Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution

doi:10.1186/s12870-022-03480-5

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	Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution
	Amenu, Sara Getachew; Wei, Neng; Wu, Lei; Oyebanji, Oyetola; Hu, Guangwan; Zhou, Yadong; Wang, Qingfeng
	2022
发表期刊	BMC PLANT BIOLOGY
卷号	22 期号:1 页码:88
摘要	Background The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. To fully understand the phylogenetic relationships and PSVs within the clade, highly reliable and sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 plastomes (40 newly sequenced and assembled and the rest from the GenBank) were comparatively analyzed to decipher the PSVs and resolve the phylogenetic relationships of the Coffeeae alliance using four molecular data matrices. Results All plastomes are typically quadripartite with the size ranging from 153,055 to 155,908 bp and contained 111 unique genes. The inverted repeat (IR) regions experienced multiple contraction and expansion; five repeat types were detected but the most abundant was SSR. The size of the Coffeeae alliance clade plastomes and its elements are affected by the IR boundary shifts and the repeat types. However, the emerging PSVs had no taxonomic and phylogenetic implications. Eight highly divergent regions were identified within the plastome regions ndhF, ccsA, ndhD, ndhA, ndhH, ycf1, rps16-trnQ-UUG, and psbM-trnD. These highly variable regions may be potential molecular markers for further species delimitation and population genetic analyses for the clade. Our plastome phylogenomic analyses yielded a well-resolved phylogeny tree with well-support at the tribal and generic levels within the Coffeeae alliance. Conclusions Plastome data could be indispensable in resolving the phylogenetic relationships of the Coffeeae alliance tribes. Therefore, this study provides deep insights into the PSVs and phylogenetic relationships of the Coffeeae alliance and the Rubiaceae family as a whole.
关键词	Coffeeae alliance Phylogenomic Plastome Plastome structural variations (PSVs) Rubiaceae COMPLETE CHLOROPLAST GENOME CODON USAGE BIAS INVERTED REPEAT SEQUENCE ALIGNMENT GENE SUBFAMILIES CONTRACTION ANGIOSPERMS EXPANSION
DOI	10.1186/s12870-022-03480-5
收录类别	SCI
WOS记录号	WOS:000761329100002
引用统计	被引频次：22[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74706
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Amenu, Sara Getachew,Wei, Neng,Wu, Lei,et al. Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution[J]. BMC PLANT BIOLOGY,2022,22(1):88.
APA	Amenu, Sara Getachew.,Wei, Neng.,Wu, Lei.,Oyebanji, Oyetola.,Hu, Guangwan.,...&Wang, Qingfeng.(2022).Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution.BMC PLANT BIOLOGY,22(1),88.
MLA	Amenu, Sara Getachew,et al."Phylogenomic and comparative analyses of Coffeeae alliance (Rubiaceae): deep insights into phylogenetic relationships and plastome evolution".BMC PLANT BIOLOGY 22.1(2022):88.

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