Biased distributions and decay of long interspersed nuclear elements in the chicken genome

Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap

Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PR domain-containing protein 9, a key determinant of recombination dynamics in most metazoans. Historical recombination maps in birds show an apparent stasis in positioning recombination events. This highly conserved recombination pattern over long timescales may constrain the evolution of recombination in birds. At the same time, extensive variation in recombination rate is observed across the genome and between different species of birds. Here, we characterize the fine-scale historical recombination map of an iconic migratory songbird, the Eurasian blackcap (Sylvia atricapilla), using a linkage disequilibrium-based approach that accounts for population demography. Our results reveal variable recombination rates among and within chromosomes, which associate positively with nucleotide diversity and GC content and negatively with chromosome size. Recombination rates increased significantly at regulatory regions but not necessarily at gene bodies. CpG islands are associated strongly with recombination rates, though their specific position and local DNA methylation patterns likely influence this relationship. The association with retrotransposons varied according to specific family and location. Our results also provide evidence of heterogeneous intrachromosomal conservation of recombination maps between the blackcap and its closest sister taxon, the garden warbler. These findings highlight the considerable variability of recombination rates at different scales and the role of specific genomic features in shaping this variation. This study opens the possibility of further investigating the impact of recombination on specific population-genomic features.

Taming transposable elements in livestock and poultry: a review of their roles and applications

Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.

Whole-genome identification of transposable elements reveals the equine repetitive element insertion polymorphism in Chinese horses

Transposable elements (TEs) are diverse, abundant, and complicated in genomes. They not only can drive the genome evolution process but can also act as special resources for adaptation. However, little is known about the evolutionary processes that shaped horses. In this work, 126 horse assemblages involved in most horse breeds in China were used to investigate the patterns of TE variation for the first time. By using RepeatMasker and melt software, we found that the horse-specific short interspersed repetitive elements family, equine repetitive elements (ERE1), exhibited polymorphisms in horse genomes. Phylogenetic analysis based on these ERE1 loci (minor allele frequency ≥0.05) revealed three major horse groups, namely, those in northern China, southern China, and Qinghai-Tibetan, which mirrors the result determined by SNPs to some extent. The present ERE1 family emerged ~0.26 to 1.77 Mya ago, with an activity peak at ~0.49 Mya, which matches the early stage of the horse lineage and decreases after the divergence of Equus caballus and Equus ferus przewalskii. To detect the functional ERE1(s) associated with adaptation, locus-specific branch length, genome-wide association study, and absolute allele frequency difference analyses were conducted and resulted in two common protein-coding genes annotated by candidate ERE1s. They were clustered into the vascular smooth muscle contraction (p = 0.01, EDNRA) and apelin signalling pathways (p = 0.02, NRF1). Notably, ERE1 insertion into the EDNRA gene showed a higher association with adaptation among southern China horses and other horses in 15 populations and 451 individuals (p = 4.55 e-8). Our results provide a comprehensive understanding of TE variations to analyse the phylogenetic relationships and traits relevant to adaptive evolution in horses.

Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase

Mobile elements (MEs) collectively contribute to at least 50% of the human genome. Due to their past incremental accumulation and ongoing DNA transposition, MEs serve as a significant source for both inter- and intra-species genetic and phenotypic diversity during primate and human evolution. By making use of the most recent genome sequences for human and many other closely related primates and robust multi-way comparative genomic approach, we identified a total of 14,870 human-specific MEs (HS-MEs) with more than 8,000 being newly identified. Collectively, these HS-MEs contribute to a total of 14.2 Mbp net genome sequence increase. Several new observations were made based on these HS-MEs, including the finding of Y chromosome as a strikingly hot target for HS-MEs and a strong mutual preference for SINE-R/VNTR/Alu (SVAs). Furthermore, ∼8,000 of these HS-MEs were found to locate in the vicinity of ∼4,900 genes, and collectively they contribute to ∼84 kb sequences in the human reference transcriptome in association with over 300 genes, including protein-coding sequences for 40 genes. In conclusion, our results demonstrate that MEs made a significant contribution to the evolution of human genome by participating in gene function in a human-specific fashion.

