Genome evolution

Many animal genomes are characterized by highly conserved chromosomal homologies that predate the ancient origin of this clade. Despite such conservation, the evolutionary forces behind the retention, expansion, and contraction of chromosomal elements, and the resulting macroevolutionary implications, are unknown. Here we present a comprehensive stem-cell resolved genomic and transcriptomic study of the fresh-water cnidarian Hydra, an animal characterized by its high regenerative capacity, the ability to propagate clonally, and an apparent lack of aging. Using single-haplotype telomere-to-telomere genome assemblies of two recently diverged hydra strains, we show how the macro-evolutionary history of chromosomal elements is shaped by both old and recent transposable element (TE) expansions. Unique features of hydra biology allowed us to compare the individual genomes of hydra's three stem cell lineages. We show that distinct TE families are active at both transcriptional and genomic levels via non-random insertions in the genomes of each of these lineages. In transcriptomes, over 14,000 transcripts were composed of nearly complete TE sequences, and further classification into families, subfamilies, and individual loci reveals cell type-specific TE expression. The active TEs include elements that differentially contribute to changes in the genome size as well as persistent structural variants around loci associated with cell proliferation. Our study reveals 14 active TE families that primarily act in this role and are predominantly composed of DNA elements. Evolutionary analysis revealed that these families constitute a highly conserved TE core in eukaryotic and metazoan genomes. Our results suggest an ancient role for these core TEs as self-renewing genomic components that persist beyond ancient chromosomal homologies.

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2,000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two ...

In this study we showed that constitutive heterochromatin, GC-rich DNA and rDNA are implicated in chromosomal rearrangements during the basic chromosome number changing (dysploidy) in Reichardia genus. This small Mediterranean genus comprises 8-10 species and presents three basic chromosome numbers (x = 9, 8 and 7). To assess genome evolution and differentiation processes, studies were conducted in a dysploid series of six species: R. dichotoma, R. macrophylla and R. albanica (2n = 18), R. tingitana and R. gaditana (2n = 16), and R. picroides (2n = 14). The molecular phylogeny reconstruction comprised three additional species (R. crystallina and R. ligulata, 2n = 16 and R. intermedia, 2n = 14). Our results indicate that the way of dysploidy is descending. During this process, a positive correlation was observed between chromosome number and genome size, rDNA loci number and pollen size, although only the correlation between chromosome number and genome size is still recovered significant once considering the phylogenetic effect. Fluorescent in situ hybridisation also evidenced changes in number, position and organisation of two rDNA families (35S and 5S), including the reduction of loci number and, consequently, reduction in the number of secondary constrictions and nuclear organising regions from three to one per diploid genome. The potential mechanisms of chromosomal and genome evolution, strongly implicating heterochromatin, are proposed and discussed, with particular consideration for Reichardia genus.

Recent phylogenomic studies have failed to conclusively resolve certain branches of the placental mammalian tree, despite the evolutionary analysis of genomic data from 32 species. Previous analyses of single genes and retroposon insertion data yielded support for different phylogenetic scenarios for the most basal divergences. The results indicated that some mammalian divergences were best interpreted not as a single bifurcating tree, but as an evolutionary network. In these studies the relationships among some orders of the super-clade Laurasiatheria were poorly supported, albeit not studied in detail. Therefore, 4775 protein-coding genes (6,196,263 nucleotides) were collected and aligned in order to analyze the evolution of this clade. Additionally, over 200,000 introns were screened in silico, resulting in 32 phylogenetically informative long interspersed nuclear elements (LINE) insertion events. The present study shows that the genome evolution of Laurasiatheria may best be understood as an evolutionary network. Thus, contrary to the common expectation to resolve major evolutionary events as a bifurcating tree, genome analyses unveil complex speciation processes even in deep mammalian divergences. We exemplify this on a subset of 1159 suitable genes that have individual histories, most likely due to incomplete lineage sorting or introgression, processes that can make the genealogy of mammalian genomes complex. These unexpected results have major implications for the understanding of evolution in general, because the evolution of even some higher level taxa such as mammalian orders may sometimes not be interpreted as a simple bifurcating pattern.

The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin.

Among Teleosts, Perciformes are the largest order of fishes and include numerous species of commercial importance. Perciformes also comprise species of primary interest for evolutionary studies and analysis of the sex determination systems and sex chromosome plasticity. Unfortunately, genomics tools and resources for Perciformes remain to be developed. Here, we report the production of a seabream whole-genome radiation hybrid (RH) panel in which quality was ascertained by the construction of a 2-Mb-resolution RH map. The map encompasses 440 markers (288 microsatellites, 82 gene-based markers, and 70 STS) suitable for linkage analysis and comparative mapping studies. Achievement of a RH panel and a whole-genome RH map should contribute to establishing seabream as a fish model among the Perciformes and should be of importance in aquaculture for marker-assisted selection, improvement of growth performance, and disease management. Development of RH maps in a costeffective manner for other fishes with the described methodology will offer a powerful approach in aquaculture and will provide extended capabilities for comparing vertebrate genome evolution.

