The complete chloroplast genome sequence of Paris nitida G.W.Hu, Z.Wang & Q.F.Wang 2017 (Melanthiaceae), an endemic herb in China

Abstract

Paris nitida G.W.Hu, Z.Wang & Q.F.Wang 2017 (Melanthiaceae) is a perennial herb that was first identified in China in 2017. In this study, we determined the circular chloroplast genome of P. nitida through de novo assembly. The 164,734 bp genome exhibits an AT content of 62.89%. We annotated 131 genes, including 36 tRNA genes, eight rRNA genes, and 87 protein-coding genes. Phylogenetic analysis revealed that P. nitida is closely related to Paris fargesii and forms a cluster with Paris dunniana. These findings provide significant genomic information for further research on the evolutionary, taxonomic, and phylogenetic aspects of the genus Paris.

Keywords: Paris nitida; chloroplast genome; illumina sequencing; melanthiaceae.

Figure 1.

Pictures of P. nitida (voucher specimen number YHH_2023_LiDu_HAF). (A) Habit, (B) Flower. All photos were taken by Prof. Xujun Wang from Liulin, Dujiaping, Yuanling, Huaihua, Hunan, P. R. China (28°27′33.58″ N, 110°53′23.95″ E).

Figure 2.

Circular representation of the chloroplast genome of P. nitida. The genes depicted both inside and outside the circle are transcribed in a counterclockwise and clockwise direction, respectively. Various colors illustrate genes categorized by their functions. The dashed area in the inner circle displays the GC and AT content, represented by dark and light grey, respectively. Abbreviations: LSC refers to the large single-copy region; IR denotes the inverted repeat; and SSC indicates the small single-copy region.

Figure 3.

Phylogenetic tree based on complete chloroplast genome sequences of 11 species. The following sequences were used: P. nitida OP425116 (this study), P. fargesii NC_033513 (unpublished), P. dunniana NC_033512 (unpublished), P. marmorata NC_033516 (Gao et al. 2018), P. polyphylla NC_046458, P. axialis NC_046459 (unpublished), P. thibetica NC_038161, trillium tschonoskii NC_027739 (unpublished), T. camschatcense NC_046451 (Guan et al. 2021), P. verticillata NC_024560 (Gao et al. 2018), Fritillaria cirrhosa NC_024728 (Li et al. 2015). Supports for nodes were calculated via 1000 standard bootstrap replicates. Scale bar = 0.01.