Chloroplast genome features of an important medicinal and edible plant: Houttuynia cordata (Saururaceae)

Abstract

Houttuynia cordata (Saururaceae), an ancient and relic species, has been used as an important medicinal and edible plant in most parts of Asia. However, because of the lack of genome information and reliable molecular markers, studies on its population structure, or phylogenetic relationships with other related species are still rare. Here, we de novo assembled the complete chloroplast (cp) genome of H. cordata using the integration of the long PacBio and short Illumina reads. The cp genome of H. cordata showed a typical quadripartite cycle of 160,226 bp. This included a pair of inverted repeats (IRa and IRb) of 26,853 bp, separated by a large single-copy (LSC) region of 88,180 bp and a small single-copy (SSC) region of 18,340 bp. A total of 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes, were identified in this cp genome. Eighty-one genes were located on the LSC region, 13 genes were located on the SSC region, and 17 twocopy genes were located on the IR region. Additionally, 48 repeat sequences and 86 SSR loci, which can be used as genomic markers for population structure analysis, were also detected. Phylogenetic analysis using 21 cp genomes of the Piperales family demonstrated that H. cordata had a close relationship with the species within the Aristolochia genus. Moreover, the results of mVISTA analysis and comparisons of IR regions demonstrated that the cp genome of H. cordata was conserved with that of the Aristolochia species. Our results provide valuable information for analyzing the genetic diversity and population structure of H. cordata, which can contribute to further its genetic improvement and breeding.

Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae

“…All five cp genomes displayed a high sequence similarity (>85%), but several short and long inserted regions were also observed ( Fig 4 ). Our results show that coding regions were more conserved than non-coding regions ( Fig 4 ), consistent with earlier research [ 29 ]. The most highly conserved cp genes were the rRNA and tRNA genes ( Fig 4 ), and the most divergent genes were ycf1 , accD , ycf2 , rpl14 , and atpA ( Fig 4 ).…”

Comparative Genomics and Phylogenetic Relationships of Two Endemic and Endangered Species (Handeliodendron Bodinieri and Eurycorymbus Cavaleriei) of two Monotypic Genera within Sapindales

“…Moreover, the ndings of this study revealed that most codons ended with A or U when RSCU values more than 1.00. As a common phenomenon in cp genomes of plants, similar results have been reported in previous studies [72,[88][89][90].…”

“…The full-length of H. bodinieri cp genome is 151,271 bp and is also different from that of the previous report [49]. Their genome exhibited a typical quadripartite structure, including a pair of inverted repeats (IRs), a large single copy (LSC) region, and a small single copy (SSC) region, which was the same as that reported for most other angiosperms [71][72][73]. This study revealed that gene content and gene order in H. bodinieri and E. cavaleriei cp genomes were quite similar to that of other published Sapindaceae species [74][75][76].…”

Morphological and genomic evidence for a new species of Corallorhiza (Orchidaceae: Epidendroideae) from SW China

“…The complete plastome of C. sinensis was sequenced, assembled, and analyzed in comparison with these members of subtribe Calypsoinae. The plastome of C. sinensis shows a typical quadripartite structure, as reported for most angiosperms ( Khayi et al., 2020 ; Wu et al., 2020 ; Zhu et al., 2020 ). A total of 109 unique genes were identified in the plastome, which contains 68 protein-coding genes, 30 tRNAs, and four rRNAs.…”