A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.

Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra ...

Chromosome number changes during the evolution of angiosperms are likely to have played a major role in speciation. Their study is of utmost importance, especially now, as a probabilistic model is available to study chromosome evolution within a phylogenetic framework. In the present study, likelihood models of chromosome number evolution were fitted to the largest family of flowering plants, the Asteraceae. Specifically, a phylogenetic supertree of this family was used to reconstruct the ancestral chromosome number and infer genomic events. Our approach inferred that the ancestral chromosome number of the family is n = 9. Also, according to the model that best explained our data, the evolution of haploid chromosome numbers in Asteraceae was a very dynamic process, with genome duplications and descending dysploidy being the most frequent genomic events in the evolution of this family. This model inferred more than one hundred whole genome duplication events; however, it did not find evidence for a paleopolyploidization at the base of this family, which has previously been hypothesized on the basis of sequence data from a limited number of species. The obtained results and potential causes of these discrepancies are discussed.

Chromosome number changes during the evolution of angiosperms are likely to have played a major role in speciation. Their study is of utmost importance, especially now, as a probabilistic model is available to study chromosome evolution within a phylogenetic framework. In the present study, likelihood models of chromosome number evolution were fitted to the largest family of flowering plants, the Asteraceae. Specifically, a phylogenetic supertree of this family was used to reconstruct the ancestral chromosome number and infer genomic events. Our approach inferred that the ancestral chromosome number of the family is n = 9. Also, according to the model that best explained our data, the evolution of haploid chromosome numbers in Asteraceae was a very dynamic process, with genome duplications and descending dysploidy being the most frequent genomic events in the evolution of this family. This model inferred more than one hundred whole genome duplication events, however it did not find ...

Let f be a homeomorphism of the closed annulus A isotopic to the identity, and let X ⊂ IntA be an f -invariant continuum which separates A into two domains, the upper domain U + and the lower domain U -. Fixing a lift of f to the universal cover of A, one defines the rotation set ρ(X) of X by means of the invariant probabilities on X. For any rational number p/q ∈ ρ(X), f is shown to admit a p/q periodic point in X, provided that (1) X consists of nonwandering points or (2) X is an attractor and the frontiers of U -and U + coincides with X. Also the Carathéodory rotation numbers of U ± are shown to be in ρ(X) for any separating invariant continuum X.

Motivation: It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an aÀproteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree. Results: We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees.

Motivation It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α−proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree. Results We address the problem of inferring the evolution of a gene family th...

The successful hybridization of cosmid clones from Drosophila melanogaster (Sophophora subgenus) to the salivary gland chromosomes of other species as distantly related as those in the Drosophila subgenus attests their great potential for unravelling genome evolution. We have carried out, using 28 cosmids and 13 gene clones, a study of the organization of the D. melanogaster 95A-96A chromosomal region in three Drosophila subgenus species: D. repleta, D. buzzattii and D. virilis. These clones were first used to built an accurate map of this 1.6 Mb region of D. melanogaster chromosome 3R (Muller's element E). Then, they were hybridized and mapped to the homologous chromosome 2 of the other three distantly related species. The studied region is disseminated over 13 different sites of chromosome 2 in the Drosophila subgenus species, which implies a minimum of 12 inversion breakpoints fixed between the two subgenera. Extrapolation to the entire chromosome gives 90 fixed inversions. The D. melanogaster Pp1-96A-Acr96Aa segment conserved in D. repleta and D. buzzatii is longer than previously thought and is also conserved in D. virilis. In addition, three other D. melanogaster segments conserved in the three Drosophila subgenus species were found. Finally, our data indicate significant statistical differences in the evolution rate of Muller's element E among lineages, a result that agrees well with the previous cytogenetic data.

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provi...

Background Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, Brussels sprouts. This diversity along with its phylogenetic membership in a group of three diploid and three tetraploid species, and the recent availability of genome sequences within Brassica provide an unprecedented opportunity to study intra- and inter-species divergence and evolution in this species and its close relatives. Description We have developed a comprehensive database, Bolbase, which provides access to the B. oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 predicted genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomics information is available, including syntenic regions among B. oleracea,...

BackgroundThe orderly progression through mitosis is regulated by the Anaphase-Promoting Complex (APC), a large multiprotein E3ubiquitin ligase that targets key cell-cycle regulators for destruction by the 26 S proteasome. The APC is composed of at least 11 subunits and associates with additional regulatory activators during mitosis and interphase cycles. Despite extensive research on APC and activator functions in the cell cycle, only a few components have been functionally characterized in plants.ResultsHere, we describe an in-depth search for APC subunits and activator genes in the Arabidopsis, rice and poplar genomes. Also, searches in other genomes that are not completely sequenced were performed. Phylogenetic analyses indicate that some APC subunits and activator genes have experienced gene duplication events in plants, in contrast to animals. Expression patterns of paralog subunits and activators in rice could indicate that this duplication, rather than complete redundancy, c...

