title: Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing.
abstract: Many phylogenomic studies based on transcriptomes have been limited to "single-copy" genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups.
authors.affiliation: Department of Ecology & Evolutionary Biology, University of Michigan yangya@umich.edu eebsmith@umich.edu.
authors.forename: Ya
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Department of Biology, Oberlin College, Science Center K111, Oberlin, OH.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Moore
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Samuel F
authors.initials: SF
authors.lastname: Brockington
authors.affiliation: Department of Biology, University of Florida Florida Museum of Natural History, University of Florida Genetics Institute, University of Florida.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada Department of Medicine, University of Alberta, Edmonton, AB, Canada BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Carpenter
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
authors.forename: Zhixiang
authors.initials: Z
authors.lastname: Yan
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
authors.forename: Yinlong
authors.initials: Y
authors.lastname: Xie
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
authors.forename: Rowan F
authors.initials: RF
authors.lastname: Sage
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Sarah
authors.initials: S
authors.lastname: Covshoff
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Julian M
authors.initials: JM
authors.lastname: Hibberd
authors.affiliation: School of Plant Biology, The University of Western Australia, Crawley, WA, Australia.
authors.forename: Matthew N
authors.initials: MN
authors.lastname: Nelson
authors.affiliation: Department of Ecology & Evolutionary Biology, University of Michigan yangya@umich.edu eebsmith@umich.edu.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Smith
mesh_terms: D029748:Caryophyllaceae / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000502:physiology*; D018745:Genome, Plant / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D059467:Transcriptome / Q000502:physiology*
keywords: Caryophyllales; RNA-seq; paleopolyploidy; substitution rate heterogeneity
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