Next-Generation Genome Sequencing of Sedum plumbizincicola Sheds Light on the Structural Evolution of Plastid rRNA Operon and Phylogenetic Implications within Saxifragales

Abstract

The genus Sedum, with about 470 recognized species, is classified in the family Crassulaceae of the order Saxifragales. Phylogenetic relationships within the Saxifragales are still unresolved and controversial. In this study, the plastome of S. plumbizincicola was firstly presented, with a focus on the structural analysis of rrn operon and phylogenetic implications within the order Saxifragaceae. The assembled complete plastome of S. plumbizincicola is 149,397 bp in size, with a typical circular, double-stranded, and quadripartite structure of angiosperms. It contains 133 genes, including 85 protein-coding genes (PCGs), 36 tRNA genes, 8 rRNA genes, and four pseudogenes (one ycf1, one rps19, and two ycf15). The predicted secondary structure of S. plumbizincicola 16S rRNA includes three main domains organized in 74 helices. Further, our results confirm that 4.5S rRNA of higher plants is associated with fragmentation of 23S rRNA progenitor. Notably, we also found the sequence of putative rrn5 promoter has some evolutionary implications within the order Saxifragales. Moreover, our phylogenetic analyses suggested that S. plumbizincicola had a closer relationship with S. sarmentosum than S. oryzifolium, and supported the taxonomic revision of Phedimus. Our findings of the present study will be useful for further investigation of the evolution of plastid rRNA operon and phylogenetic relationships within Saxifragales.

The Mitogenome of Sedum plumbizincicola (Crassulaceae): Insights into RNA Editing, Lateral Gene Transfer, and Phylogenetic Implications

“…According to the Angiosperm Phylogeny Group (APG) system IV [ 118 ], the order Saxifragales includes 15 families. Our mitophylogenetic tree divided 16 species into two clades and five families, which were generally congruent with the framework phylogeny of Saxifragales reported by Folk et al (nuclear data) [ 119 ], Ding et al (plastid data) [ 51 ], and Han et al (plastid data) [ 120 ]. Nevertheless, there are still some unsolved phylogenetic problems within Saxifragales.…”

“…For example, the exact taxonomic position of S. plumbizincicola is not entirely clear. Ding et al [ 51 ] indicated that the S. plumbizincicola mitogenome was close to S. sarmentosum Bunge. Han et al [ 120 ] subsequently implied that S. plumbizincicola had a closer relationship with S. tricarpum Makino than S. sarmentosum by increasing sampling size.…”

“…The first dataset consists of 29 concatenated mitochondrial PCGs. The other includes 79 combined plastid PCGs (data were retrieved from our previous research [ 51 ]). The nonsynonymous substitutions rates (dN), synonymous substitutions rates (dS), and their ratios (ω) were calculated with PAML v4.9 (The ω > 1, =1, and <1 indicate positive, neutral, and purifying selection, respectively) [ 52 ].…”

“…MTPTs and NUMTs were identified by using BLASTn with our previous plastomic data (MN185459) [ 51 ] as a reference and our current nuclear genome (unpublished), respectively. The lost mitochondrial non-core genes were detected in nuclear genome and transcriptomes by using BLASTn with corresponding reference sequences from mitogenomes of H. parviflora (KR559021) [ 63 ], Vitis vinifera L. (NC_012119) [ 64 ], and Amborella trichopoda Baill.…”

Ten Plastomes of Crassula (Crassulaceae) and Phylogenetic Implications

“…In angiosperms, the plastid genome (plastome) generally exhibits a conserved quadripartite circular structure with a size of 120–170 kb, comprising two single copy regions (larger and small regions, namely LSC and SSC, respectively) and two inverted repeat regions (IRs) [ 14 , 15 , 16 ]. Owing to the low level of recombination, uniparental inheritance, and without interference from paralogs, plastome has been extensively utilized as a super-barcode for plant species identification and evolutionary studies [ 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 ]. Due to the rapid development and widespread application of high-throughput sequencing technologies (such as Illumina, PacBio, and Nanopore sequencing technologies), an increasing number of complete Crassulaceae plastomes (more than 70 sequences) have been deposited in public databases.…”