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Citation for Study 24472

Citation title: "Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.".

Study name: "Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.".

This study is part of submission 24472 (Status: Published).

Citation

Li Y., & Jin X. 2019. Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes. Molecular Phylogenetics and Evolution, 139: 106540.

Authors

• Li Y. 18259157968
• Jin X. 861062836582

Abstract

To advance our knowledge of orchid relationships and timing of their relative divergences, we used 76 protein-coding genes from plastomes (ptCDS) and 38 protein-coding genes from mitochondrial genomes (mtCDS) of 74 orchids representing the five subfamilies and 18 tribes of Orchidaceae, to reconstruct the phylogeny and temporal evolution of the Orchidaceae. Our results indicated the backbone of Orchidaceae is well supported with both datasets, but there are conflicts between these trees. The phylogenetic positions of two subfamilies (Vanilloideae and Cypripedioideae) are reversed in these two analyses. The phylogenetic positions of several tribes and subtribes, such as Epipogiinae, Gastrodieae, Nerviliinae, and Tropidieae, are well resolved in mtCDS tree. Thaieae have a different position among higher Epidendroideae, instead of sister to the higher Epidendroideae. Interrelationships of several recently radiated tribes within Epidendroideae, including Vandeae, Collabieae, Cymbidieae, Epidendreae, Podochileae, and Vandeae, were resolved with good support in the ptCDS tree, but most are not in the mtCDS tree. Conflicts between the two datasets may be attributed to the different substitution rates in these two genomes and heterogeneity of substitution rate of plastome. Molecular dating indicated that the first three subfamilies, Apostasioideae, Cypripedioideae and Vanilloideae, diverged relatively quickly, and then there was a longer period before the last two subfamilies, Orchidoideae and Epidendroideae, began to radiate. Most mycoheterotrophic clades of Orchidaceae evolved in the last 30 million years with the exception of Gastrodieae.

Keywords

Cypripedioideae, mitochondrial genome, mycoheterotrophic orchids, Orchidaceae, plastid genome, Vanilloideae

External links

• DOI: 10.1016/j.ympev.2019.106540

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S24472
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref29629,
  	 author = {yunxia  li and Xiao-Hua  Jin},
  	 title = {Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.},
  	 year = {2019},
  	 keywords = {Cypripedioideae, mitochondrial genome, mycoheterotrophic orchids, Orchidaceae, plastid genome, Vanilloideae},
  	 doi = {10.1016/j.ympev.2019.106540},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Phylogenetics and Evolution},
  	 volume = {139},
  	 number = {},
  	 pages = {106540},
  	 abstract = {To advance our knowledge of orchid relationships and timing of their relative divergences, we used 76 protein-coding genes from plastomes (ptCDS) and 38 protein-coding genes from mitochondrial genomes (mtCDS) of 74 orchids representing the five subfamilies and 18 tribes of Orchidaceae, to reconstruct the phylogeny and temporal evolution of the Orchidaceae. Our results indicated the backbone of Orchidaceae is well supported with both datasets, but there are conflicts between these trees. The phylogenetic positions of two subfamilies (Vanilloideae and Cypripedioideae) are reversed in these two analyses. The phylogenetic positions of several tribes and subtribes, such as Epipogiinae, Gastrodieae, Nerviliinae, and Tropidieae, are well resolved in mtCDS tree. Thaieae have a different position among higher Epidendroideae, instead of sister to the higher Epidendroideae. Interrelationships of several recently radiated tribes within Epidendroideae, including Vandeae, Collabieae, Cymbidieae, Epidendreae, Podochileae, and Vandeae, were resolved with good support in the ptCDS tree, but most are not in the mtCDS tree. Conflicts between the two datasets may be attributed to the different substitution rates in these two genomes and heterogeneity of substitution rate of plastome. Molecular dating indicated that the first three subfamilies, Apostasioideae, Cypripedioideae and Vanilloideae, diverged relatively quickly, and then there was a longer period before the last two subfamilies, Orchidoideae and Epidendroideae, began to radiate. Most mycoheterotrophic clades of Orchidaceae evolved in the last 30 million years with the exception of Gastrodieae. }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 29629
  AU  - li,yunxia 
  AU  - Jin,Xiao-Hua 
  T1  - Phylogenomics of Orchidaceae based on plastid and mitochondrial genomes.
  PY  - 2019
  KW  - Cypripedioideae
  KW  - mitochondrial genome
  KW  - mycoheterotrophic orchids
  KW  - Orchidaceae
  KW  - plastid genome
  KW  - Vanilloideae
  UR  - http://dx.doi.org/10.1016/j.ympev.2019.106540
  N2  - To advance our knowledge of orchid relationships and timing of their relative divergences, we used 76 protein-coding genes from plastomes (ptCDS) and 38 protein-coding genes from mitochondrial genomes (mtCDS) of 74 orchids representing the five subfamilies and 18 tribes of Orchidaceae, to reconstruct the phylogeny and temporal evolution of the Orchidaceae. Our results indicated the backbone of Orchidaceae is well supported with both datasets, but there are conflicts between these trees. The phylogenetic positions of two subfamilies (Vanilloideae and Cypripedioideae) are reversed in these two analyses. The phylogenetic positions of several tribes and subtribes, such as Epipogiinae, Gastrodieae, Nerviliinae, and Tropidieae, are well resolved in mtCDS tree. Thaieae have a different position among higher Epidendroideae, instead of sister to the higher Epidendroideae. Interrelationships of several recently radiated tribes within Epidendroideae, including Vandeae, Collabieae, Cymbidieae, Epidendreae, Podochileae, and Vandeae, were resolved with good support in the ptCDS tree, but most are not in the mtCDS tree. Conflicts between the two datasets may be attributed to the different substitution rates in these two genomes and heterogeneity of substitution rate of plastome. Molecular dating indicated that the first three subfamilies, Apostasioideae, Cypripedioideae and Vanilloideae, diverged relatively quickly, and then there was a longer period before the last two subfamilies, Orchidoideae and Epidendroideae, began to radiate. Most mycoheterotrophic clades of Orchidaceae evolved in the last 30 million years with the exception of Gastrodieae. 
  L3  - 10.1016/j.ympev.2019.106540
  JF  - Molecular Phylogenetics and Evolution
  VL  - 139
  IS  - 
  ER  -