The complete nucleotide sequence of the mitochondrial (mt) genome was determined for specimens of the coral species Montipora cactus (Bernard 1897) and Anacropora matthai (Pillai 1973), representing two morphologically distinct genera of the family Acroporidae. These sequences were compared with the published mt genome sequence for the confamilial species, Acropora tenuis (Dana 1846). The size of the mt genome was 17,887 bp and 17,888 bp for M. cactus and A. matthai. Gene content and organization was found to be very similar among the three Acroporidae mt genomes with a group I intron occurring in the NADH dehyrogenase 5 (nad5) gene. The intergenic regions were also similar in length among the three corals. The control region located between the small ribosomal RNA (ms) and the cytochrome oxidase 3 (cox3) gene was significantly smaller in M. cactus and A. matthai (both 627 bp) than in A. tenuis (1086 bp). Only one set of repeated sequences was identified at the 3¢-end of the control regions in M. cactus and A. matthai. A lack of the abundant repetitive elements which have been reported for A. tenuis, accounts for the relatively short control regions in M. cactus and A. matthai. Pairwise distances and relative rate analyses of 13 protein coding genes, the group I intron and the largest intergenic region, igr3, revealed significant differences in the rate of molecular evolution of the mt genome among the three species, with an extremely slow rate being seen between Montipora and Anacropora. It is concluded that rapid mt genome evolution is taking place in genus Acropora relative to the confamilial genera Montipora and Anacropora although all are within the relatively slow range thought to be typical of Anthozoa.

The complete nucleotide sequence of the mitochondrial (mt) genome was determined for specimens of the coral species Montipora cactus (Bernard 1897) and Anacropora matthai (Pillai 1973), representing two morphologically distinct genera of the family Acroporidae. These sequences were compared with the published mt genome sequence for the confamilial species, Acropora tenuis (Dana 1846). The size of the mt genome was 17,887 bp and 17,888 bp for M. cactus and A. matthai. Gene content and organization was found to be very similar among the three Acroporidae mt genomes with a group I intron occurring in the NADH dehyrogenase 5 (nad5) gene. The intergenic regions were also similar in length among the three corals. The control region located between the small ribosomal RNA (ms) and the cytochrome oxidase 3 (cox3) gene was significantly smaller in M. cactus and A. matthai (both 627 bp) than in A. tenuis (1086 bp). Only one set of repeated sequences was identified at the 3¢-end of the control regions in M. cactus and A. matthai. A lack of the abundant repetitive elements which have been reported for A. tenuis, accounts for the relatively short control regions in M. cactus and A. matthai. Pairwise distances and relative rate analyses of 13 protein coding genes, the group I intron and the largest intergenic region, igr3, revealed significant differences in the rate of molecular evolution of the mt genome among the three species, with an extremely slow rate being seen between Montipora and Anacropora. It is concluded that rapid mt genome evolution is taking place in genus Acropora relative to the confamilial genera Montipora and Anacropora although all are within the relatively slow range thought to be typical of Anthozoa.

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped superscaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.

New mutations leading to structural variation (SV) in genomes-in the form of mobile element insertions, large deletions, gene duplications, and other chromosomal rearrangements-can play a key role in microbial evolution. Yet, SV is considerably more difficult to predict from short-read genome resequencing data than single-nucleotide substitutions and indels (SN), so it is not yet routinely identified in studies that profile population-level genetic diversity over time in evolution experiments. We implemented an algorithm for detecting polymorphic SV as part of the breseq computational pipeline. This procedure examines split-read alignments, in which the two ends of a single sequencing read match disjoint locations in the reference genome, in order to detect structural variants and estimate their frequencies within a sample. We tested our algorithm using simulated Escherichia coli data and then applied it to 500-and 1000-generation population samples from the Lenski E. coli long-term evolution experiment (LTEE). Knowledge of genes that are targets of selection in the LTEE and mutations present in previously analyzed clonal isolates allowed us to evaluate the accuracy of our procedure. Overall, SV accounted for ∼25% of the genetic diversity found in these samples. By profiling rare SV, we were able to identify many cases where alternative mutations in key genes transiently competed within a single population. We also found, unexpectedly, that mutations in two genes that rose to prominence at these early time points always went extinct in the long term. Because it is not limited by the base-calling error rate of the sequencing technology, our approach for identifying rare SV in whole-population samples may have a lower detection limit than similar predictions of SNs in these data sets. We anticipate that this functionality of breseq will be useful for providing a more complete picture of genome dynamics during evolution experiments with haploid microorganisms.

