Journal Article

Comparative Chloroplast Genomics Reveals the Evolution of Pinaceae Genera and Subfamilies

Ching-Ping Lin, Jen-Pan Huang, Chung-Shien Wu, Chih-Yao Hsu and Shu-Miaw Chaw

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 2, issue , pages 504-517
Published in print January 2010 |
Published online July 2010 | e-ISSN: 1759-6653 | DOI:

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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 AbiesKeteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or LarixPseudotsuga. 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, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix–Pseudotsuga–PiceaeCathayaPinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix–Pseudotsuga, and PiceaeCathayaPinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix–Pseudotsuga, Picea, and CathayaPinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.

Keywords: chloroplast genome; Cedrus; Cathaya; Pesudotsuga; Pinaceae phylogeny; molecular dating

Journal Article.  7900 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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