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Citation for Study 15625

Citation title: "Infrageneric phylogeny and temporal divergences in Sorghum (Andropogonodae, Poaceae) based on low-copy nuclear and plastid sequences".

Study name: "Infrageneric phylogeny and temporal divergences in Sorghum (Andropogonodae, Poaceae) based on low-copy nuclear and plastid sequences".

This study is part of submission 15625 (Status: Published).

Citation

Liu Q., Liu H., Wen J., & Peterson P.M. 2014. Infrageneric phylogeny and temporal divergences in Sorghum (Andropogonodae, Poaceae) based on low-copy nuclear and plastid sequences. PLoS ONE, .

Authors

• Liu Q. (submitter) 086-020-37252567
• Liu H.
• Wen J.
• Peterson P.M.

Abstract

The infrageneric phylogeny and temporal divergence of Sorghum were explored in the present study. Sequence data of two low-copy nuclear (LCN) genes, phosphoenolpyruvate carboxylase 4 (Pepc4) and granule-bound starch synthase I (GBSSI), from 79 accessions of Sorghum plus Cleistachne sorghoides together with those from outgroups were used for maximum likelihood (ML) and Bayesian inference (BI) analyses. Bayesian dating based on three plastid DNA markers (ndhA intron, rpl32-trnL, and rps16 intron) was used to estimate the ages of major diversification events in Sorghum. The monophyly of Sorghum plus Cleistachne sorghoides (with the latter nested within Sorghum) was strongly supported by the Pepc4 data using BI analysis, and the monophyly of Sorghum was strongly supported by GBSSI data using both ML and BI analyses. Sorghum was divided into three clades in the Pepc4, GBSSI, and plastid phylograms: the subg. Sorghum lineage; the subg. Parasorghum and Stiposorghum lineage; and the subg. Chaetosorghum and Heterosorghum lineage. Two LCN homoeologous loci of Cleistachne sorghoides were first discovered in the same accession. Sorghum arundinaceum, S. bicolor, S. × drummondii, S. propinquum, and S. virgatum were closely related to S. × almum in the Pepc4, GBSSI, and plastid phylograms, suggesting that they may be potential genome donors to S. almum. Multiple LCN and plastid allelic variants have been identified in S. halepense of subg. Sorghum. The crown ages of Sorghum plus Cleistachne sorghoides and subg. Sorghum are estimated to be 12.7 million years ago (Mya) and 8.6 Mya, respectively. Molecular results support the recognition of three distinct subgenera in Sorghum: subg. Chaetosorghum with two sections, each with a single species, subg. Parasorghum with 17 species, and subg. Sorghum with nine species and we also provide a new nomenclatural combination, Sorghum sorghoides.

Keywords

Africa, chloroplast markers, Australia, Sorghum, low-copy nuclear markers, molecular phylogeny, Poaceae.