Phylogenetic relationships among strepsirhines are enigmatic. Comparative chromosome painting using Zoo-FISH techniques can provide independent verification of phylogenetic trees derived from classical or molecular data. We compared chromosomal features of 11 representative species (8 within Lemuriformes and 3 from both lineages of Lorisiformes) using parsimony. Chromosomal syntenies were used to build a binary matrix of characters in PAUP 4.0b1, and subsequently analyzed by the bootstrap method. The chromosome complement of Tupaia belangieri (Scandentia) was used as the outgroup. An exhaustive search retrieved 8 equally parsimonious trees. Four characters ancestral for eutherians (HSA3+21, 7+16, 12+22 and 14+15) have been retained in all strepsirhine species, and one ancestral eutherian association (HSA16+19) was unique to Daubentonia madagascariensis. Among lorisiforms and other lemuriforms, chromosomes 16 and 19 have undergone different, and presumably successive, associations. The analysis also revealed a large number of autapomorphies (i.e. HSA1+5, 3+7, 8+11, 16+22) for most of the families investigated here. Three of the remaining associations (HSA1+7, 6+14, 12+19) shared by at least two species within the same family, are considered to be convergent in our chromosomal phylogeny. Most, but not all, molecular phylogenies reconstruct D. madagascariensis as the basal divergence of the Malagasy lemurs, and nested within the living strepsirhines. Under this interpretation, the 16+19 association, shared with non-primate mammals, would be considered a convergent autapomorphy. However, the morphological peculiarities that characterize this species, and a few molecular phylogenies, allow the possibility that this association is an ancient retention.

The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution. In 1938 Marjorie Courtenay-Latimer, the curator of a small natural history museum in East London, South Africa, discovered a large, unusual-looking fish among the many specimens delivered to her by a local fish trawler. Latimeria chalumnae, named after its discoverer 1 , was over 1 m long, bluish in colour and had conspicuously fleshy fins that resembled the limbs of terrestrial vertebrates. This discovery is considered to be one of the most notable zoological finds of the twentieth century. Latimeria is the only living member of an ancient group of lobe-finned fishes that was known previously only from fossils and believed to have been extinct since the Late Cretaceous period, approximately 70 million years ago (Myr ago) 1 . It was almost 15 years before a second specimen of this elusive species was discovered in the

This chapter explores polyploidy breeding as a transformative approach in crop improvement. It outlines the fundamentals of polyploidy, distinguishing between autopolyploids and allopolyploids, and describes both natural and induced methods for increasing chromosome sets. The chapter discusses the advantages of polyploidy, such as enhanced cell size, increased vigor, and novel trait expression, while also addressing challenges like reduced fertility and genetic instability. Modern techniques, including chemical induction and tissue culture, along with emerging genomic tools, are highlighted as key to advancing polyploid breeding for improved crop performance and sustainability.

Background: Transposable elements (TEs) are considered to be an important source of genome size variation and genetic and phenotypic plasticity in eukaryotes. Most of our knowledge about TEs comes from large genomic projects and studies focused on model organisms. However, TE dynamics among related taxa from natural populations and the role of TEs at the species or supra-species level, where genome size and karyotype evolution are modulated in concert with polyploidy and chromosomal rearrangements, remain poorly understood. We focused on the holokinetic genus Eleocharis (Cyperaceae), which displays large variation in genome size and the occurrence of polyploidy and agmatoploidy/symploidy. We analyzed and quantified the long terminal repeat (LTR) retrotransposons Ty1-copia and Ty3-gypsy in relation to changes in both genome size and karyotype in Eleocharis. We also examined how this relationship is reflected in the phylogeny of Eleocharis. Results: Using flow cytometry, we measured the genome sizes of members of the genus Eleocharis (Cyperaceae). We found positive correlation between the independent phylogenetic contrasts of genome size and chromosome number in Eleocharis. We analyzed PCR-amplified sequences of various reverse transcriptases of the LTR retrotransposons Ty1-copia and Ty3-gypsy (762 sequences in total). Using real-time PCR and dot blot approaches, we quantified the densities of Ty1-copia and Ty3-gypsy within the genomes of the analyzed species. We detected an increasing density of Ty1-copia elements in evolutionarily younger Eleocharis species and found a positive correlation between Ty1-copia densities and C /n -values (an alternative measure of monoploid genome size) in the genus phylogeny. In addition, our analysis of Ty1-copia sequences identified a novel retrotransposon family named Helos1, which is responsible for the increasing density of Ty1-copia. The transition:transversion ratio of Helos1 sequences suggests that Helos1 recently transposed in later-diverging Eleocharis species. Conclusions: Using several different approaches, we were able to distinguish between the roles of LTR retrotransposons, polyploidy and agmatoploidy/symploidy in shaping Eleocharis genomes and karyotypes. Our results confirm the occurrence of both polyploidy and agmatoploidy/symploidy in Eleocharis. Additionally, we introduce a new player in the process of genome evolution in holokinetic plants: LTR retrotransposons.

