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

Liu L, Jin X, Chen N, Li X, Li P, Fu C - PLoS ONE (2015)

Bottom Line: 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.All three methods significantly favored the topology of (((M. rubra, M. adenophora), M. nana), M. esculenta).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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.

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.

No MeSH data available.


Related in: MedlinePlus

GO classifications of annotated contigs of M. rubra.
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pone.0139840.g005: GO classifications of annotated contigs of M. rubra.

Mentions: According to the results of Nr protein database annotation, 6730, 5287, and 6769 contigs for M. rubra, M. nana and M. esculenta respectively were implemented in Blast2GO for functional classification. For M. rubra, genes involved in cellular processes (GO: 0009987) and metabolic processes (GO: 0008152) are the top two most abundant subcategories in the biological process. Cell (GO: 0005623) and Cell part (GO: 0044464) are highly represented under the cellular component category. Binding (GO: 0005488) represents the major proportion of molecular function (Fig 5). M. nana and M. esculenta showed similar results (S3 Fig).


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

Liu L, Jin X, Chen N, Li X, Li P, Fu C - PLoS ONE (2015)

GO classifications of annotated contigs of M. rubra.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591994&req=5

pone.0139840.g005: GO classifications of annotated contigs of M. rubra.
Mentions: According to the results of Nr protein database annotation, 6730, 5287, and 6769 contigs for M. rubra, M. nana and M. esculenta respectively were implemented in Blast2GO for functional classification. For M. rubra, genes involved in cellular processes (GO: 0009987) and metabolic processes (GO: 0008152) are the top two most abundant subcategories in the biological process. Cell (GO: 0005623) and Cell part (GO: 0044464) are highly represented under the cellular component category. Binding (GO: 0005488) represents the major proportion of molecular function (Fig 5). M. nana and M. esculenta showed similar results (S3 Fig).

Bottom Line: 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.All three methods significantly favored the topology of (((M. rubra, M. adenophora), M. nana), M. esculenta).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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.

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.

No MeSH data available.


Related in: MedlinePlus