Leveraging plastomes for comparative analysis and phylogenomic inference within Scutellarioideae (Lamiaceae)

Abstract

Scutellaria, or skullcaps, are medicinally important herbs in China, India, Japan, and elsewhere. Though Scutellaria is the second largest and one of the more taxonomically challenging genera within Lamiaceae, few molecular systematic studies have been undertaken within the genus; in part due to a paucity of available informative markers. The lack of informative molecular markers for Scutellaria hinders our ability to accurately and robustly reconstruct phylogenetic relationships, which hampers our understanding of the diversity, phylogeny, and evolutionary history of this cosmopolitan genus. Comparative analyses of 15 plastomes, representing 14 species of subfamily Scutellarioideae, indicate that plastomes within Scutellarioideae contain about 151,000 nucleotides, and possess a typical quadripartite structure. In total, 590 simple sequence repeats, 489 longer repeats, and 16 hyper-variable regions were identified from the 15 plastomes. Phylogenetic relationships among the 14 species representing four of the five genera of Scutellarioideae were resolved with high support values, but the current infrageneric classification of Scutellaria was not supported in all analyses. Complete plastome sequences provide better resolution at an interspecific level than using few to several plastid markers in phylogenetic reconstruction. The data presented here will serve as a foundation to facilitate DNA barcoding, species identification, and systematic research within Scutellaria, which is an important medicinal plant resource worldwide.

An updated tribal classification of Lamiaceae based on plastome phylogenomics

“…Scutellarioideae had been thought to be sister to Lamioideae [31,44], but with the separation of Cymarioideae from the Lamioideae [19], Scutellarioideae is sister to the Cymarioideae-Lamioideae clade. Based on previous studies and our phylogenomic results, Tinnea and Holmskioldia are successive sister groups to Scutellaria, with Wenchengia sister to the rest of Scutellarioideae [15,16,19,31,44,66,136]. However, relationships within Scutellarioideae remain unresolved because Renschia has never been included in a molecular phylogenetic study.…”

“…In this study, plastomes of 50 taxa were newly sequenced and 61 taxa were reassembled from the sequence read archive (SRA) database; others were acquired from previous studies [ 66 , 67 , 206 , 207 ] or downloaded from NCBI ( https://www.ncbi.nlm.nih.gov ; Additional file 8 : Table S3). In total, the ingroup sampling included 170 taxa (175 accessions), 79 genera, and represented all 15 currently recognized tribes and all 12 subfamilies within Lamiaceae [ 19 , 51 ].…”

“…However, relationships within Scutellarioideae remain unresolved because Renschia has never been included in a molecular phylogenetic study. To date, four phylogenetic studies have focused on Scutellaria [66,[138][139][140], but none included a comprehensive taxon sampling of the genus or of Scutellarioideae as a whole. Thus, relationships within Scutellaria still need to be addressed in future studies.…”

“…While the use of complete plastome sequences is not a panacea [56], it has successfully resolved previously intractable phylogenetic problems within flowering plants at multiple taxonomic levels [57][58][59][60][61][62][63][64][65]. Concordantly, recent phylogenomic studies based on plastome sequences have provided new insight into both generic and species-level relationships within Scutellarioideae [66] and Salvia [67], respectively. In order to resolve the remaining ambiguities at the tribal and subfamilial level, we sequenced and analyzed the complete plastome for 175 representative taxa from all currently recognized tribes in the 12 subfamilies of Lamiaceae.…”

“…All the newly sequenced and annotated plastomes in the present study were submitted to the National Center for Biotechnology Information (NCBI) database with accession numbers MT473738–MT473786 (Table 1 ). Other plastomes analyzed were acquired from previous studies [ 66 , 67 , 206 , 207 ] or downloaded from NCBI ( https://www.ncbi.nlm.nih.gov ;…”