Amongst the 11 eutherian-specific genes acquired from a sushi-ichi retrotransposon is the CCHC type zinc-finger protein-encoding gene SIRH11/ZCCHC16. Its contribution to eutherian brain evolution is implied because of its involvement in cognitive function in mice, possibly via the noradrenergic system. Although, the possibility that Sirh11/Zcchc16 functions as a non-coding RNA still remains, dN/dS ratios in pairwise comparisons between its orthologs have provided supportive evidence that it acts as a protein. It became a pseudogene in armadillos (Cingulata) and sloths (Pilosa), the only two extant orders of xenarthra, which prompted us to examine the lineage-specific variations of SIRH11/ZCCHC16 in eutherians. We examined the predicted SIRH11/ZCCHC16 open reading frame (ORF) in 95 eutherian species based on the genomic DNA information in GenBank. A large variation in the SIRH11/ZCCHC16 ORF was detected in several lineages. These include a lack of a CCHC RNA-binding domain in its C-terminus, observed in gibbons (Hylobatidae: Primates) and megabats (Megachiroptera: Chiroptera). A lack of the N-terminal half, on the other hand, was observed in New World monkeys (Platyrrhini: Primates) and species belonging to New World and African Hystricognaths (Caviomorpha and Bathyergidae: Rodents) along with Cetacea and Ruminantia (Cetartiodactyla). Among the hominoids, interestingly, three out of four genera of gibbons have lost normal SIRH11/ZCCHC16 function by deletion or the lack of the CCHC RNA-binding domain. Our extensive dN/dS analysis suggests that such truncated SIRH11/ZCCHC16 ORFs are functionally diversified even within lineages. Combined, our results show that SIRH11/ZCCHC16 may contribute to the diversification of eutherians by lineage-specific structural changes after its domestication in the common eutherian ancestor, followed by putative species-specific functional changes that enhanced fitness and occurred as a consequence of complex natural selection events.

Euteleost fishes seem to have more copies of many genes than their tetrapod relatives. Three different mechanisms could explain the origin of these 'extra' fish genes. The duplicates may have been produced during a fishspecific genome duplication event. A second explanation is an increased rate of independent gene duplications in fish. A third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. These three hypotheses have been tested by phylogenetic tree reconstruction. Phylogenetic analyses of sequences from human, mouse, chicken, frog (Xenopus laevis), zebrafish (Danio rerio) and pufferfish (Takifugu rubripes) suggest that ray-finned fishes are likely to have undergone a whole genome duplication event between 200 and 450 million years ago. We also comment here on the evolutionary consequences of this ancient genome duplication.

It has been suggested that fish have more genes than humans. Whether most of these additional genes originated through a complete (fish-specific) genome duplication or through many lineage-specific tandem gene or smaller block duplications and family expansions continues to be debated. We analyzed the complete genome of the pufferfish Takifugu rubripes (Fugu) and compared it with the paranome of humans. We show that most paralogous genes of Fugu are the result of three complete genome duplications. Both relative and absolute dating of the complete predicted set of protein-coding genes suggest that initial genome duplications, estimated to have occurred at least 600 million years ago, shaped the genome of all vertebrates. In addition, analysis of >150 block duplications in the Fugu genome clearly supports a fish-specific genome duplication (≈320 million years ago) that coincided with the vast radiation of most modern ray-finned fishes. Unlike the human genome, Fugu contains very f...

Most species of flowering plants and vertebrates have descended from ancestors who doubled their genomes, either through autopolyploidy or allopolyploidy. Evidence from cytogenetic analyses, morphological studies of fossil and extant species and, more recently, whole-genome and EST analyses suggests that most (60-70%) flowering plants have a polyploid ancestry 1,2-4 . In flowering plants, polyploids form at a frequency of 1 per 100,000 individuals 5 , and ∼2-4% of speciation events involve polyploidization 6 . As a result, many plants, and most of our domesticated crop species, are polyploid 7 . Although polyploidy is much rarer in animals than in plants, there are hundreds of known insects and vertebrate species that are polyploid, mainly amphibians and fish 6 . Whole-genome duplications (WGDs) have also been documented for unicellular organisms: the first ancient WGD to be discovered in eukaryotes was that of the yeast Saccharomyces cerevisiae 8 . More recently, it was shown that the unicellular ciliate Paramecium tetraurelia has also undergone several WGDs 9 . Because ancient WGDs in plants and animals gave rise to some particularly species-rich groups, some have argued that polyploidy is not an evolutionary dead end but that it provides novel opportunities for evolutionary success . However, most polyploidy events have occurred near the tips of the evolutionary tree of life rather than at deeper branches. Although many species are currently polyploid, few ancient polyploidy events have survived. During 500-600 million years of vertebrate evolution, no more than two (or three for teleosts) WGDs have persisted. Since the rise of the flowering plants 150-200 million years ago (mya) , the number of inferred ancient WGDs in any angiosperm lineage is at most four . In the fungal lineage, for which many more genome sequences are known, there is only evidence for a single ancient WGD event . Paleopolyploidy events therefore seem to be exceedingly rare, and polyploids, or rather their descendants, have not been established tens or hundreds of times. However, all vertebrates seem to have shared two ancient WGD events, whereas all teleosts, and probably also eudicots, are derived from a lineage that experienced a WGD event . This would suggest that, although descendants of WGD events do not survive often, when they do survive their evolutionary lineage can be very successful. The observation that these WGDs often gave rise to species-rich groups of organisms, such as >25,000 species of fish and >350,000 species of flowering plants, suggests that polyploidy can facilitate

