Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.

Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a...

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Autores principales:	Nemanja Vukašinović, Fatima Cvrčková, Marek Eliáš, Rex Cole, John E Fowler, Viktor Žárský, Lukáš Synek
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/84d67cbbf7b74340951bb17d21ce6493
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spelling	oai:doaj.org-article:84d67cbbf7b74340951bb17d21ce64932021-11-18T08:23:39ZDissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.1932-620310.1371/journal.pone.0094077https://doaj.org/article/84d67cbbf7b74340951bb17d21ce64932014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24728280/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethering complex, we examined whether this could be explained by a hidden gene duplication. Re-sequencing and manual assembly of the Arabidopsis thaliana SEC10 (At5g12370) locus revealed that this locus, comprising a single gene in the reference genome assembly, indeed contains two paralogous genes in tandem, SEC10a and SEC10b, and that a sequence segment of 7 kb in length is missing from the reference genome sequence. Differences between the two paralogs are concentrated in non-coding regions, while the predicted protein sequences exhibit 99% identity, differing only by substitution of five amino acid residues and an indel of four residues. Both SEC10 genes are expressed, although varying transcript levels suggest differential regulation. Homozygous T-DNA insertion mutants in either paralog exhibit a wild-type phenotype, consistent with proposed extensive functional redundancy of the two genes. By these observations we demonstrate that recently duplicated genes may remain hidden even in well-characterized genomes, such as that of A. thaliana. Moreover, we show that the use of the existing A. thaliana reference genome sequence as a guide for sequence assembly of new Arabidopsis accessions or related species has at least in some cases led to error propagation.Nemanja VukašinovićFatima CvrčkováMarek EliášRex ColeJohn E FowlerViktor ŽárskýLukáš SynekPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 4, p e94077 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nemanja Vukašinović Fatima Cvrčková Marek Eliáš Rex Cole John E Fowler Viktor Žárský Lukáš Synek Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.
description	Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethering complex, we examined whether this could be explained by a hidden gene duplication. Re-sequencing and manual assembly of the Arabidopsis thaliana SEC10 (At5g12370) locus revealed that this locus, comprising a single gene in the reference genome assembly, indeed contains two paralogous genes in tandem, SEC10a and SEC10b, and that a sequence segment of 7 kb in length is missing from the reference genome sequence. Differences between the two paralogs are concentrated in non-coding regions, while the predicted protein sequences exhibit 99% identity, differing only by substitution of five amino acid residues and an indel of four residues. Both SEC10 genes are expressed, although varying transcript levels suggest differential regulation. Homozygous T-DNA insertion mutants in either paralog exhibit a wild-type phenotype, consistent with proposed extensive functional redundancy of the two genes. By these observations we demonstrate that recently duplicated genes may remain hidden even in well-characterized genomes, such as that of A. thaliana. Moreover, we show that the use of the existing A. thaliana reference genome sequence as a guide for sequence assembly of new Arabidopsis accessions or related species has at least in some cases led to error propagation.
format	article
author	Nemanja Vukašinović Fatima Cvrčková Marek Eliáš Rex Cole John E Fowler Viktor Žárský Lukáš Synek
author_facet	Nemanja Vukašinović Fatima Cvrčková Marek Eliáš Rex Cole John E Fowler Viktor Žárský Lukáš Synek
author_sort	Nemanja Vukašinović
title	Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.
title_short	Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.
title_full	Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.
title_fullStr	Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.
title_full_unstemmed	Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.
title_sort	dissecting a hidden gene duplication: the arabidopsis thaliana sec10 locus.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/84d67cbbf7b74340951bb17d21ce6493
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Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.

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