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

• Main Authors: Ying Zhang, Jing-Wen Zhang, Yong Yang, Xin-Nian Li
• Format: Article
• Language: English
• Published: MDPI AG 2019-11-01
• Series: Forests
• Subjects: endangered mangrove; <i>scyphiphora hydrophyllacea</i>; rubiaceae; gentianales; chloroplast genome; phylogenetic analysis
• Online Access: https://www.mdpi.com/1999-4907/10/11/1000

<i>Scyphiphora hydrophyllacea</i> Gaertn. f. (Rubiaceae) is an endangered mangrove species found in China, and its only known location is in Hainan Island. Previous studies conducted on <i>S. hydrophyllaceae</i> 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 <i>S. hydrophyllaceae</i> by comparing with it related Rubiaceae species. The chloroplast genome of <i>S. hydrophyllaceae</i> 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 <i>S. hydrophyllacea</i> 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 <i>matK</i>, <i>rps</i>16, and <i>atpF</i>. 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 <i>S. hydrophyllaceae</i> is closer to the <i>Coffeeae</i> genus than to <i>Cinchoneae</i>, <i>Naucleeae</i>, <i>Morindeae</i>, and <i>Rubieae</i> 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.