Complete chloroplast genomes of medicinally importantTeucriumspecies and comparative analyses with related species from Lamiaceae

Abstract

Teucrium is one of the most economically and ecologically important genera in the Lamiaceae family; however, it is currently the least well understood at the plastome level. In the current study, we sequenced the complete chloroplast (cp) genomes of T. stocksianum subsp. stenophyllum R.A.King (TSS), T. stocksianum subsp. stocksianum Boiss. (TS) and T. mascatense Boiss. (TM) through next-generation sequencing and compared them with the cp genomes of related species in Lamiaceae (Ajuga reptans L., Caryopteris mongholica Bunge, Lamium album L., Lamium galeobdolon (L.) Crantz, and Stachys byzantina K.Koch). The results revealed that the TSS, TS and TM cp genomes have sizes of 150,087, 150,076 and 150,499 bp, respectively. Similarly, the large single-copy (LSC) regions of TSS, TS and TM had sizes of 81,707, 81,682 and 82,075 bp, respectively. The gene contents and orders of these genomes were similar to those of other angiosperm species. However, various differences were observed at the inverted repeat (IR) junctions, and the extent of the IR expansion into ψrps19 was 58 bp, 23 bp and 61 bp in TSS, TS and TM, respectively. Similarly, in all genomes, the pbsA gene was present in the LSC at varying distances from the JLA (IRa-LSC) junction. Furthermore, 89, 72, and 92 repeats were identified in the TSS, TM and TS cp genomes, respectively. The highest number of simple sequence repeats was found in TSS (128), followed by TS (127) and TM (121). Pairwise alignments of the TSS cp genome with related cp genomes showed a high degree of synteny. However, relatively lower sequence identity was observed when various coding regions were compared to those of related cp genomes. The average pairwise divergence among the complete cp genomes showed that TSS was more divergent from TM (0.018) than from TS (0.006). The current study provides valuable genomic insight into the genus Teucrium and its subspecies that may be applied to a more comprehensive study.

Complete Chloroplast Genome Characterization of Oxalis Corniculata and Its Comparison with Related Species from Family Oxalidaceae

“…The study of different repeats (palindromic, forward, and tandem) in our sequenced cp genome showed variation in the number of repeats, which is similar to other species previously studied [ 59 ]. In all types of repeats, tandem repeats were found more than palindromic and forward repeats in four cp genomes; these results are consistent with previous reports of Teucrium and Commiphora species [ 60 , 61 ], as well as S. miltiorrhiza [ 62 ]. Similarly, simple sequence repeats (SSRs) usually have a higher rate of mutation compared with other neutral regions of DNA due to slipped strand mispairing.…”

Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

“…For example, in the same family (Acanthaceae), Ding, et al 42 and Huang, et al 44 previously reported the size of protein coding genes, rRNA, tRNA, number of genes, number of protein coding genes, number of rRNA and number of tRNA in A. paniculate and A. knappiae www.nature.com/scientificreports/ which is similar to what we found in the A. marina. Similarly, almost same results were observed in the recently reported chloroplast genomes of C. gileadensis 50 , Teucrium species 53 , Vachellia nilotica and Senegalia senegal 54 . In the chloroplast genome, microsatellites or SSRs distributed in the genome with the length of almost 1 bp to 6 bp.…”

Comparative Chloroplast Genomics of Endangered Euphorbia Species: Insights into Hotspot Divergence, Repetitive Sequence Variation, and Phylogeny

“…The number of repeats, including forward, tandem, and palindromic repeats, were studied in the chloroplast genomes sequenced and compared, and were found in a larger amount than in the previously reported cp genome of V. fordii (49 repeats) [32]. Among these repeats, tandem repeats were found several times more than palindromic and forward repeats, which are consistent with the Teucrium and Commiphora species [30,31], as well as S. miltiorrhiza [39], as previously reported.…”

“…All of them were assembled into a single chloroplast genome presenting a typical quadripartite structure. Analysis of two sequenced Euphorbia genomes revealed that, like most of the higher angiosperm genomes, they comprised the tetrahedral structure containing two pairs of inverted repeats, one large single-copy region and one small single-copy region [4,31]. There was a 186 bp difference observed between the two sequenced chloroplast genomes, and the size was also comparable with other compared Euphorbia species, as well as the Vernicia fordii chloroplast genome, which is 161,528 bp in length [32], suggesting that chloroplast genomes are conserved.…”

“…Out of these 18 introns containing genes, five are tRNAs, and three genes, ycf3, clpP, and rps12, contain double introns ( Table 2). The base composition analyzed in sequenced and compared genomes reveal that adenine (A) at the first position was 31.0%, 31 38.6%, and 38.4%, respectively. Furthermore, the abundance of "G" and "C" at the first, second, and third positions were observed less than the abundance of "A" and "T" (Table 3).…”