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

Abstract

The plant “False Lily of the Valley”, Speirantha gardenii is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of S. gardenii and this is the first report on the chloroplast genome sequence of Speirantha. The complete S. gardenii chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, KA/KS nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that S. gardenii species has a closer genetic relationship to the Reineckea, Rohdea and Convallaria genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum Spruceanum, Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

“…Guanine-cytosine (GC) content has been a very useful tool to characterize in general terms the behavior of genomes [ 54 , 55 ].The GC content in the IR region was much higher than in the LSC and SSC regions in the C. spruceanum cp genome, probably due to the presence of eight ribosomal RNA (rRNA) genes in this region, which is consistent with previous analyses in other Ixoroideae [ 43 , 46 ] and in other angiosperms cp genomes [ 21 , 56 , 57 ]. The IR (A/B) region has always been considered consistent and stable in the cp genome, and it is also common in the evolution of plants with contraction or expansion events in the border region [ 43 ].…”

“…Although the chloroplast genomes of angiosperms are highly conserved, mutational events occur, such as structural rearrangement, insertions, and deletions, inversions, translocations, and variations in the number of copies. This polymorphism in the chloroplast genome provides valuable information about population genetics and structure, phylogeny, species barcode analysis, and endangered species conservation and breeding improvement [ 21 ]. In addition, the chloroplast genome will provide us information about the codon usage bias.…”

Unlocking the Complete Chloroplast Genome of a Native Tree Species from the Amazon Basin, Capirona (Calycophyllum spruceanum Benth., Rubiaceae), and Its Comparative Analysis with Other Ixoroideae Species

“…In total, 41 perfect SSRs were detected in C. sprucearum cp genome distributed in the LSC, SSC, and IR regions with strong A/T bias. Similarly, previous studies also revealed that the noncoding region contained more SSRs than the coding regions [14,16]. Also our results are comparable to those of several previous studies showing that SSRs in cp genomes are highly rich in polythymine (poly T) or polyadenine (polyA) as reported for cp genomes of other plants species [32][33][34].…”

“…The GC content in the IR region was much higher than in the LSC and SSC region in C. spruceanum cp genome, probably due to the presence of eight ribosomal RNA (rRNA) genes in this region, which is consistent with previous analyses in other Ixoroideae [15,16], and in other angiosperms cp genomes [14,22,23]. The IR (A/B) region has always been considered consistent and stable in the cp genome, and it is also common in the evolution of plants with contraction or expansion events in the border region [16].…”

“…Although the chloroplast genomes of angiosperms are highly conserved, mutational events occur, such as structural rearrangement, insertions, and deletions (InDels), inversions, translocations and variations in the number of copies (CNV). This polymorphism in the chloroplast genome provides invaluable information about population genetics and structure, phylogeny, species barcode analysis, and endangered species conservation and breeding improvement [14]. To date, there is no report on the application of Next Generation Sequencing (NGS) techniques to study Calycophyllum spp.…”