Accumulation of transposable elements in selfing populations of Arabidopsis lyrata supports the ectopic recombination model of transposon evolution

Transposable elements (TE) can constitute a large fraction of plant genomes, yet our understanding of their evolution and fitness effect is still limited. Here we tested several models of evolution that make specific predictions about differences in TE abundance between selfing and outcrossing taxa, and between small and large populations. We estimated TE abundance in multiple populations of North American Arabidopsis lyrata differing in mating system and long-term size, using transposon insertion display on several TE families. Selfing populations had higher TE copy numbers per individual and higher TE allele frequencies, supporting models which assume that selection against TEs acts predominantly against heterozygotes via the process of ectopic recombination. In outcrossing populations differing in long-term size, the data supported neither a model of density-regulated transposition nor a model of direct deleterious effect. Instead, the population structure of TEs revealed that outcrossing populations tended to split into western and eastern groups - as previously detected using microsatellite markers - whereas selfing populations from west and east were less differentiated. This, too, agrees with the model of ectopic recombination. Overall, our results suggest that TE elements are nearly neutral except for their deleterious potential to disturb meiosis in the heterozygous state.

Coevolution between transposable elements and recombination

One of the most striking patterns of genome structure is the tight, typically negative, association between transposable elements (TEs) and meiotic recombination rates. While this is a highly recurring feature of eukaryotic genomes, the mechanisms driving correlations between TEs and recombination remain poorly understood, and distinguishing cause versus effect is challenging. Here, we review the evidence for a relation between TEs and recombination, and discuss the underlying evolutionary forces. Evidence to date suggests that overall TE densities correlate negatively with recombination, but the strength of this correlation varies across element types, and the pattern can be reversed. Results suggest that heterogeneity in the strength of selection against ectopic recombination and gene disruption can drive TE accumulation in regions of low recombination, but there is also strong evidence that the regulation of TEs can influence local recombination rates. We hypothesize that TE insertion polymorphism may be important in driving within-species variation in recombination rates in surrounding genomic regions. Furthermore, the interaction between TEs and recombination may create positive feedback, whereby TE accumulation in non-recombining regions contributes to the spread of recombination suppression. Further investigation of the coevolution between recombination and TEs has important implications for our understanding of the evolution of recombination rates and genome structure.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.

New high copy tandem repeat in the content of the chicken W chromosome

The content of repetitive DNA in avian genomes is considerably less than in other investigated vertebrates. The first descriptions of tandem repeats were based on the results of routine biochemical and molecular biological experiments. Both satellite DNA and interspersed repetitive elements were annotated using library-based approach and de novo repeat identification in assembled genome. The development of deep-sequencing methods provides datasets of high quality without preassembly allowing one to annotate repetitive elements from unassembled part of genomes. In this work, we search the chicken assembly and annotate high copy number tandem repeats from unassembled short raw reads. Tandem repeat (GGAAA)_n has been identified and found to be the second after telomeric repeat (TTAGGG)n most abundant in the chicken genome. Furthermore, (GGAAA)_n repeat forms expanded arrays on the both arms of the chicken W chromosome. Our results highlight the complexity of repetitive sequences and update data about organization of sex W chromosome in chicken.

Low diversity, activity, and density of transposable elements in five avian genomes

In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes. Phylogenetic analysis revealed that CR1 clade was more diverse in the family structure compared with R2 clade in birds; avian ERVs were classified into four clades (alpha, beta, gamma, and ERV-L) and belonged to three classes of ERV with an uneven distributed in these lineages. The activities of DNA and SINE TEs were very low in the evolution history of avian genomes; most LINEs and LTRs were ancient copies with a substantial decrease of activity in recent, with only LTRs and LINEs in chicken and zebra finch exhibiting weak activity in very recent, and very few TEs were intact; however, the recent activity may be underestimated due to the sequencing/assembly technologies in some species. Overall, this study demonstrates low diversity, activity, and density of TEs in the five avian species; highlights the differences of TEs in these lineages; and suggests that the current and recent activity of TEs in avian genomes is very limited, which may be one of the reasons of small genome sizes in birds.

