AUTHOR=Shen Jun , Zhang Xu , Landis Jacob B. , Zhang Huajie , Deng Tao , Sun Hang , Wang Hengchang 

TITLE=Plastome Evolution in Dolomiaea (Asteraceae, Cardueae) Using Phylogenomic and Comparative Analyses

JOURNAL=Frontiers in Plant Science

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2020.00376

DOI=10.3389/fpls.2020.00376

ISSN=1664-462X

ABSTRACT=<p><italic>Dolomiaea</italic> is a medicinally important genus of Asteraceae endemic to alpine habitats of the Qinghai-Tibet Plateau (QTP) and adjacent areas. Despite significant medicinal value, genomic resources of <italic>Dolomiaea</italic> are still lacking, impeding our understanding of its evolutionary history. Here, we sequenced and annotated plastomes of four <italic>Dolomiaea</italic> species. All analyzed plastomes share the gene content and structure of most Asteraceae plastomes, indicating the conservation of plastome evolutionary history of <italic>Dolomiaea</italic>. Eight highly divergent regions (<italic>rps</italic>16<italic>-trn</italic>Q, <italic>trn</italic>C<italic>-pet</italic>N, <italic>trn</italic>E<italic>-rpo</italic>B, <italic>trn</italic>T<italic>-trn</italic>L<italic>-trn</italic>F, <italic>psb</italic>E<italic>-pet</italic>L, <italic>ndh</italic>F<italic>-rpl</italic>32<italic>-trn</italic>L, <italic>rps</italic>15<italic>-ycf</italic>1, and <italic>ycf</italic>1), along with a total of 51–61 simple sequence repeats (SSRs) were identified as valuable molecular markers for further species delimitation and population genetic studies. Phylogenetic analyses confirmed the evolutionary position of <italic>Dolomiaea</italic> as a clade within the subtribe Saussureinae, while revealing the discordance between the molecular phylogeny and morphological treatment. Our analysis also revealed that the plastid genes, <italic>rpo</italic>C2 and <italic>ycf</italic>1, which are rarely used in Asteraceae phylogenetic inference, exhibit great phylogenetic informativeness and promise in further phylogenetic studies of tribe Cardueae. Analysis for signatures of selection identified four genes that contain sites undergoing positive selection (<italic>atp</italic>A, <italic>ndh</italic>F, <italic>rbc</italic>L, and <italic>ycf</italic>4). These genes may play important roles in the adaptation of <italic>Dolomiaea</italic> to alpine environments. Our study constitutes the first investigation on the sequence and structural variation, phylogenetic utility and positive selection of plastomes of <italic>Dolomiaea</italic>, which will facilitate further studies of its taxonomy, evolution and conservation.</p>