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S15625
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref23055,
  	 author = {Qing  Liu and Huan  Liu and Jun   Wen and Paul M. Peterson},
  	 title = {Infrageneric phylogeny and temporal divergences in Sorghum (Andropogonodae, Poaceae) based on low-copy nuclear and plastid sequences},
  	 year = {2014},
  	 keywords = {Africa, chloroplast markers, Australia, Sorghum, low-copy nuclear markers, molecular phylogeny, Poaceae.},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {PLoS ONE},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {The infrageneric phylogeny and temporal divergence of Sorghum were explored in the present study. Sequence data of two low-copy nuclear (LCN) genes, phosphoenolpyruvate carboxylase 4 (Pepc4) and granule-bound starch synthase I (GBSSI), from 79 accessions of Sorghum plus Cleistachne sorghoides together with those from outgroups were used for maximum likelihood (ML) and Bayesian inference (BI) analyses. Bayesian dating based on three plastid DNA markers (ndhA intron, rpl32-trnL, and rps16 intron) was used to estimate the ages of major diversification events in Sorghum. The monophyly of Sorghum plus Cleistachne sorghoides (with the latter nested within Sorghum) was strongly supported by the Pepc4 data using BI analysis, and the monophyly of Sorghum was strongly supported by GBSSI data using both ML and BI analyses. Sorghum was divided into three clades in the Pepc4, GBSSI, and plastid phylograms: the subg. Sorghum lineage; the subg. Parasorghum and Stiposorghum lineage; and the subg. Chaetosorghum and Heterosorghum lineage. Two LCN homoeologous loci of Cleistachne sorghoides were first discovered in the same accession. Sorghum arundinaceum, S. bicolor, S. × drummondii, S. propinquum, and S. virgatum were closely related to S. × almum in the Pepc4, GBSSI, and plastid phylograms, suggesting that they may be potential genome donors to S. almum. Multiple LCN and plastid allelic variants have been identified in S. halepense of subg. Sorghum. The crown ages of Sorghum plus Cleistachne sorghoides and subg. Sorghum are estimated to be 12.7 million years ago (Mya) and 8.6 Mya, respectively. Molecular results support the recognition of three distinct subgenera in Sorghum: subg. Chaetosorghum with two sections, each with a single species, subg. Parasorghum with 17 species, and subg. Sorghum with nine species and we also provide a new nomenclatural combination, Sorghum sorghoides.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 23055
  AU  - Liu,Qing 
  AU  - Liu,Huan 
  AU  - Wen,Jun  
  AU  - Peterson,Paul M.
  T1  - Infrageneric phylogeny and temporal divergences in Sorghum (Andropogonodae, Poaceae) based on low-copy nuclear and plastid sequences
  PY  - 2014
  KW  - Africa
  KW  - chloroplast markers
  KW  - Australia
  KW  - Sorghum
  KW  - low-copy nuclear markers
  KW  - molecular phylogeny
  KW  - Poaceae.
  UR  - http://dx.doi.org/
  N2  - The infrageneric phylogeny and temporal divergence of Sorghum were explored in the present study. Sequence data of two low-copy nuclear (LCN) genes, phosphoenolpyruvate carboxylase 4 (Pepc4) and granule-bound starch synthase I (GBSSI), from 79 accessions of Sorghum plus Cleistachne sorghoides together with those from outgroups were used for maximum likelihood (ML) and Bayesian inference (BI) analyses. Bayesian dating based on three plastid DNA markers (ndhA intron, rpl32-trnL, and rps16 intron) was used to estimate the ages of major diversification events in Sorghum. The monophyly of Sorghum plus Cleistachne sorghoides (with the latter nested within Sorghum) was strongly supported by the Pepc4 data using BI analysis, and the monophyly of Sorghum was strongly supported by GBSSI data using both ML and BI analyses. Sorghum was divided into three clades in the Pepc4, GBSSI, and plastid phylograms: the subg. Sorghum lineage; the subg. Parasorghum and Stiposorghum lineage; and the subg. Chaetosorghum and Heterosorghum lineage. Two LCN homoeologous loci of Cleistachne sorghoides were first discovered in the same accession. Sorghum arundinaceum, S. bicolor, S. × drummondii, S. propinquum, and S. virgatum were closely related to S. × almum in the Pepc4, GBSSI, and plastid phylograms, suggesting that they may be potential genome donors to S. almum. Multiple LCN and plastid allelic variants have been identified in S. halepense of subg. Sorghum. The crown ages of Sorghum plus Cleistachne sorghoides and subg. Sorghum are estimated to be 12.7 million years ago (Mya) and 8.6 Mya, respectively. Molecular results support the recognition of three distinct subgenera in Sorghum: subg. Chaetosorghum with two sections, each with a single species, subg. Parasorghum with 17 species, and subg. Sorghum with nine species and we also provide a new nomenclatural combination, Sorghum sorghoides.
  L3  - 
  JF  - PLoS ONE
  VL  - 
  IS  - 
  ER  -