Comparative genome analysis revealed gene inversions, boundary expansions and contractions, and gene loss in the Stemona sessilifolia (Miq.) Miq. chloroplast genome

Abstract

Stemona sessilifolia (Miq.) Miq., commonly known as Baibu, is one of the most popular herbal medicines in Asia. In the Chinese Pharmacopoeia, Baibu has multiple authentic sources and there are many similar herbs sold as Baibu in herbal medicine markets. The existence of counterfeits of Baibu brings challenges to its identification. To assist in its accurate identification, we sequenced and analyzed the complete chloroplast genome of S. sessilifolia using next-generation sequencing technology. The genome was found to be 154,037 bp in length, possessing a typical quadripartite structure consisting of a pair of inverted repeats (IRs: 27,090 bp) separated by a large single copy (LSC: 81,949 bp) and a small single copy (SSC: 17,908 bp). A total of 112 unique genes were identified, including 80 protein-coding, 28 transfer RNA and four ribosomal RNA genes. In addition, 45 tandem, 27 forward, 23 palindromic and 104 simple sequence repeats were detected in the genome by repeated analysis. Compared with its counterfeits (Asparagus officinalis and Carludovica palmata) we found that IR expansion and SSC contraction events of S. sessilifolia resulted in two copies of the rpl22 gene in the IR regions and a partial duplication of the ndhF gene in the SSC region. An approximately 3-kb-long inversion was also identified in the LSC region, leading to the petA and cemA genes being presented in the complementary strand of the chloroplast DNA molecule. Comparative analysis revealed some highly variable regions, including trnF-GAA_ndhJ, atpB_rbcL, rps15_ycf1, trnG-UCC_trnR-UCU, ndhF_rpl32, accD_psaI, rps2_rpoC2, trnS-GCU_trnG-UCC, trnT-UGU_trnL-UAA and rps16_trnQ-UUG. Finally, gene loss events were investigated in the context of phylogenetic relationships. In summary, the complete plastome of S. sessilifolia will provide valuable information for the distinction between Baibu and its counterfeits and assist in elucidating the evolution of S. sessilifolia.

The First Complete Chloroplast Genome Sequence of Mortiño (Vaccinium floribundum) and Comparative Analyses with Other Vaccinium Species

“…Therefore, in relation to other Vaccinium species cp genomes, the V. floribundum cp genome could have undergone a possible expansion/contraction in its IR regions, shifting its IR/SSC-IR/LSC boundaries. This has been reported previously in cp genomes of different genera, such as Litsea [75], Punica [76], Paphiopedilum [77], and Stemona [78]. Additionally, the expansion/contraction of the IR regions could justify the difference in plastome sizes within the Vaccinium genus and contribute to the different gene arrangements of their cp genomes [75][76][77][78][79].…”

“…This has been reported previously in cp genomes of different genera, such as Litsea [75], Punica [76], Paphiopedilum [77], and Stemona [78]. Additionally, the expansion/contraction of the IR regions could justify the difference in plastome sizes within the Vaccinium genus and contribute to the different gene arrangements of their cp genomes [75][76][77][78][79].…”

The complete chloroplast genome of Hibiscus syriacus using long-read sequencing: Comparative analysis to examine the evolution of the tribe Hibisceae

“…Contraction or expansion of the single-copy and IR regions commonly occurs in various angiosperms ( Jian et al., 2018 ; Li and Zheng, 2018 ; Henriquez et al., 2020 ; Guo et al., 2021 ; Liu et al., 2021 ). These alterations are considered a major mechanism that causes size variation of the chloroplast genome and evolutionary events ( Zhu et al., 2016 ; Liang et al., 2022 ; Lu et al., 2022 ).…”

Comparative phylogenetic analysis of oolong tea (Phoenix Dancong tea) using complete chloroplast genome sequences

“…The IR region of oolong tea was not only highly conserved in terms of length, but the locations and sizes of the boundary genes, rps19 , ycf1 and trnH were also relatively stable. Although the positions of these boundary genes are slightly different from those of other plants, the gene types are almost the same, which also exists in Stemona sessilifolia [ 45 ], Myristicaceae [ 46 ], and Brassicaceae [ 47 ]. Accordingly, we infer that there should be no simple phylogenetic signals at the IR boundary.…”