4.6 Article

Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: Dark Repeatome and Its Abundance in Conifer and Gnetum Species

期刊

LIFE-BASEL
卷 11, 期 11, 页码 -

出版社

MDPI
DOI: 10.3390/life11111234

关键词

gymnosperms; repetitive elements; principal component analysis

资金

  1. University of Gottingen
  2. Laszlo N. Tauber Family Foundation
  3. Government of the Russian Federation [14.Y26.31.0004]

向作者/读者索取更多资源

This study focused on analyzing the repeatome content and abundance patterns in the genomes of 10 gymnosperm species using raw genomic NGS reads. The results showed that known and newly discovered putative repeats in the genomes were specific to phylogenetically close groups of species and aligned with biological taxa. The abundances of known and newly discovered putative repeats closely matched the known taxonomic relations among the species.
Repetitive elements (RE) and transposons (TE) can comprise up to 80% of some plant genomes and may be essential for regulating their evolution and adaptation. The repeatome information is often unavailable in assembled genomes because genomic areas of repeats are challenging to assemble and are often missing from final assembly. However, raw genomic sequencing data contain rich information about RE/TEs. Here, raw genomic NGS reads of 10 gymnosperm species were studied for the content and abundance patterns of their repeatome. We utilized a combination of alignment on databases of repetitive elements and de novo assembly of highly repetitive sequences from genomic sequencing reads to characterize and calculate the abundance of known and putative repetitive elements in the genomes of 10 conifer plants: Pinus taeda, Pinus sylvestris, Pinus sibirica, Picea glauca, Picea abies, Abies sibirica, Larix sibirica, Juniperus communis, Taxus baccata, and Gnetum gnemon. We found that genome abundances of known and newly discovered putative repeats are specific to phylogenetically close groups of species and match biological taxa. The grouping of species based on abundances of known repeats closely matches the grouping based on abundances of newly discovered putative repeats (kChains) and matches the known taxonomic relations.

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