Whole genome sequencing of Gyeongbuk Araucana, a newly developed blue-egg laying chicken breed, reveals its origin and genetic characteristics

Chicken, Gallus gallus, is a valuable species both as a food source and as a model organism for scientific research. Here, we sequenced the genome of Gyeongbuk Araucana, a rare chicken breed with unique phenotypic characteristics including flight ability, large body size, and laying blue-shelled eggs, to identify its genomic features. We generated genomes of Gyeongbuk Araucana, Leghorn, and Korean Native Chicken at a total of 33.5, 35.82, and 33.23 coverage depth, respectively. Along with the genomes of 12 Chinese breeds, we identified genomic variants of 16.3 million SNVs and 2.3 million InDels in mapped regions. Additionally, through assembly of unmapped reads and selective sweep, we identified candidate genes that fall into heart, vasculature and muscle development and body growth categories, which provided insight into Gyeongbuk Araucana's phenotypic traits. Finally, genetic variation based on the transposable element insertion pattern was investigated to elucidate the features of transposable elements related to blue egg shell formation. This study presents results of the first genomic study on the Gyeongbuk Araucana breed; it has potential to serve as an invaluable resource for future research on the genomic characteristics of this chicken breed as well as others.

Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes

Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians.

Losing identity: structural diversity of transposable elements belonging to different classes in the genome of Anopheles gambiae

Background

Transposable elements (TEs), both DNA transposons and retrotransposons, are genetic elements with the main characteristic of being able to mobilize and amplify their own representation within genomes, utilizing different mechanisms of transposition. An almost universal feature of TEs in eukaryotic genomes is their inability to transpose by themselves, mainly as the result of sequence degeneration (by either mutations or deletions). Most of the elements are thus either inactive or non-autonomous. Considering that the bulk of some eukaryotic genomes derive from TEs, they have been conceived as “TE graveyards.” It has been shown that once an element has been inactivated, it progressively accumulates mutations and deletions at neutral rates until completely losing its identity or being lost from the host genome; however, it has also been shown that these “neutral sequences” might serve as raw material for domestication by host genomes.

Results

We have analyzed the sequence structural variations, nucleotide divergence, and pattern of insertions and deletions of several superfamilies of TEs belonging to both class I (long terminal repeats [LTRs] and non-LTRs [NLTRs]) and II in the genome of Anopheles gambiae, aiming at describing the landscape of deterioration of these elements in this particular genome. Our results describe a great diversity in patterns of deterioration, indicating lineage-specific differences including the presence of Solo-LTRs in the LTR lineage, 5′-deleted NLTRs, and several non-autonomous and MITEs in the class II families. Interestingly, we found fragments of NLTRs corresponding to the RT domain, which preserves high identity among them, suggesting a possible remaining genomic role for these domains.

Conclusions

We show here that the TEs in the An. gambiae genome deteriorate in different ways according to the class to which they belong. This diversity certainly has implications not only at the host genomic level but also at the amplification dynamic and evolution of the TE families themselves.

