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Citation for Study 27799

Citation title: " Insights into Phylogenetic Relationships and Genome Evolution of Subfamily Commelinoideae (Commelinaceae Mirb.) Inferred from Complete Chloroplast Genomes".

Study name: " Insights into Phylogenetic Relationships and Genome Evolution of Subfamily Commelinoideae (Commelinaceae Mirb.) Inferred from Complete Chloroplast Genomes".

This study is part of submission 27799 (Status: Published).

Citation

Jung J., Kim C., & Kim J. 2021. Insights into Phylogenetic Relationships and Genome Evolution of Subfamily Commelinoideae (Commelinaceae Mirb.) Inferred from Complete Chloroplast Genomes. BMC Genomics, 22: 231.

Authors

• Jung J. (submitter) +8201093799715
• Kim C. +821042418922
• Kim J.

Abstract

Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia and Streptolirion,). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of the Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bps length, four CDS (ndhH, rpoC2, matK, ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinaceae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.

Keywords

Commelinaceae, chloroplast genome, nucleotide diversity, phylogenomics, plastome

External links

• DOI: 10.21203/rs.3.rs-116972/v1

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S27799
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref31818,
  	 author = {Joonhyung  Jung and Changkyun  Kim and Joo-Hwan  Kim},
  	 title = { Insights into Phylogenetic Relationships and Genome Evolution of Subfamily Commelinoideae (Commelinaceae Mirb.) Inferred from Complete Chloroplast Genomes},
  	 year = {2021},
  	 keywords = {Commelinaceae, chloroplast genome, nucleotide diversity, phylogenomics, plastome},
  	 doi = {10.21203/rs.3.rs-116972/v1},
  	 url = {http://},
  	 pmid = {},
  	 journal = {BMC Genomics},
  	 volume = {22},
  	 number = {},
  	 pages = {231},
  	 abstract = {Background
  Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time.
  Results 
  All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia and Streptolirion,). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of the Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bps length, four CDS (ndhH, rpoC2, matK, ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes.
  Conclusions
  	In this study, we provide detailed information on the 15 complete plastid genomes of Commelinaceae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 31818
  AU  - Jung,Joonhyung 
  AU  - Kim,Changkyun 
  AU  - Kim,Joo-Hwan 
  T1  -  Insights into Phylogenetic Relationships and Genome Evolution of Subfamily Commelinoideae (Commelinaceae Mirb.) Inferred from Complete Chloroplast Genomes
  PY  - 2021
  KW  - Commelinaceae
  KW  - chloroplast genome
  KW  - nucleotide diversity
  KW  - phylogenomics
  KW  - plastome
  UR  - http://dx.doi.org/10.21203/rs.3.rs-116972/v1
  N2  - Background
  Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time.
  Results 
  All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia and Streptolirion,). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of the Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bps length, four CDS (ndhH, rpoC2, matK, ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes.
  Conclusions
  	In this study, we provide detailed information on the 15 complete plastid genomes of Commelinaceae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.
  L3  - 10.21203/rs.3.rs-116972/v1
  JF  - BMC Genomics
  VL  - 22
  IS  - 
  ER  -