Reference-free comparative genomics of 174 chloroplasts.

Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Chai-Shian Kua, Jue Ruan, John Harting, Cheng-Xi Ye, Matthew R Helmus, Jun Yu, Charles H Cannon
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a0889bd0f6b3498d9393f89743c533c8
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:a0889bd0f6b3498d9393f89743c533c8
record_format	dspace
spelling	oai:doaj.org-article:a0889bd0f6b3498d9393f89743c533c82021-11-18T08:08:11ZReference-free comparative genomics of 174 chloroplasts.1932-620310.1371/journal.pone.0048995https://doaj.org/article/a0889bd0f6b3498d9393f89743c533c82012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23185288/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ~18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid [2] to a massive algal chloroplast [3], including gnetophytes [4] and cycads [5]. The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied genomes and rapid discovery of informative candidate regions.Chai-Shian KuaJue RuanJohn HartingCheng-Xi YeMatthew R HelmusJun YuCharles H CannonPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 11, p e48995 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Chai-Shian Kua Jue Ruan John Harting Cheng-Xi Ye Matthew R Helmus Jun Yu Charles H Cannon Reference-free comparative genomics of 174 chloroplasts.
description	Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ~18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid [2] to a massive algal chloroplast [3], including gnetophytes [4] and cycads [5]. The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied genomes and rapid discovery of informative candidate regions.
format	article
author	Chai-Shian Kua Jue Ruan John Harting Cheng-Xi Ye Matthew R Helmus Jun Yu Charles H Cannon
author_facet	Chai-Shian Kua Jue Ruan John Harting Cheng-Xi Ye Matthew R Helmus Jun Yu Charles H Cannon
author_sort	Chai-Shian Kua
title	Reference-free comparative genomics of 174 chloroplasts.
title_short	Reference-free comparative genomics of 174 chloroplasts.
title_full	Reference-free comparative genomics of 174 chloroplasts.
title_fullStr	Reference-free comparative genomics of 174 chloroplasts.
title_full_unstemmed	Reference-free comparative genomics of 174 chloroplasts.
title_sort	reference-free comparative genomics of 174 chloroplasts.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/a0889bd0f6b3498d9393f89743c533c8
work_keys_str_mv	AT chaishiankua referencefreecomparativegenomicsof174chloroplasts AT jueruan referencefreecomparativegenomicsof174chloroplasts AT johnharting referencefreecomparativegenomicsof174chloroplasts AT chengxiye referencefreecomparativegenomicsof174chloroplasts AT matthewrhelmus referencefreecomparativegenomicsof174chloroplasts AT junyu referencefreecomparativegenomicsof174chloroplasts AT charleshcannon referencefreecomparativegenomicsof174chloroplasts
_version_	1718422184763850752

Reference-free comparative genomics of 174 chloroplasts.

Ejemplares similares