Recombination drives vertebrate genome contraction

Selective and/or neutral processes may govern variation in DNA content and, ultimately, genome size. The observation in several organisms of a negative correlation between recombination rate and intron size could be compatible with a neutral model in which recombination is mutagenic for length changes. We used whole-genome data on small insertions and deletions within transposable elements from chicken and zebra finch to demonstrate clear links between recombination rate and a number of attributes of reduced DNA content. Recombination rate was negatively correlated with the length of introns, transposable elements, and intergenic spacer and with the rate of short insertions. Importantly, it was positively correlated with gene density, the rate of short deletions, the deletion bias, and the net change in sequence length. All these observations point at a pattern of more condensed genome structure in regions of high recombination. Based on the observed rates of small insertions and deletions and assuming that these rates are representative for the whole genome, we estimate that the genome of the most recent common ancestor of birds and lizards has lost nearly 20% of its DNA content up until the present. Expansion of transposable elements can counteract the effect of deletions in an equilibrium mutation model; however, since the activity of transposable elements has been low in the avian lineage, the deletion bias is likely to have had a significant effect on genome size evolution in dinosaurs and birds, contributing to the maintenance of a small genome. We also demonstrate that most of the observed correlations between recombination rate and genome contraction parameters are seen in the human genome, including for segregating indel polymorphisms. Our data are compatible with a neutral model in which recombination drives vertebrate genome size evolution and gives no direct support for a role of natural selection in this process.

One major implication from genetic work done several decades ago is that the genome contains a lot of sequences that do not constitute genes or other functional elements. The total amount of DNA—the genome size—is thus not necessarily an indicator of DNA complexity or organismal complexity, an observation often referred to as the C-value paradox (C-value being a measure of DNA content). What then is it that determines genome size? One model posits that the evolution of genome size is not a consequence of natural selection but is instead governed by the incidence and character of naturally occurring mutations that affect the length of DNA, a process that is not affected by selection. Here we present the results of an analysis of how recombination affects the size of avian and human genomes. We find strong evidence that the rate of recombination is a driving force of genome size evolution. In regions of the genome where recombination occurs frequently, the loss of DNA caused by small deletions is particularly pronounced. Our simulations show that the effect of such recombination-driven genome contraction can be profound over evolutionary time scales. These observations lead to a model in which recombination is mutagenic for length changes and that the incidence of deletions increases with increasing recombination rate. Although we cannot formally exclude that natural selection contributes to the observed relationship between recombination and genome contraction, we find no evidence to support such a scenario.

Insertion of an intact CR1 retrotransposon in a cadherin gene linked with Bt resistance in the pink bollworm, Pectinophora gossypiella

Three mutations in the Pectinophora gossypiella cadherin gene PgCad1 are linked with resistance to Bacillus thuringiensis (Bt) toxin Cry1Ac. Here we show that the r3 mutation entails recent insertion into PgCad1 of an active chicken repeat (CR1) retrotransposon, designated CR1-1_Pg. Unlike most other CR1 elements, CR1-1_Pg is intact, transcribed by a flanking promoter, contains target site duplications and has a relatively low number of copies. Examination of transcripts from the PgCad1 locus revealed that CR1-1_Pg disrupts both the cadherin protein and a long noncoding RNA of unknown function. Together with previously reported data, these findings show that transposable elements disrupt eight of 12 cadherin alleles linked with resistance to Cry1Ac in three lepidopteran species, indicating that the cadherin locus is a common target for disruption by transposable elements.

The transposable element profile of the anolis genome: How a lizard can provide insights into the evolution of vertebrate genome size and structure

The recent sequencing of the lizard genome provides a unique opportunity to examine the evolution of vertebrate genomes in a phylogenetic context. The lizard genome contains an extraordinary diversity of active transposable elements that far exceeds the diversity reported in extant mammals and birds. Retrotransposons and DNA transposons are represented by multiple active families, contributing to the very diverse repetitive landscape of the lizard. Surprisingly, ancient transposon copies are relatively rare suggesting that the transposon copy number is tightly controlled in lizard. This bias in favor of young copies results from the joint effect of purifying selection acting on novel insertions and a high rate of DNA loss. Recent analyses have revealed that the repetitive landscape of reptiles differ drastically from other extant amniotes by their diversity but also by the dynamics of amplification of their transposons. Thus, from the point of view of mobile elements, reptile genomes show more similarity to fish and amphibians than to other amniotes.

