Complete chloroplast genome of Reineckia carnea and its implications for the phylogenetic position within Nolinoideae (Asparagaceae)

Abstract

Reineckia carnea is an important horticultural and medicinal plant in East Asia. Here, we determined the first complete chloroplast genome of R. carnea using genome skimming approach. The cp genome was 157,059 bp long, with a large single-copy region (LSC) of 85,474 bp and a small single-copy region (SSC) of 18,535 bp separated by a pair of inverted repeats (IRs) of 26,525 bp. It encodes 132 genes, including 86 protein-coding genes, 38 tRNA genes, and eight ribosomal RNA genes. The phylogenetic analysis indicated that R. carnea is close related to Rohdea chinensis.

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

“…So, in the present study, we constructed a maximum-likelihood phylogenetic tree based on concatenated 75 protein-coding genes of 19 Nolinoideae species and revealed that all the species formed a monophyletic group and S. gardenii formed a cluster with R. carnea, R. chinensis and C. keiskei. The previous studies also support this phylogenetic tree where similar results were obtained that showed weakly supported bootstrap value in some nodes of the Nolinoideae phylogeny [9][10][11][12][13][14][15]48]. The phylogenetic result also showed that Speirantha, Rohdea, Reineckea and Convallaria genus are constantly clustered in the same clade with a high-resolution value, even though high sequence divergence is noted in few protein-coding genes of these chloroplast genomes.…”

“…Until recently, only a few complete chloroplast genome sequences for this Nolinoideae subfamily have been deposited in GenBank, with the very first being that of Polygonatum cyrtonema in 2015. Owing to the development of high-throughput sequencing technologies, additional Nolinoideae chloroplast genomes were sequenced [9][10][11][12][13][14][15], but the genus Speirantha has to date remained unexplored. Therefore, in the present study, we sequenced the S. gardenii chloroplast genome and compared it with its closed related other Nolinoideae members.…”

“…Usually, the length of the infA gene is 234 bp. Most of the species of the Nolinoideae subfamily do not contain an infA gene or contain it as a pseudogene except Maianthemum dilatatum, M. bicolor, R. carnea and R. chinensis [9,10,13]. Meanwhile, the deletion of two bp at the 180th bp position in the infA gene of C. keiskei, causes frameshift mutation to a premature stop codon and thus leads to the formation of infA pseudogene [12].…”

“…Moreover, in the Polygonateae clade, several Polygonatum species were characterized and their phylogenetic relationships have been resolved recently [9,11,14,15]. In contrast, only a few studies have been carried out in the Aspidistreae tribe clade [10,12,13]. So, in the present study, we constructed a maximum-likelihood phylogenetic tree based on concatenated 75 protein-coding genes of 19 Nolinoideae species and revealed that all the species formed a monophyletic group and S. gardenii formed a cluster with R. carnea, R. chinensis and C. keiskei.…”

“…Among these, Nolinoideae is a subfamily, with more than 100 species, of the 2 of 16 Asparagaceae family belonging to the monocot flowering plants. In the past decade, a few species of Nolinoideae have been characterized at the molecular level and phylogenetic implications with other species were identified [9][10][11][12][13][14][15]. The genus Speirantha belongs to the subfamily Nolinoideae and consists of only one species, S. gardenii and its common name is "False Lily of the Valley".…”