Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies.

Genome Biology and Evolution
Ching-Ping LinShu-Miaw Chaw

Abstract

As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies-Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix-Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, ...Continue Reading

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Citations

Feb 13, 2013·Journal of Molecular Evolution·Juan P Jaramillo-CorreaJean Bousquet
Mar 10, 2012·Genome Biology and Evolution·Ching-Ping LinShu-Miaw Chaw
Jan 15, 2013·Genome Biology and Evolution·Chung-Shien WuYa-Yi Huang
Jan 7, 2014·PloS One·Leila do Nascimento VieiraMiguel Pedro Guerra
Mar 27, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Dong-Keun YiKyung Choi
Jun 30, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Jia LiTing Wang
Sep 4, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Jong Cheol YangKyung Choi
Dec 10, 2015·Genome Biology and Evolution·Shaun D JackmanInanç Birol
Aug 2, 2015·Molecular Phylogenetics and Evolution·Jin-Hua RanXiao-Quan Wang
Nov 14, 2013·Ecology and Evolution·Sofia BodareMartin Lascoux
Feb 26, 2014·Molecular Phylogenetics and Evolution·Xiao-Quan Wang, Jin-Hua Ran
Jun 28, 2015·Genome Biology and Evolution·Chung-Shien Wu, Shu-Miaw Chaw
Jul 23, 2013·Molecular Phylogenetics and Evolution·Jared D LockwoodSusanne S Renner
Nov 28, 2012·Annals of Allergy, Asthma & Immunology : Official Publication of the American College of Allergy, Asthma, & Immunology·Richard W Weber
Jun 25, 2016·Genome Biology·Henry DaniellWan-Jung Chang
Jun 30, 2016·Genome Biology and Evolution·Edi SudiantoShu-Miaw Chaw
May 2, 2017·Genome Biology and Evolution·Zhen LiYves Van de Peer
Sep 12, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·ZhouXian NiLi-An Xu
Mar 25, 2018·The New Phytologist·Christine Strullu-DerrienFrancis M Martin

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Datasets Mentioned

BETA
AB547400
AB547462
AB547461
AB547460

Methods Mentioned

BETA
PCR
electrophoresis

Software Mentioned

PAUP
GARLI
MEGA
CONSEL
Mulan
Dual Organellar GenoMe Annotator
PHYLIP
r8s
MrBayes
SEQBOOT

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