A genome-wide view of mutation rate co-variation using multivariate analyses

Background

While the abundance of available sequenced genomes has led to many studies of regional heterogeneity in mutation rates, the co-variation among rates of different mutation types remains largely unexplored, hindering a deeper understanding of mutagenesis and genome dynamics. Here, utilizing primate and rodent genomic alignments, we apply two multivariate analysis techniques (principal components and canonical correlations) to investigate the structure of rate co-variation for four mutation types and simultaneously explore the associations with multiple genomic features at different genomic scales and phylogenetic distances.

Results

We observe a consistent, largely linear co-variation among rates of nucleotide substitutions, small insertions and small deletions, with some non-linear associations detected among these rates on chromosome X and near autosomal telomeres. This co-variation appears to be shaped by a common set of genomic features, some previously investigated and some novel to this study (nuclear lamina binding sites, methylated non-CpG sites and nucleosome-free regions). Strong non-linear relationships are also detected among genomic features near the centromeres of large chromosomes. Microsatellite mutability co-varies with other mutation rates at finer scales, but not at 1 Mb, and shows varying degrees of association with genomic features at different scales.

Conclusions

Our results allow us to speculate about the role of different molecular mechanisms, such as replication, recombination, repair and local chromatin environment, in mutagenesis. The software tools developed for our analyses are available through Galaxy, an open-source genomics portal, to facilitate the use of multivariate techniques in future large-scale genomics studies.

Effects of L1-ORF2 fragments on green fluorescent protein gene expression

The retrotransposon known as long interspersed nuclear element-1 (L1) is 6 kb long, although most L1s in mammalian and other eukaryotic cells are truncated. L1 contains two open reading frames, ORF1 and ORF2, that code for an RNA-binding protein and a protein with endonuclease and reverse transcriptase activities, respectively. In this work, we examined the effects of full length L1-ORF2 and ORF2 fragments on green fluorescent protein gene (GFP) expression when inserted into the pEGFP-C1 vector downstream of GFP. All of the ORF2 fragments in sense orientation inhibited GFP expression more than when in antisense orientation, which suggests that small ORF2 fragments contribute to the distinct inhibitory effects of this ORF on gene expression. These results provide the first evidence that different 280-bp fragments have distinct effects on the termination of gene transcription, and that when inserted in the antisense direction, fragment 280-9 (the 3' end fragment of ORF2) induces premature termination of transcription that is consistent with the effect of ORF2.

Control of chicken CR1 retrotransposons is independent of Dicer-mediated RNA interference pathway

BACKGROUND

Dicer is an RNase III-ribonuclease that initiates the formation of small interfering RNAs as a defence against genomic parasites such as retrotransposons. Despite intensive characterization in mammalian species, the biological functions of Dicer in controlling retrotransposable elements of the non-mammalian vertebrate are poorly understood. In this report, we examine the role of chicken Dicer in controlling the activity of chicken CR1 retrotransposable elements in a chicken-human hybrid DT40 cell line employing a conditional loss-of-Dicer function.

RESULTS

Retrotransposition is detrimental to host genome stability and thus eukaryotic cells have developed mechanisms to limit the expansion of retrotransposons by Dicer-mediated RNAi silencing pathways. However, the mechanisms that control the activity and copy numbers of transposable elements in chicken remain unclear. Here, we describe how the loss of Dicer in chicken cells does not reactivate endogenous chicken CR1 retrotransposons with impaired RNAi machinery, suggesting that the control of chicken CR1 is independent of Dicer-induced RNAi silencing. In contrast, upon introduction of a functionally active human L1 retrotransposable element that contains an active 5' UTR promoter, the Dicer-deficient chicken cells show a strong increase in the accumulation of human L1 transcripts and retrotransposition activity, highlighting a major difference between chicken CR1 and other mammalian L1 retrotransposons.

CONCLUSION

Our data provide evidence that chicken CR1 retrotransposons, unlike their mammalian L1 counterparts, do not undergo retrotransposition because most CR1 retrotransposons are truncated or mutated at their 5'UTR promoters and thus are not subjected to Dicer-mediated RNAi-silencing control.