Microsporidia are obligate intracellular parasites that have long been considered to be primitive eukaryotes, both on the basis of morphological features and on the basis of molecular, mainly ribosomal RNA-based, phylogenies. However, accumulating sequence data and the use of more sophisticated tree construction methods now seem to suggest that microsporidia share a common origin with fungi and are therefore most probably just curious fungi. In this paper, we describe the current views on the phylogenetic position of the microsporidia and present additional evidence for a close relationship between fungi and microsporidia on the basis of reanalysed ribosomal RNA data. In this respect, the importance of incorporating detailed knowledge of the substitution pattern of sequences into phylogenetic methods is discussed.

The availability of complete genome sequences for 12 Drosophila species provides an unprecedented resource for largescale studies of genome evolution. In this study, we looked for correlated shifts in the patterns of genome and proteome evolution within the genus Drosophila. Specifically, we asked if the nucleotide composition of the Drosophila willistoni genome-which is significantly less GC rich than the other 11 sequenced Drosophila genomes-is reflected in an altered pattern of amino acid substitutions in the encoded proteins. Our results show that this is indeed the case: There are large and highly significant asymmetries in the patterns of amino acid substitution between D. willistoni and Drosophila melanogaster, and they are in the direction predicted by the nucleotide biases. The implication of this result, combined with previous studies on long-term proteome evolution, is that substitutional biases at the DNA level can be a major factor in determining both the long-term and the short-term directions of proteome evolution.

Two genes, petB and petD, encoding cytochrome b6 and subunit IV of the cytochrome b,/fcomplex, respectively, of the chloroplast genome of Marchantia polymorpha, a liverwort, have been mapped between the psbH and rpoA genes and each of the petB and petD genes has been predicted to contain a group II intron in its coding sequence [(1986) Nature 322, 572-5741. Primer extension analysis of the liverwort chloroplast RNA using two synthetic oligodeoxyribonucleotides, complementary to parts of the coding sequences of the petB and petD transcripts, as primers has provided evidence that the two genes are co-transcribed to a precursor mRNA which is then precisely spliced at the predicted sites. Chloroplast; Cytochrome b,/fcomplex; RNA splicing; Primer extension; (Marchantia polymorpha

ABSTRACTLong Interspersed Element 1 (LINE-1/L1) is an abundant retrotransposon that has greatly impacted human genome evolution. LINE-1s are responsible for the generation of millions of insertions in the current human population. The characterization of sporadic cases of mosaic individuals carrying pathogenic L1-insertions, suggest that heritable insertions occurs during early embryogenesis. However, the timing and potential genomic impact of LINE-1 mobilization during early embryogenesis is unknown. Here, we demonstrate that inner cell mass of human pre-implantation embryos support the expression and retrotransposition of LINE −1s. Additionally, we show that LINE-1s are expressed in trophectoderm cells of embryos, and identify placenta-restricted endogenous LINE-1 insertions in newborns. Using human embryonic stem cells as a model of post-implantation epiblast cells, we demonstrate ongoing LINE-1 retrotransposition, which can impact expression of targeted genes. Our data demonstra...

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have .21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host-and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

Grain yield in wheat (Triticum aestivum L.) is a polygenic trait representing many developmental processes and their interactions with environment. Among them, tillering capacity is an important agronomic trait for plant architecture and grain yield, but the genetic basis of tiller formation in wheat remains largely unknown. In this study, we identi ed a tiller inhibition mutant (tin5) from ethyl methane sulfonate (EMS) treated G1812 (Triticum urartu Thumanjan ex Gandilyan). A mapping population was constructed with tin5/G3146. Based on the sequence differences between G1812 and G3146, large InDels (≧5 bp) were selected and veri ed, and a skeleton physical map was constructed with genome-wide 168 polymorphic InDel markers. Genetic analysis revealed that the low-tiller phenotype was controlled by a single recessive locus, which we named TIN5. This locus was mapped to a 2.1-Mb region that contained 24 annotated genes in chromosome Tu7. Among these annotated genes, 16 genes expressed at the seedling stage, but only TuG1812G0700004539 showed a non-synonymous polymorphism between tin5 and WT. Our nding will facilitate its map-based cloning and pave the way for an in-depth analysis of the underlying genetic basis of tillering formation and regulation patterns. A tiller inhibition gene TIN5 was delimited into an approximate 2.1 Mb genomic region on chromosome Tu7 that contains 24 annotated genes.

