A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.

The genus Fragaria encompasses species at ploidy levels ranging from diploid to decaploid. The cultivated strawberry, Fragaria×ananassa, and its two immediate progenitors, F. chiloensis and F. virginiana, are octoploids. To elucidate the ancestries of these octoploid species, we performed a phylogen...

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Autores principales:	Laura M DiMeglio, Günter Staudt, Hongrun Yu, Thomas M Davis
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/912201cc32fa47c98cec36281595012c
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spelling	oai:doaj.org-article:912201cc32fa47c98cec36281595012c2021-11-25T06:06:33ZA phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.1932-620310.1371/journal.pone.0102237https://doaj.org/article/912201cc32fa47c98cec36281595012c2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25078607/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The genus Fragaria encompasses species at ploidy levels ranging from diploid to decaploid. The cultivated strawberry, Fragaria×ananassa, and its two immediate progenitors, F. chiloensis and F. virginiana, are octoploids. To elucidate the ancestries of these octoploid species, we performed a phylogenetic analysis using intron-containing sequences of the nuclear ADH-1 gene from 39 germplasm accessions representing nineteen Fragaria species and one outgroup species, Dasiphora fruticosa. All trees from Maximum Parsimony and Maximum Likelihood analyses showed two major clades, Clade A and Clade B. Each of the sampled octoploids contributed alleles to both major clades. All octoploid-derived alleles in Clade A clustered with alleles of diploid F. vesca, with the exception of one octoploid allele that clustered with the alleles of diploid F. mandshurica. All octoploid-derived alleles in clade B clustered with the alleles of only one diploid species, F. iinumae. When gaps encoded as binary characters were included in the Maximum Parsimony analysis, tree resolution was improved with the addition of six nodes, and the bootstrap support was generally higher, rising above the 50% threshold for an additional nine branches. These results, coupled with the congruence of the sequence data and the coded gap data, validate and encourage the employment of sequence sets containing gaps for phylogenetic analysis. Our phylogenetic conclusions, based upon sequence data from the ADH-1 gene located on F. vesca linkage group II, complement and generally agree with those obtained from analyses of protein-encoding genes GBSSI-2 and DHAR located on F. vesca linkage groups V and VII, respectively, but differ from a previous study that utilized rDNA sequences and did not detect the ancestral role of F. iinumae.Laura M DiMeglioGünter StaudtHongrun YuThomas M DavisPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 7, p e102237 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Laura M DiMeglio Günter Staudt Hongrun Yu Thomas M Davis A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.
description	The genus Fragaria encompasses species at ploidy levels ranging from diploid to decaploid. The cultivated strawberry, Fragaria×ananassa, and its two immediate progenitors, F. chiloensis and F. virginiana, are octoploids. To elucidate the ancestries of these octoploid species, we performed a phylogenetic analysis using intron-containing sequences of the nuclear ADH-1 gene from 39 germplasm accessions representing nineteen Fragaria species and one outgroup species, Dasiphora fruticosa. All trees from Maximum Parsimony and Maximum Likelihood analyses showed two major clades, Clade A and Clade B. Each of the sampled octoploids contributed alleles to both major clades. All octoploid-derived alleles in Clade A clustered with alleles of diploid F. vesca, with the exception of one octoploid allele that clustered with the alleles of diploid F. mandshurica. All octoploid-derived alleles in clade B clustered with the alleles of only one diploid species, F. iinumae. When gaps encoded as binary characters were included in the Maximum Parsimony analysis, tree resolution was improved with the addition of six nodes, and the bootstrap support was generally higher, rising above the 50% threshold for an additional nine branches. These results, coupled with the congruence of the sequence data and the coded gap data, validate and encourage the employment of sequence sets containing gaps for phylogenetic analysis. Our phylogenetic conclusions, based upon sequence data from the ADH-1 gene located on F. vesca linkage group II, complement and generally agree with those obtained from analyses of protein-encoding genes GBSSI-2 and DHAR located on F. vesca linkage groups V and VII, respectively, but differ from a previous study that utilized rDNA sequences and did not detect the ancestral role of F. iinumae.
format	article
author	Laura M DiMeglio Günter Staudt Hongrun Yu Thomas M Davis
author_facet	Laura M DiMeglio Günter Staudt Hongrun Yu Thomas M Davis
author_sort	Laura M DiMeglio
title	A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.
title_short	A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.
title_full	A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.
title_fullStr	A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.
title_full_unstemmed	A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.
title_sort	phylogenetic analysis of the genus fragaria (strawberry) using intron-containing sequence from the adh-1 gene.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/912201cc32fa47c98cec36281595012c
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A phylogenetic analysis of the genus Fragaria (strawberry) using intron-containing sequence from the ADH-1 gene.

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