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Citation for Study 23649

Citation title: "Whole Chloroplast Genome and Gene Locus Phylogenies Reveal the Taxonomic Placement and Relationship of Tripidium (Panicoideae: Andropogoneae) to Sugarcane".

Study name: "Whole Chloroplast Genome and Gene Locus Phylogenies Reveal the Taxonomic Placement and Relationship of Tripidium (Panicoideae: Andropogoneae) to Sugarcane".

This study is part of submission 23649 (Status: Published).

Citation

Lloyd evans D., Joshi S.V., & Wang J. 2019. Whole Chloroplast Genome and Gene Locus Phylogenies Reveal the Taxonomic Placement and Relationship of Tripidium (Panicoideae: Andropogoneae) to Sugarcane. BMC Evolutionary Biology, .

Authors

• Lloyd evans D. (submitter) +27747503010
• Joshi S.V.
• Wang J.

Abstract

Background For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the ?Saccharum Complex?, an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. Results Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. Conclusion For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are eight million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the ?Saccharum complex? to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.

Keywords

Tripidium, saccharinae, saccharum complex, plastids, phylogenetics, taxonomy, sorghinae, assembly, gene loci

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S23649
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref29067,
  	 author = {Dyfed  Lloyd Evans and Shailesh Vinay Joshi and Jianping  Wang},
  	 title = {Whole Chloroplast Genome and Gene Locus Phylogenies Reveal the Taxonomic Placement and Relationship of Tripidium (Panicoideae: Andropogoneae) to Sugarcane},
  	 year = {2019},
  	 keywords = {Tripidium, saccharinae, saccharum complex, plastids, phylogenetics, taxonomy, sorghinae, assembly, gene loci},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC Evolutionary Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Background
  For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the ?Saccharum Complex?, an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae.
  Results
  Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented.
  Conclusion
  For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are eight million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the ?Saccharum complex? to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 29067
  AU  - Lloyd Evans,Dyfed 
  AU  - Joshi,Shailesh Vinay
  AU  - Wang,Jianping 
  T1  - Whole Chloroplast Genome and Gene Locus Phylogenies Reveal the Taxonomic Placement and Relationship of Tripidium (Panicoideae: Andropogoneae) to Sugarcane
  PY  - 2019
  KW  - Tripidium
  KW  - saccharinae
  KW  - saccharum complex
  KW  - plastids
  KW  - phylogenetics
  KW  - taxonomy
  KW  - sorghinae
  KW  - assembly
  KW  - gene loci
  UR  - http://dx.doi.org/
  N2  - Background
  For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the ?Saccharum Complex?, an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae.
  Results
  Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented.
  Conclusion
  For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are eight million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the ?Saccharum complex? to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.
  
  L3  - 
  JF  - BMC Evolutionary Biology
  VL  - 
  IS  - 
  ER  -