Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and <i>Gnetum</i> 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 of...

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Autores principales:	Avi Titievsky, Yuliya A. Putintseva, Elizaveta A. Taranenko, Sofya Baskin, Natalia V. Oreshkova, Elia Brodsky, Alexandra V. Sharova, Vadim V. Sharov, Julia Panov, Dmitry A. Kuzmin, Leonid Brodsky, Konstantin V. Krutovsky
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	gymnosperms repetitive elements principal component analysis Science Q
Acceso en línea:	https://doaj.org/article/405290e96a494cba8566672ffe00de22
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spelling	oai:doaj.org-article:405290e96a494cba8566672ffe00de222021-11-25T18:11:25ZComparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and <i>Gnetum</i> Species10.3390/life111112342075-1729https://doaj.org/article/405290e96a494cba8566672ffe00de222021-11-01T00:00:00Zhttps://www.mdpi.com/2075-1729/11/11/1234https://doaj.org/toc/2075-1729Repetitive 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: <i>Pinus taeda</i>, <i>Pinus sylvestris</i>, <i>Pinus sibirica</i>, <i>Picea glauca</i>, <i>Picea abies</i>, <i>Abies sibirica</i>, <i>Larix sibirica</i>, <i>Juniperus communis</i>, <i>Taxus baccata</i>, and <i>Gnetum gnemon</i>. 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 (<i>kChains</i>) and matches the known taxonomic relations.Avi TitievskyYuliya A. PutintsevaElizaveta A. TaranenkoSofya BaskinNatalia V. OreshkovaElia BrodskyAlexandra V. SharovaVadim V. SharovJulia PanovDmitry A. KuzminLeonid BrodskyKonstantin V. KrutovskyMDPI AGarticlegymnospermsrepetitive elementsprincipal component analysisScienceQENLife, Vol 11, Iss 1234, p 1234 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	gymnosperms repetitive elements principal component analysis Science Q
spellingShingle	gymnosperms repetitive elements principal component analysis Science Q Avi Titievsky Yuliya A. Putintseva Elizaveta A. Taranenko Sofya Baskin Natalia V. Oreshkova Elia Brodsky Alexandra V. Sharova Vadim V. Sharov Julia Panov Dmitry A. Kuzmin Leonid Brodsky Konstantin V. Krutovsky Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and <i>Gnetum</i> Species
description	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: <i>Pinus taeda</i>, <i>Pinus sylvestris</i>, <i>Pinus sibirica</i>, <i>Picea glauca</i>, <i>Picea abies</i>, <i>Abies sibirica</i>, <i>Larix sibirica</i>, <i>Juniperus communis</i>, <i>Taxus baccata</i>, and <i>Gnetum gnemon</i>. 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 (<i>kChains</i>) and matches the known taxonomic relations.
format	article
author	Avi Titievsky Yuliya A. Putintseva Elizaveta A. Taranenko Sofya Baskin Natalia V. Oreshkova Elia Brodsky Alexandra V. Sharova Vadim V. Sharov Julia Panov Dmitry A. Kuzmin Leonid Brodsky Konstantin V. Krutovsky
author_facet	Avi Titievsky Yuliya A. Putintseva Elizaveta A. Taranenko Sofya Baskin Natalia V. Oreshkova Elia Brodsky Alexandra V. Sharova Vadim V. Sharov Julia Panov Dmitry A. Kuzmin Leonid Brodsky Konstantin V. Krutovsky
author_sort	Avi Titievsky
title	Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and <i>Gnetum</i> Species
title_short	Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and <i>Gnetum</i> Species
title_full	Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and <i>Gnetum</i> Species
title_fullStr	Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and <i>Gnetum</i> Species
title_full_unstemmed	Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and <i>Gnetum</i> Species
title_sort	comparative genomics analysis of repetitive elements in ten gymnosperm species: “dark repeatome” and its abundance in conifer and <i>gnetum</i> species
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/405290e96a494cba8566672ffe00de22
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Comparative Genomics Analysis of Repetitive Elements in Ten Gymnosperm Species: “Dark Repeatome” and Its Abundance in Conifer and <i>Gnetum</i> Species

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