The role of LINEs and CpG islands in dosage compensation on the chicken Z chromosome

Most avian Z genes are expressed more highly in ZZ males than ZW females, suggesting that chromosome-wide mechanisms of dosage compensation have not evolved. Nevertheless, a small percentage of Z genes are expressed at similar levels in males and females, an indication that a yet unidentified mechanism compensates for the sex difference in copy number. Primary DNA sequences are thought to have a role in determining chromosome gene inactivation status on the mammalian X chromosome. However, it is currently unknown whether primary DNA sequences also mediate chicken Z gene compensation status. Using a combination of chicken DNA sequences and Z gene compensation profiles of 310 genes, we explored the relationship between Z gene compensation status and primary DNA sequence features. Statistical analysis of different Z chromosomal features revealed that long interspersed nuclear elements (LINEs) and CpG islands are enriched on the Z chromosome compared with 329 other DNA features. Linear support vector machine (SVM) classifiers, using primary DNA sequences, correctly predict the Z compensation status for >60% of all Z-linked genes. CpG islands appear to be the most accurate classifier and alone can correctly predict compensation of 63% of Z genes. We also show that LINE CR1 elements are enriched 2.7-fold on the chicken Z chromosome compared with autosomes and that chicken chromosomal length is highly correlated with percentage LINE content. However, the position of LINE elements is not significantly associated with dosage compensation status of Z genes. We also find a trend for a higher proportion of CpG islands in the region of the Z chromosome with the fewest dosage-compensated genes compared with the region containing the greatest concentration of compensated genes. Comparison between chicken and platypus genomes shows that LINE elements are not enriched on sex chromosomes in platypus, indicating that LINE accumulation is not a feature of all sex chromosomes. Our results suggest that CpG islands are not randomly distributed on the Z chromosome and may influence Z gene dosage compensation status.

Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats

Chicken Repeat 1 (CR1) repeats are the most abundant family of repeats in the chicken genome, with more than 200,000 copies accounting for approximately 80% of the chicken interspersed repeats. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to the 22 CR1 subfamilies as previously reported in Repbase. We performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the chicken genome. We identified and validated 57 chicken CR1 subfamilies and further analyzed the correlation between these subfamilies and their regional GC contents. We also discovered one novel lineage-specific CR1 subfamilies in turkeys when compared with chickens. We built an evolutionary tree of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.

Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes

Discovery of a large number of conserved non-coding elements (CNEs) in vertebrate genomes provides a cornerstone to elucidate molecular mechanisms of macroevolution. Extensive comparative genomics has proven that transposons such as short interspersed elements (SINEs) were an important source of CNEs. We recently characterized AmnSINE1, a SINE family in Amniota genomes, some of which are present in CNEs, and demonstrated that two AmnSINE1 loci play an important role in mammalian-specific brain development by functioning as an enhancer (Sasaki et al. Proc. Natl. Acad. Sci. USA 2008). To get more information about AmnSINE1s, we here performed a multi-species search for AmnSINE1, and revealed the distribution and evolutionary history of these SINEs in amniote genomes. The number of AmnSINE1 regions in amniotes ranged from 160 to 1200; the number in the eutherians were under 500 and the largest was that in chicken. Phylogenetic analysis established that each AmnSINE1 locus has evolved uniquely, primarily since the divergence of mammals from reptiles. These results support the notion that AmnSINE1s were amplified as an ancient retroposon in a common ancestor of Amniota and subsequently have survived for 300 Myr because of functions acquired by mutation-coupled exaptation prior mammalian radiation. On the basis of sequence homology and conserved synteny, we detected the orthologs of AmnSINE1 for candidates of further enhancer analysis, which are more conserved than two loci that were shown to have been involved in mammalian brain development. The present work provides a comprehensive data set to test the role of AmnSINE1s, many of which were exapted and contributed to mammalian macroevolution.