Dataset Information

Segmental duplications: evolution and impact among the current Lepidoptera genomes.

ABSTRACT: Structural variation among genomes is now viewed to be as important as single nucleoid polymorphisms in influencing the phenotype and evolution of a species. Segmental duplication (SD) is defined as segments of DNA with homologous sequence.Here, we performed a systematic analysis of segmental duplications (SDs) among five lepidopteran reference genomes (Plutella xylostella, Danaus plexippus, Bombyx mori, Manduca sexta and Heliconius melpomene) to understand their potential impact on the evolution of these species. We find that the SDs content differed substantially among species, ranging from 1.2% of the genome in B. mori to 15.2% in H. melpomene. Most SDs formed very high identity (similarity higher than 90%) blocks but had very few large blocks. Comparative analysis showed that most of the SDs arose after the divergence of each linage and we found that P. xylostella and H. melpomene showed more duplications than other species, suggesting they might be able to tolerate extensive levels of variation in their genomes. Conserved ancestral and species specific SD events were assessed, revealing multiple examples of the gain, loss or maintenance of SDs over time. SDs content analysis showed that most of the genes embedded in SDs regions belonged to species-specific SDs ("Unique" SDs). Functional analysis of these genes suggested their potential roles in the lineage-specific evolution. SDs and flanking regions often contained transposable elements (TEs) and this association suggested some involvement in SDs formation. Further studies on comparison of gene expression level between SDs and non-SDs showed that the expression level of genes embedded in SDs was significantly lower, suggesting that structure changes in the genomes are involved in gene expression differences in species.The results showed that most of the SDs were "unique SDs", which originated after species formation. Functional analysis suggested that SDs might play different roles in different species. Our results provide a valuable resource beyond the genetic mutation to explore the genome structure for future Lepidoptera research.

SUBMITTER: Zhao Q

PROVIDER: S-EPMC5499213 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Segmental duplications: evolution and impact among the current Lepidoptera genomes.

Zhao Qian Q Ma Dongna D Vasseur Liette L You Minsheng M

BMC evolutionary biology 20170706 1

<h4>Background</h4>Structural variation among genomes is now viewed to be as important as single nucleoid polymorphisms in influencing the phenotype and evolution of a species. Segmental duplication (SD) is defined as segments of DNA with homologous sequence.<h4>Results</h4>Here, we performed a systematic analysis of segmental duplications (SDs) among five lepidopteran reference genomes (Plutella xylostella, Danaus plexippus, Bombyx mori, Manduca sexta and Heliconius melpomene) to understand the ...[more]

PMID: 28683762

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Project description:Segmental duplications play fundamental roles in both genomic disease and gene evolution. To understand their organization within the human genome, we have developed the computational tools and methods necessary to detect identity between long stretches of genomic sequence despite the presence of high copy repeats and large insertion-deletions. Here we present our analysis of the most recent genome assembly (January 2001) in which we focus on the global organization of these segments and the role they play in the whole-genome assembly process. Initially, we considered only large recent duplication events that fell well-below levels of draft sequencing error (alignments 90%-98% similar and > or =1 kb in length). Duplications (90%-98%; > or =1 kb) comprise 3.6% of all human sequence. These duplications show clustering and up to 10-fold enrichment within pericentromeric and subtelomeric regions. In terms of assembly, duplicated sequences were found to be over-represented in unordered and unassigned contigs indicating that duplicated sequences are difficult to assign to their proper position. To assess coverage of these regions within the genome, we selected BACs containing interchromosomal duplications and characterized their duplication pattern by FISH. Only 47% (106/224) of chromosomes positive by FISH had a corresponding chromosomal position by comparison. We present data that indicate that this is attributable to misassembly, misassignment, and/or decreased sequencing coverage within duplicated regions. Surprisingly, if we consider putative duplications >98% identity, we identify 10.6% (286 Mb) of the current assembly as paralogous. The majority of these alignments, we believe, represent unmerged overlaps within unique regions. Taken together the above data indicate that segmental duplications represent a significant impediment to accurate human genome assembly, requiring the development of specialized techniques to finish these exceptional regions of the genome. The identification and characterization of these highly duplicated regions represents an important step in the complete sequencing of a human reference genome.

Project description:BackgroundSegmental duplications (SDs), also known as low-copy repeats, are DNA sequences of length greater than 1 kb which are duplicated with a high degree of sequence identity (greater than 90%) causing instability in genomes. SDs are generally found in the genome as mosaic forms of duplicated sequences which are generated by a two-step process: first, multiple duplicated sequences are aggregated at specific genomic regions, and then, these primary duplications undergo multiple secondary duplications. However, the mechanism of how duplicated sequences are aggregated in the first place is not well understood.ResultsBy analyzing the distribution of microsatellite sequences among twenty insect species in a genome-wide manner it was found that pairs of microsatellites along with the intervening sequences were duplicated multiple times in each genome. They were found as low copy repeats or segmental duplications when the duplicated loci were greater than 1 kb in length and had greater than 90% sequence similarity. By performing a sliding-window genomic analysis for number of paired microsatellites and number of segmental duplications, it was observed that regions rich in repetitive paired microsatellites tend to get richer in segmental duplication suggesting a "rich-gets-richer" mode of aggregation of the duplicated loci in specific regions of the genome. Results further show that the relationship between number of paired microsatellites and segmental duplications among the species is independent of the known phylogeny suggesting that association of microsatellites with segmental duplications may be a species-specific evolutionary process. It was also observed that the repetitive microsatellite pairs are associated with gene duplications but those sequences are rarely retained in the orthologous genes between species. Although some of the duplicated sequences with microsatellites as termini were found within transposable elements (TEs) of Drosophila, most of the duplications are found in the TE-free and gene-free regions of the genome.ConclusionThe study clearly suggests that microsatellites are instrumental in extensive sequence duplications that may contribute to species-specific evolution of genome plasticity in insects.

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Segmental duplications: evolution and impact among the current Lepidoptera genomes.

Publications

Segmental duplications: evolution and impact among the current Lepidoptera genomes.

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