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

Abstract

Dolomiaea 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 Dolomiaea are still lacking, impeding our understanding of its evolutionary history. Here, we sequenced and annotated plastomes of four Dolomiaea species. All analyzed plastomes share the gene content and structure of most Asteraceae plastomes, indicating the conservation of plastome evolutionary history of Dolomiaea. Eight highly divergent regions (rps16-trnQ, trnC-petN, trnE-rpoB, trnT-trnL-trnF, psbE-petL, ndhF-rpl32-trnL, rps15-ycf1, and ycf1), 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 Dolomiaea 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, rpoC2 and ycf1, 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 (atpA, ndhF, rbcL, and ycf4). These genes may play important roles in the adaptation of Dolomiaea to alpine environments. Our study constitutes the first investigation on the sequence and structural variation, phylogenetic utility and positive selection of plastomes of Dolomiaea, which will facilitate further studies of its taxonomy, evolution and conservation.

Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences fromAldama(Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera

“…The conservation of plastome features has been recorded in several Angiosperm groups ( Cai et al, 2015 ; Reginato et al, 2016 ; Sun et al, 2019 ; Yan et al, 2019 ) and our results corroborate that plastomes are highly conserved in Asteraceae, even at the generic or subtribal level, in size, GC content, number of genes and gene order ( Wang et al, 2015 ; Salih et al, 2017 ; Shen et al, 2020 ).…”

“…Size variation between the smallest ( A. vernonioides ) and largest ( A. squalida ) Aldama plastomes is very low (178 bp) ( Table 1 ). This is similar to the variation found between the plastomes of different species of Atractylodes (60 bp; Wang et al, 2020 ) , Echinacea (98 bp; Zhang et al, 2017 ) , Dendrosenecio (59 bp; Gichira et al, 2019 ) , Dolomiaea (179 bp; Shen et al, 2020 ) and Senecio (209 bp) ( Gichira et al, 2019 ), but greatly inferior to the variation found between 20 Saussurea species (1,148 bp; Zhang et al, 2019 ) . Among genera in Heliantheae, D. asperatum, from subtribe Ecliptinae, presents the largest genome, exceeding the smallest one ( A. vernonioides ) by only 641 bp.…”

“…1 ). Expansions of the IRs and contractions of the LSC are frequent in Asterids (e.g., Downie & Jansen, 2015 ; Firetti et al, 2017 ; Thode & Lohmann, 2019 ), but were not observed at the generic level in our results or in other studies in Asteraceae ( Zhang et al, 2017 ; Cho et al, 2019 ; Gichira et al, 2019 ; Shahzadi et al, 2019 ; Shen et al, 2020 ; Wang et al, 2020 ; Zhang et al, 2019 ), except for a recent study in the genus Aster ( Tyagi et al, 2020 ). The IR/SC boundaries are highly conserved in all Aldama and Heliantheae genera sequenced in this study ( Fig.…”

“…While coding regions normally accumulate genetic differences more slowly than non-coding regions ( Fazekas et al, 2008 ; Lahaye et al, 2008 ), one exception is the gene ycf1 , which evolves at a faster pace ( Dong et al, 2012 ; Shaw et al, 2014 ). This region is frequently cited as one of the most variable in Asteraceae plastomes ( Wang et al, 2015 ; Zhang et al, 2017 ; Cho et al, 2019 ; Zhang et al, 2019 ; Shen et al, 2020 ; Wang et al, 2020 ) but seems to have been used as a marker only once, in a phylogenetic study within the tribe Astereae ( Costa, 2014 ). Nonetheless, ycf1 was successfully used in phylogenetic inferences of other angiosperm groups, such as Fabaceae (e.g., Dastpak et al, 2018 ) and orchids (e.g., Neubig et al, 2009 ) .…”

Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes

“…Subsequently, remaining high-quality reads were assembled into contigs using NOVOPlasty v.2.7.2 [ 61 ]. Following the description of Shen et al [ 62 ], a seed-and-extend algorithm was employed with the plastome sequence of Swertia mussotii (Genbank accession: NC_031155.1) as the seed input, and other parameters were kept at default settings (see NOVOPlasty manual). Assembled plastomes were then annotated using Plastid Genome Annotator (PGA) [ 63 ].…”