Evolution and Diversity of Transposable Elements in Vertebrate Genomes

Sotero-Caio, Cibele G.; Platt, Roy N.; Suh, Alexander; Ray, David A.

doi:10.1093/gbe/evw264

Cited by 246 publications

(262 citation statements)

References 231 publications

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“…The availability of comprehensive repeat annotation for the collared flycatcher (Suh et al., ) allowed us to explore such putative exaptations for the first time in an avian species. In contrast to mammals, where TEs account for more than half of many species’ genomes (Sotero‐Caio, Platt, Suh, & Ray, ), birds generally have far fewer TEs, with the number of copies ranging from 130,000 to 350,000 and genomic TE densities from 4.1% to 9.8% in most species so far investigated (Kapusta & Suh, ; Zhang et al., ). The current collared flycatcher genome assembly and annotation contains 209,730 TEs, spanning 5.4% of the genome.…”

Section: Discussionmentioning

confidence: 99%

Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)

Craig

Suh

et al. 2018

Molecular Ecology

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It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence are particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts. We report that~6.6% of the collared flycatcher genome (74.0 Mb) is spanned by~1.28 million CEs, a higher proportion of the genome but a lower total amount of conserved sequence than has been reported in mammals. We identified >200,000 CEs specific to either the archosaur, avian, neoavian or passeridan lineages, constituting candidates for lineage-specific adaptations.Importantly, no less than~71% of CE sites were nonexonic (52.6 Mb), and conserved nonexonic sequence density was negatively correlated with functional exonic density at local genomic scales. Additionally, nucleotide diversity was strongly reduced at nonexonic conserved sites (0.00153) relative to intergenic nonconserved sites (0.00427). By integrating deep transcriptome sequencing and additional genome annotation, we identified novel protein-coding genes, long noncoding RNA genes and transposon-derived (exapted) CEs. The approach taken here based on the use of a PRO-GRESSIVE CACTUS whole-genome alignment to identify CEs should be readily applicable to nonmodel organisms in general and help to reveal the rich repertoire of putatively functional noncoding sequence as targets for selection.

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Section: Discussionmentioning

confidence: 99%

Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)

Craig

Suh

et al. 2018

Molecular Ecology

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“…vertebrates is the abundance and diversity of transposable elements (TEs) Sotero-Caio et al, 2017]. TE is an umbrella term that covers a large diversity of mobile DNA sequences that have the ability to replicate and multiply in the genome of their host.…”

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confidence: 99%

The Mobilome of Reptiles: Evolution, Structure, and Function

Boissinot¹,

Bourgeois²,

Manthey

et al. 2019

Cytogenet Genome Res

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Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

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“…These genomes are typically in a draft form, consisting of tens of thousands of scaffolds that comprise the majority of the assembly. Long‐insert libraries greater than 8 Kbp are needed to span long interspersed nuclear elements (LINEs), some of the most common repetitive elements in eukaryotic genomes (Sotero‐Caio, Platt, Suh, & Ray, ; Treangen & Salzberg, ; van Heesch et al, ). However, even 20–25 Kbp long‐insert libraries cannot span and thus resolve repetitive elements such as long segmental duplications in eukaryotic genomes (Bailey, ; Feng et al, ; Treangen & Salzberg, ).…”

Section: Introductionmentioning

confidence: 99%

Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary

Elbers

Rogers

Perelman

et al. 2019

Molecular Ecology Resources

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Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate‐pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi‐C and Dovetail Genomics Chicago libraries and long‐read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high‐quality contiguous reference genome is the dromedary ( Camelus dromedarius ). Draft genomes exist but are highly fragmented, and a high‐quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi‐C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome‐level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi‐C libraries increased the longest scaffold over 12‐fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50‐fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long‐read sequencing.

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Evolution and Diversity of Transposable Elements in Vertebrate Genomes

Cited by 246 publications

References 231 publications

Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)

Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)

The Mobilome of Reptiles: Evolution, Structure, and Function

Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary

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