The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.

<h4>Background</h4>Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of m...

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Autores principales:	Wenqin Wang, Yongrui Wu, Joachim Messing
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ca743fca802e4ed2a77176517b13362a
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spelling	oai:doaj.org-article:ca743fca802e4ed2a77176517b13362a2021-11-18T08:13:11ZThe mitochondrial genome of an aquatic plant, Spirodela polyrhiza.1932-620310.1371/journal.pone.0046747https://doaj.org/article/ca743fca802e4ed2a77176517b13362a2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23056432/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mt genomes in plant.<h4>Methods</h4>Spirodela polyrhiza mt genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA using the SOLiD platform. Using a genome copy number sensitive assembly algorithm, the mt genome was successfully assembled. Gap closure and accuracy was determined with PCR products sequenced with the dideoxy method.<h4>Conclusions</h4>This is the most compact monocot mitochondrial genome with 228,493 bp. A total of 57 genes encode 35 known proteins, 3 ribosomal RNAs, and 19 tRNAs that recognize 15 amino acids. There are about 600 RNA editing sites predicted and three lineage specific protein-coding-gene losses. The mitochondrial genes, pseudogenes, and other hypothetical genes (ORFs) cover 71,783 bp (31.0%) of the genome. Imported plastid DNA accounts for an additional 9,295 bp (4.1%) of the mitochondrial DNA. Absence of transposable element sequences suggests that very few nuclear sequences have migrated into Spirodela mtDNA. Phylogenetic analysis of conserved protein-coding genes suggests that Spirodela shares the common ancestor with other monocots, but there is no obvious synteny between Spirodela and rice mtDNAs. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly four-fifths of the Spirodela mitochondrial genome is of unknown origin and function. Although it contains a similar chloroplast DNA content and range of RNA editing as other monocots, it is void of nuclear insertions, active gene loss, and comprises large regions of sequences of unknown origin in non-coding regions. Moreover, the lack of synteny with known mitochondrial genomic sequences shed new light on the early evolution of monocot mitochondrial genomes.Wenqin WangYongrui WuJoachim MessingPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 10, p e46747 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wenqin Wang Yongrui Wu Joachim Messing The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.
description	<h4>Background</h4>Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mt genomes in plant.<h4>Methods</h4>Spirodela polyrhiza mt genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA using the SOLiD platform. Using a genome copy number sensitive assembly algorithm, the mt genome was successfully assembled. Gap closure and accuracy was determined with PCR products sequenced with the dideoxy method.<h4>Conclusions</h4>This is the most compact monocot mitochondrial genome with 228,493 bp. A total of 57 genes encode 35 known proteins, 3 ribosomal RNAs, and 19 tRNAs that recognize 15 amino acids. There are about 600 RNA editing sites predicted and three lineage specific protein-coding-gene losses. The mitochondrial genes, pseudogenes, and other hypothetical genes (ORFs) cover 71,783 bp (31.0%) of the genome. Imported plastid DNA accounts for an additional 9,295 bp (4.1%) of the mitochondrial DNA. Absence of transposable element sequences suggests that very few nuclear sequences have migrated into Spirodela mtDNA. Phylogenetic analysis of conserved protein-coding genes suggests that Spirodela shares the common ancestor with other monocots, but there is no obvious synteny between Spirodela and rice mtDNAs. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly four-fifths of the Spirodela mitochondrial genome is of unknown origin and function. Although it contains a similar chloroplast DNA content and range of RNA editing as other monocots, it is void of nuclear insertions, active gene loss, and comprises large regions of sequences of unknown origin in non-coding regions. Moreover, the lack of synteny with known mitochondrial genomic sequences shed new light on the early evolution of monocot mitochondrial genomes.
format	article
author	Wenqin Wang Yongrui Wu Joachim Messing
author_facet	Wenqin Wang Yongrui Wu Joachim Messing
author_sort	Wenqin Wang
title	The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.
title_short	The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.
title_full	The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.
title_fullStr	The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.
title_full_unstemmed	The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.
title_sort	mitochondrial genome of an aquatic plant, spirodela polyrhiza.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/ca743fca802e4ed2a77176517b13362a
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The mitochondrial genome of an aquatic plant, Spirodela polyrhiza.

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