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

BMC Plant Biology

Lei Wu¹  Yadong Zhou²  Qingfeng Wang²  Guangwan Hu²  Sara Getachew Amenu³  Neng Wei³  Oyetola Oyebanji⁴ 

[1]College of Forestry, Central South University of Forestry and Technology, 410004, Changsha, Hunan, People’s Republic of China

[2]Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 430074, Wuhan, Hubei, People’s Republic of China

[3]Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 430074, Wuhan, Hubei, People’s Republic of China

[4]Sino-Africa Joint Research Center (SAJOREC), Chinese Academy of Sciences, 430074, Wuhan, Hubei, People’s Republic of China

[5]Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 430074, Wuhan, Hubei, People’s Republic of China

[6]University of Chinese Academy of Sciences, 100049, Beijing, People’s Republic of China

[7]University of Chinese Academy of Sciences, 100049, Beijing, People’s Republic of China

[8]Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, People’s Republic of China

[9]Department of Botany, Faculty of Science, University of Lagos, Lagos, Nigeria

关键词: Coffeeae alliance;    Phylogenomic;    Plastome;    Plastome structural variations (PSVs);    Rubiaceae;   

DOI  :  10.1186/s12870-022-03480-5

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsAll 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.ConclusionsPlastome 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.

【 授权许可】

CC BY