Grain yield in wheat (Triticum aestivum L.) is a polygenic trait representing many developmental processes and their interactions with environment. Among them, tillering capacity is an important agronomic trait for plant architecture and grain yield, but the genetic basis of tiller formation in wheat remains largely unknown. In this study, we identi ed a tiller inhibition mutant (tin5) from ethyl methane sulfonate (EMS) treated G1812 (Triticum urartu Thumanjan ex Gandilyan). A mapping population was constructed with tin5/G3146. Based on the sequence differences between G1812 and G3146, large InDels (≧5 bp) were selected and veri ed, and a skeleton physical map was constructed with genome-wide 168 polymorphic InDel markers. Genetic analysis revealed that the low-tiller phenotype was controlled by a single recessive locus, which we named TIN5. This locus was mapped to a 2.1-Mb region that contained 24 annotated genes in chromosome Tu7. Among these annotated genes, 16 genes expressed at the seedling stage, but only TuG1812G0700004539 showed a non-synonymous polymorphism between tin5 and WT. Our nding will facilitate its map-based cloning and pave the way for an in-depth analysis of the underlying genetic basis of tillering formation and regulation patterns. A tiller inhibition gene TIN5 was delimited into an approximate 2.1 Mb genomic region on chromosome Tu7 that contains 24 annotated genes.

Tomato (Lycopersicon esculentum) is a model species for molecular biology research and a candidate for large-scale genome sequencing. Pericentromeric heterochromatin constitutes a large portion of the tomato chromosomes. However, the knowledge of the structure, organization, and evolution of such regions remains very limited. Here, we report the analysis of a 198-kb sequence near the FER gene, located in a distal part of pericentromeric heterochromatin on the long arm of tomato chromosome 6. Nine genes, one pseudogene, and 55 transposable elements (TEs) were identified, showing a low gene density (19.8 kb/gene) and a high content of transposable elements (>45% of the sequence). Six genes (56B23_g3, g5, g7, g8, g9, and g10) have perfect matches (>98% identity) with tomato expressed sequence tags. Two genes (56B23_g1 and g6), which share <98% sequence identity with expressed sequence tags, were confirmed for transcriptional activity by reverse transcription-PCR. The genes wer...

Naegleria gruberi amoebae, EGs strain, containing viruslike particles (VLP) were grown at temperatures of 21" and 37°C. At 21"C, the amoebae displayed the morphological structures associated with development of the VLP's. At 37"C, however, gross morphological modifications and new structures appeared. When amoebae were at 37°C for less than 12 hr, nuclei were found to have a larger number of VLP's than amoebae at 21°C. Exposure of the amoebae to the higher temperature for 1224 hr resulted in. a scarcity of particles. Large bundles of microtubulelike fibrils were present in the nucleoplasm of amoebae at 37"C, and, in addition, the nuclei showed degenerative modifications. The fibrillar changes were not due to the elevated temperature alone since a substrain of EGs ( = EGB) not infected with VLP's exhibited no nuclear modifications. It is assumed that the elevated temperature acaeleratrd upon the cells. and enhanced a lytic effect of the VLP's

MotivationSynthetic genomics as a field seeks to synthesize large regions of genomes from the ground up. Such large-scale projects, especially in complex genomes can rely on pre-existing BAC (Bacterial Artificial Chromosome) libraries as starting material to reduce cost. However, choosing BACs that cover long DNA regions, especially those that require many BACs, is a manual, idiosyncratic, time consuming, and error prone process. Automating this work would make the assembly of large DNA constructs more efficient.ResultsWe have developed MenDEL – a web-based DNA design application, that provides efficient tools for finding BACs that cover long regions of interest and allow for sorting results based on multiple user defined criteria - total length, number of BACs, longest BAC. etc. In addition, it enables the user to find a combination of BACs from pre-existing libraries that cover a region of interest not found in any single BAC.Availability and ImplementationMenDEL application is av...

Previously, we reported the generation of a virusinduced systemic signal that increased the somatic and meiotic recombination rates in tobacco mosaic virus (TMV)-infected tobacco plants. Here, we analyzed the progeny of plants that received the signal and found that these plants also have a higher frequency of rearrangements in the loci carrying the homology to LRR region of the gene of resistance to TMV (N-gene). Analysis of the stability of repetitive elements from Nicotiana tabacum loci and 5.8S ribosomal RNA loci did not show any changes. Further analysis of the changes in the progeny of infected plants revealed that they had substantially hypermethylated genomes. At the same time, loci-specific methylation analysis showed: (1) profound hypomethylation in several LRR-containing loci; (2) substantial hypermethylation of actin loci and (3) no change in methylation in the loci of repetitive elements from N. tabacum or 5.8S ribosomal RNA. Global genome hypermethylation of the progeny is believed to be part of a general protection mechanism against stress, whereas locus-specific hypomethylation is associated with a higher frequency of rearrangements. Increased recombination events combined with the specific methylation pattern induced by pathogen attack could be a sign of an adaptive response by plants.

