Structural and Comparative Analysis of the Complete Chloroplast Genome of a Mangrove Plant: Scyphiphora hydrophyllacea Gaertn. f. and Related Rubiaceae Species

Abstract

Scyphiphora hydrophyllacea Gaertn. f. (Rubiaceae) is an endangered mangrove species found in China, and its only known location is in Hainan Island. Previous studies conducted on S. hydrophyllaceae have mainly focused on its location, biological characteristics, and medical effects. However, to date, there has been no published report regarding the genetics or genome of this endangered mangrove species. In this study, we developed valuable chloroplast genome-related molecular resources of S. hydrophyllaceae by comparing with it related Rubiaceae species. The chloroplast genome of S. hydrophyllaceae was found to be a circular molecule with a total size of 155,132 bp, and it is observed to have a quadripartite structure. The whole chloroplast genome contains 132 genes, of which 88 and 36 are protein-coding and transfer RNA genes, respectively; it also contains four ribosomal RNA genes with an overall GC content of 37.60%. A total of 52 microsatellites were detected in the S. hydrophyllacea chloroplast genome, and microsatellite marker detection identified A/T mononucleotides as majority simple sequence repeats in all nine Rubiaceae chloroplast genomes. Comparative analyses of these nine chloroplast genomes revealed variable regions, including matK, rps16, and atpF. All nine species shared 13 RNA-editing sites distributed across eight coding genes. Phylogenetic analyses based on the complete sequences of the chloroplast genomes revealed that the position of S. hydrophyllaceae is closer to the Coffeeae genus than to Cinchoneae, Naucleeae, Morindeae, and Rubieae in the Rubiaceae family. The genome information reported in this study could find further application in the evolution and population genetic studies, and it helps improve our understanding of the endangered mechanism and the development of conservation strategies of this endangered mangrove plant.

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]. Also, these results suggest that the cp genome in this subfamily had rather conserved genome organization [15,16].…”

“…In fact, the complete cp genome of C. spruceanum was 154,480pb, similar to other Ixoroideae genomes [15,17], with a quadripartite structure (LSC, SSC and two IR regions) which is a common characteristics in higher plants [11]. The annotation of C. spruceanum cp genome predicted 87 proteincoding genes (CDS), and similar patterns of protein-coding genes are also present in other Rubiaceae plants [16]. Similar to other studies [18,19], there were three genes (rps12, clpP1 and ycf3) that included two intron regions in the cp genome of capirona.…”

“…Until very recently, only a few complete chloroplast genome sequences for the Ixoroideae subfamily have been deposited to GenBank, with the very first being that of Coffea canephora in 2016. Nevertheless, with the development of Next Generation Sequencing (NGS), the chloroplast (cp) genome of most species of Ixoroideae subfamily has been obtained [2, [15][16][17], however, to date, cp genome of members of the genus Calycophyllum remained unknown. Thus, in the present study we sequenced for the first time the C. spruceanum chloroplast genome (accession number: OK326865.1) and compared with other members of the sub family Ixoroideae that are closely related.…”

“…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]. Also, these results suggest that the cp genome in this subfamily had rather conserved genome organization [15,16]. We identified that in the seven sequences of the cp genome are some highly divergent regions including psbA-trnH-GUG, rps16-matK, atpI-atpH, ndhJ-rps4, rbcL-psaI, psaI-petA, ycf1-rps15, and rpl32-ndhF.…”