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Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

Identifieur interne : 000503 ( Main/Exploration ); précédent : 000502; suivant : 000504

Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

Auteurs : Luxian Liu [République populaire de Chine] ; Xinjie Jin [République populaire de Chine] ; Nan Chen [République populaire de Chine] ; Xian Li [République populaire de Chine] ; Pan Li [République populaire de Chine] ; Chengxin Fu [République populaire de Chine]

Source :

RBID : PMC:4591994

Abstract

Phylogenetic relationships among Chinese species of Morella (Myricaceae) are unresolved. Here, we use restriction site-associated DNA sequencing (RAD-seq) to identify candidate loci that will help in determining phylogenetic relationships among Morella rubra, M. adenophora, M. nana and M. esculenta. Three methods for inferring phylogeny, maximum parsimony (MP), maximum likelihood (ML) and Bayesian concordance, were applied to data sets including as many as 4253 RAD loci with 8360 parsimony informative variable sites. All three methods significantly favored the topology of (((M. rubra, M. adenophora), M. nana), M. esculenta). Two species from North America (M. cerifera and M. pensylvanica) were placed as sister to the four Chinese species. According to BEAST analysis, we deduced speciation of M. rubra to be at about the Miocene-Pliocene boundary (5.28 Ma). Intraspecific divergence in M. rubra occurred in the late Pliocene (3.39 Ma). From pooled data, we assembled 29378, 21902 and 23552 de novo contigs with an average length of 229, 234 and 234 bp for M. rubra, M. nana and M. esculenta respectively. The contigs were used to investigate functional classification of RAD tags in a BLASTX search. Additionally, we identified 3808 unlinked SNP sites across the four populations of M. rubra and discovered genes associated with fruit ripening and senescence, fruit quality and disease/defense metabolism based on KEGG database.


Url:
DOI: 10.1371/journal.pone.0139840
PubMed: 26431030
PubMed Central: 4591994


Affiliations:


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Le document en format XML

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<p>Phylogenetic relationships among Chinese species of
<italic>Morella</italic>
(Myricaceae) are unresolved. Here, we use restriction site-associated DNA sequencing (RAD-seq) to identify candidate loci that will help in determining phylogenetic relationships among
<italic>Morella rubra</italic>
,
<italic>M</italic>
.
<italic>adenophora</italic>
,
<italic>M</italic>
.
<italic>nana</italic>
and
<italic>M</italic>
.
<italic>esculenta</italic>
. Three methods for inferring phylogeny, maximum parsimony (MP), maximum likelihood (ML) and Bayesian concordance, were applied to data sets including as many as 4253 RAD loci with 8360 parsimony informative variable sites. All three methods significantly favored the topology of (((
<italic>M</italic>
.
<italic>rubra</italic>
,
<italic>M</italic>
.
<italic>adenophora</italic>
),
<italic>M</italic>
.
<italic>nana</italic>
),
<italic>M</italic>
.
<italic>esculenta</italic>
). Two species from North America (
<italic>M</italic>
.
<italic>cerifera</italic>
and
<italic>M</italic>
.
<italic>pensylvanica</italic>
) were placed as sister to the four Chinese species. According to BEAST analysis, we deduced speciation of
<italic>M</italic>
.
<italic>rubra</italic>
to be at about the Miocene-Pliocene boundary (5.28 Ma). Intraspecific divergence in
<italic>M</italic>
.
<italic>rubra</italic>
occurred in the late Pliocene (3.39 Ma). From pooled data, we assembled 29378, 21902 and 23552 de novo contigs with an average length of 229, 234 and 234 bp for
<italic>M</italic>
.
<italic>rubra</italic>
,
<italic>M</italic>
.
<italic>nana</italic>
and
<italic>M</italic>
.
<italic>esculenta</italic>
respectively. The contigs were used to investigate functional classification of RAD tags in a BLASTX search. Additionally, we identified 3808 unlinked SNP sites across the four populations of
<italic>M</italic>
.
<italic>rubra</italic>
and discovered genes associated with fruit ripening and senescence, fruit quality and disease/defense metabolism based on KEGG database.</p>
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<name sortKey="Li, L" uniqKey="Li L">L Li</name>
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<author>
<name sortKey="Zou, J" uniqKey="Zou J">J Zou</name>
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<name sortKey="Li, J" uniqKey="Li J">J Li</name>
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<author>
<name sortKey="Fang, X" uniqKey="Fang X">X Fang</name>
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<author>
<name sortKey="Shi, Y" uniqKey="Shi Y">Y Shi</name>
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<analytic>
<author>
<name sortKey="Li, X" uniqKey="Li X">X Li</name>
</author>
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<name sortKey="He, Y" uniqKey="He Y">Y He</name>
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<biblStruct>
<analytic>
<author>
<name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name>
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<author>
<name sortKey="Miao, S" uniqKey="Miao S">S Miao</name>
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<country>
<li>République populaire de Chine</li>
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<li>Zhejiang</li>
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<li>Hangzhou</li>
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<li>Université de Zhejiang</li>
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<name sortKey="Liu, Luxian" sort="Liu, Luxian" uniqKey="Liu L" first="Luxian" last="Liu">Luxian Liu</name>
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<name sortKey="Chen, Nan" sort="Chen, Nan" uniqKey="Chen N" first="Nan" last="Chen">Nan Chen</name>
<name sortKey="Fu, Chengxin" sort="Fu, Chengxin" uniqKey="Fu C" first="Chengxin" last="Fu">Chengxin Fu</name>
<name sortKey="Jin, Xinjie" sort="Jin, Xinjie" uniqKey="Jin X" first="Xinjie" last="Jin">Xinjie Jin</name>
<name sortKey="Li, Pan" sort="Li, Pan" uniqKey="Li P" first="Pan" last="Li">Pan Li</name>
<name sortKey="Li, Xian" sort="Li, Xian" uniqKey="Li X" first="Xian" last="Li">Xian Li</name>
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