TreeBASE Search-Analyses for study 20385

@ARTICLE{TreeBASE2Ref26722, author = {Yinhuan Wang and Xiaojian Qu and Siyun Chen and Dezhu Li and Tingshuang Yi}, title = {Plastomes of Mimosoideae: structural and size variation, sequence divergence, and phylogenetic implication}, year = {2016}, keywords = {plastome, IR expansion, repeats, Mimosoideae, sequence divergence, phylogenomics}, doi = {}, url = {http://}, pmid = {}, journal = {Tree Genetics & Genomes}, volume = {}, number = {}, pages = {}, abstract = {Plastomes of Fabaceae show both significant structural and size variation, and therefore provide a good group for addressing plastome diversification and evolution. However, most published plastomes are from subfamily Papilionoideae and only a few from the other two subfamilies. We integrated 11 newly sequenced plastomes from representing genera with three previously published ones. Each mimosoid plastome presented typical quadripartite structure and contained 111 unique genes. A ca. 13 kb IR (inverted repeat) expansion into SSC (small single copy) was detected in plastomes of a clade formed by tribe Ingeae and Acacia sensu stricto (s.s.), and a ca. 1.7 kb IR expansion into and a ca. 1.9 kb contraction out of LSC (large single copy) were found in Pithecellobium flexicaule and Acacia dealbata, respectively. Size of mimosoid plastomes was found significantly affected by IR-SC boundary shift, and also associated with repeat content. A loss of both introns of clpP occurred in A. dealbata and Faidherbia albida, and a duplicated clpP copy was detected in A. dealbata. Furthermore, a 421 bp inversion that containing rps18 was found in A. dealbata. Substitution rates decreased after genes translocated from SC to IR and vice versa. Plastome coding and noncoding regions with various sequence divergence may supply valuable markers for molecular evolutionary and phylogenetic studies at different taxonomic levels. Plastid phylogenomics well resolved relationships among sampled species. Evolutionary pattern of IR expansion/contraction was traced and IR expansion into SSC was found to be the synapomorphy of the Ingeae + Acacia s.s. clade. } }