Abstract
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.
Highlights
With over 13,000 species belonging to 611 genera and 65 tribes, Rubiaceae, commonly known as coffee, madder, or bedstraw family, is the fourth-largest angiosperm family after Asteraceae, Orchidaceae and Fabaceae [1]
We aim to explore the Plastome structural variations (PSVs) and reconstruct the phylogenetic tree of the Coffeeae alliance using four data matrices: coding sequences (CDs), noncoding sequences (NCDs), protein-coding genes (PCGs), and complete plastome (CP) sequences
Plastome Organization of the Coffeeae alliance tribes Mean coverage of the newly sequenced plastome ranged between 165.7 × (Pavetta barbertonensis Bremek. of Pavetteae) and 635 × (Rubovietnamia aristata Tirveng. of Gardenieae) (Table S1)
Summary
With over 13,000 species belonging to 611 genera and 65 tribes, Rubiaceae, commonly known as coffee, madder, or bedstraw family, is the fourth-largest angiosperm family after Asteraceae, Orchidaceae and Fabaceae [1]. Despite the eminence of previous studies on the taxonomy of Rubiaceae, still the number of traditional subfamilies that should be recognized is yet to be fully substantiated [5, 6]. 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. The structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. 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
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