Author:
Amenu Sara Getachew,Wei Neng,Wu Lei,Oyebanji Oyetola,Hu Guangwan,Zhou Yadong,Wang Qingfeng
Abstract
Abstract
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.
Publisher
Springer Science and Business Media LLC
Reference77 articles.
1. Wikstrom N, Bremer B, Rydin C. Conflicting phylogenetic signals in genomic data of the coffee family (Rubiaceae). J Syst Evol. 2020;58(4):440–60.
2. Mendoza-Cifuentes H, Celis A, Tovar E, Gonzalez MA. Lintersemina (Rubiaceae: Condamineeae), a new and enigmatic genus from the Magdalena Medio region of Colombia. Phytotaxa. 2020;451(1):1–20.
3. Davis AP, Govaerts R, Bridson DM, Ruhsam M, Moat J, Brummitt NA, et al. A global assessment of distribution, diversity, endemism, and taxonomic effort in the Rubiaceae. Ann Mo Bot Gard. 2009;96(1):68–78.
4. Robbrecht E. Tropical woody Rubiaceae. Op Bot Belg. 1988;1(272):599–602.
5. Robbrecht E, Manen JF. The major evolutionary lineages of the coffee family (Rubiaceae, Angiosperms). Combined analysis (nDNA and cpDNA) to infer the position of Coptosapelta and Luculia, and supertree construction based on rbcL, rps16, trnL-trnF, and atpB-rbcL data. A new classification in two subfamilies, Cinchonoideae and Rubioideae. Syst Geogr Pl. 2006;76:85–146.
Cited by
18 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献