Data deposition: The genome data reported in this paper have been deposited in the National Center for Biotechnology Information BioProject database, www.ncbi.nlm.nih. gov/bioproject [accession nos. PRJNA53493 (tADL), PRJNA58807 (HI), PRJNA72619 (DL31), and PRJNA75121 (DL1)]; and the metagenome data have been deposited in the Genomes OnLine database, www.genomesonline.org [accession nos. Gs0000582 (13m_0.1), Gs0000585 (24m_0.8), Gs0000586 (SSU rRNA pyrotag data), Gs0000587 (24m_0.1), Gs0000592 (36m_pooled), Gs0000594 (24m_3.0), and Gs0000595 (5mRS_0.1)].

Several, stable amoebal strains which differ phenotypically from the diploid parental amoebal strain have been obtained in the Myxomycete Physarum polycephalum. They were detected using their flagellation pattern as a discriminating parameter. This approach is valid since the number of flagella by phase contrast microscopy correlates with the number of anterior centrioles obtained using three-dimensional reconstructions of the nucleo-flagellar complexes from serial thin sections. The complexity of the structures of the various nucleo-flagellar complexes suggests that in these strains the duplication time of centrioles is not strictly regulated as it is in haploid amoebae. In agreement with this hypothesis, several pro-centrioles were observed in interphase amoebae. Although the anterior centrioles are linked to the mtoc I during interphase, the number of mtoc I cannot regulate the number of centrioles since some strains possess two mtoc 1 but only one pair of centrioles. Neither the number of centrioles nor the number ofmtoc 1 are related to ploidy. Stable strains with one (all haploid strains), two (some diploid strains) and three (some diploid strains) mtoc 1 have been observed. Thus each mtoc 1 is duplicated once per cell cycle implying that it must possess some information which plays a role in the morphogenesis of the new mtoc 1. Except in one case, the number of mitotic abnormalities increases exponentially with the number of mtoc 1. This observation suggests that the mtoc 1 could correspond to the interphase state of the mitotic center.

Molecular cytogenetics and the study of genome size have been used to understand evolutionary and systematic relationships in many species. However, this approach has seldom been applied to alpine plants. A group of dysploid-polyploid high mountain Artemisia species, distributed from the European Sierra Nevada to Central Asian mountains, through the Pyrenees, the Alps and the Caucasus, is a good model to consider changes at the genome and chromosome levels. These small perennial Artemisia, found frequently in isolated populations, present highly disjunct distributions. Some are considered rare or even endangered. Here we show results for nine species and 31 populations, including genome size (2C-values), fluorochrome banding and fluorescent in situ hybridisation (FISH) of ribosomal RNA genes (rDNA). Significant intraspecific genome size variation is found in certain populations of A. eriantha and A. umbelliformis, but without taxonomic significance due to the absence of morphological or ecological differentiation. The number and position of GC-rich DNA bands is mostly coincidental with rDNA although there is an expansion of GC-rich heterochromatin in centromeres in some taxa. Ancestral character states have been reconstructed and x=9 is inferred as the likely ancestral base number, while the dysploid x=8 has appeared repeatedly during the evolution of Artemisia. On the basis of cytological observations, Robertsonian translocations are proposed for the appearance of dysploidy in the genus. A remarkable presence of x=8-based species has been detected in the clade including high mountain species, which highlights the important role of dysploidy in the diversification of high mountain Artemisia. Conversely, polyploidy, though present in the alpine species, is more common in the rest of the genus, particularly in arctic species. Hypotheses on the mechanisms underpinning the relative abundance of dysploids and scarcity of polyploids in high mountain Artemisia are discussed.

Green for Diatoms Diatoms account for 20% of global carbon fixation and, together with other chromalveolates (e.g., dinoflagellates and coccolithophorids), represent many thousands of eukaryote taxa in the world's oceans and on the tree of life. Moustafa et al. (p. 1724 ; see the Perspective by Dagan and Martin ) have discovered that the genomes of diatoms are highly chimeric, with about 10% of their nuclear genes being of foreign algal origin. Of this set of 1272 algal genes, 253 were, as expected, from a distant red algal secondary endosymbiont, but more than 1000 of the genes were derived from green algae and predated the red algal relationship. These protist taxa are important not only for genetic and genomic investigations but also for their potential in biofuel and nanotechnology applications and in global primary productivity in relation to climate change.