Comparative Analysis of the Chloroplast Genome of Cardamine hupingshanensis and Phylogenetic Study of Cardamine

Abstract

Cardamine hupingshanensis (K. M. Liu, L. B. Chen, H. F. Bai and L. H. Liu) is a perennial herbal species endemic to China with narrow distribution. It is known as an important plant for investigating the metabolism of selenium in plants because of its ability to accumulate selenium. However, the phylogenetic position of this particular species in Cardamine remains unclear. In this study, we reported the chloroplast genome (cp genome) for the species C. hupingshanensis and analyzed its position within Cardamine. The cp genome of C. hupingshanensis is 155,226 bp in length and exhibits a typical quadripartite structure: one large single copy region (LSC, 84,287 bp), one small single copy region (17,943 bp) and a pair of inverted repeat regions (IRs, 26,498 bp). Guanine-Cytosine (GC) content makes up 36.3% of the total content. The cp genome contains 111 unique genes, including 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. A total of 115 simple sequences repeats (SSRs) and 49 long repeats were identified in the genome. Comparative analyses among 17 Cardamine species identified the five most variable regions (trnH-GUG-psbA, ndhK-ndhC, trnW-CCA-trnP-UGG, rps11-rpl36 and rpl32-trnL-UAG), which could be used as molecular markers for the classification and phylogenetic analyses of various Cardamine species. Phylogenetic analyses based on 79 protein coding genes revealed that the species C. hupingshanensis is more closely related to the species C. circaeoides. This relationship is supported by their shared morphological characteristics.

Characterization of the complete plastome sequence of Korean endemic, Cardamine glechomifolia H.Lév. (Brassicaceae, Brassicales)

“…However, earlier phylogenetic studies on Cardamine indicated a close connection between clade II and clade I, as Raman and Park ( 2021 ) and Huang et al. ( 2022 ) reported. To elucidate the interrelationship among the three clades, it appears imperative to procure more samples and do further investigation.…”

“… 2020 ), Cardamine hupingshanensis (NC_065146) (Huang et al. 2022 ), Cardamine impatiens (NC_026445) (Hu et al. 2015 ), Cardamine kitaibelii (NC_049610) (Walden et al.…”

Complete Plastomes of Ten Rorippa Species (Brassicaceae): Comparative Analysis and Phylogenetic Relationships

“…Simple sequence repeats are widely served as molecular markers for population genetic analyses, polymorphism identification, and taxonomic analyses [68]. Here, we identified the SSRs in the ten Rorippa species, ranging from 102 to 111, which is comparable to other Brassicaceae in numbers [69,70]. The number of poly (G)/(C) SSRs in the Rorippa plastome is significantly less than that of poly (A)/(T), which agrees with the results of other taxa [71].…”

Cardamine libagouensis, a new species from Hubei, China

“…Genome sequence analysis indicates that the divergence between C. hirsuta and Arabidopsis thaliana occurred around 32 Mya, and that C. hirsuta and C. hupingensis diverged about 6.5 Mya. Phylogenetic analyses based on 79 protein coding genes in the chloroplast genome revealed that 17 Cardamine species formed three different clades and C. hupingshanensis is more closely related to C. circaeoides (Huang et al 2022).…”