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Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae
Huang, Y (Huang, Yuan)1,2; Wang, J (Wang, Jun)3; Yang, YP (Yang, Yongping)4; Fan, CZ (Fan, Chuanzhu)3; Chen, JH (Chen, Jiahui)1,4; Chen, JH; Fan, CZ; Yang, YP
AbstractChloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three Salix species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus Populus, which most likely results from homoplasy. By comparing three Salix chloroplast genomes with the published chloroplast genomes of other Salicaceae species, we demonstrate that the synteny and length of chloroplast genomes in Salicaceae are highly conserved but experienced dynamic evolution among species. We identify seven positively selected chloroplast genes in Salicaceae, which might be related to the adaptive evolution of Salicaceae species. Comparative chloroplast genome analysis within the family also indicates that some chloroplast genes are lost or became pseudogenes, infer that the chloroplast genes horizontally transferred to the nucleus genome. Based on the complete nucleus genome sequences from two Salicaceae species, we remarkably identify that the entire chloroplast genome is indeed transferred and integrated to the nucleus genome in the individual of the reference genome of P. trichocarpa at least once. This observation, along with presence of the large nuclear plastid DNA (NUPTs) and NUPTs-containing multiple chloroplast genes in their original order in the chloroplast genome, favors the DNA-mediated hypothesis of organelle to nucleus DNA transfer. Overall, the phylogenomic analysis using chloroplast complete genomes clearly elucidates the phylogeny of Salicaceae. The identification of positively selected chloroplast genes and dynamic chloroplast-to-nucleus gene transfers in Salicaceae provide resources to better understand the successful adaptation of Salicaceae species.
Subject Area植物学
WOS IDWOS:000403639300001
Indexed BySCI
KeywordChlamydomonas-reinhardtii Molecular Phylogeny Salix Salicaceae Maximum-likelihood Plastid Genomes Photosystem-ii Sequence Data Petd Gene Nuclear Plants
WOS Research AreaPlant Sciences
WOS SubjectPlant Sciences ; Plant Sciences
Cooperation Status国内
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Document Type期刊论文
Corresponding AuthorChen, JH; Fan, CZ; Yang, YP
Affiliation1.Chinese Acad Sci, Key Lab Plant Divers & Biogeog East Asia, Kunming, Peoples R China.
2.Yunnan Normal Univ, Sch Life Sci, Kunming, Peoples R China.
3.Wayne State Univ, Dept Biol Sci, Detroit, MI 48202 USA.
4.Chinese Acad Sci, Kunming Inst Bot, Inst Tibetan Plateau Res Kunming, Kunming, Peoples R China.
Recommended Citation
GB/T 7714
Huang, Y ,Wang, J ,Yang, YP ,et al. Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae[J]. FRONTIERS IN PLANT SCIENCE,2017,8(0):1050.
APA Huang, Y .,Wang, J .,Yang, YP .,Fan, CZ .,Chen, JH .,...&Yang, YP.(2017).Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae.FRONTIERS IN PLANT SCIENCE,8(0),1050.
MLA Huang, Y ,et al."Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae".FRONTIERS IN PLANT SCIENCE 8.0(2017):1050.
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