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.
Highlights
Scyphiphora hydrophyllacea is a shrub mangrove that belongs to the Scyphiphora genus, a monotypic genus whose distribution range extends south India and as well as Ceylon, Indochina, and Hainan in China through the Malay Archipelago and Philippines to Australia andNew Caledonia and northward to the Solomon Islands and Palau [1]
Eight protein-coding genes, four ribosomal RNA (rRNA), and seven transfer RNA (tRNA) are found to be duplicated in the inverted repeat (IR) regions
The gene rps12 is a trans-spliced gene with its 5′ terminal located at the large single-copy region (LSC) region and the endaccession with a copy located in each of thetotal twocpIRgenome regions,ofwhich is a common higher under number
Summary
Scyphiphora hydrophyllacea is a shrub mangrove that belongs to the Scyphiphora genus (family: Rubiaceae), a monotypic genus whose distribution range extends south India and as well as Ceylon, Indochina, and Hainan in China through the Malay Archipelago and Philippines to Australia andNew Caledonia and northward to the Solomon Islands and Palau [1]. Scyphiphora hydrophyllacea is a shrub mangrove that belongs to the Scyphiphora genus (family: Rubiaceae), a monotypic genus whose distribution range extends south India and as well as Ceylon, Indochina, and Hainan in China through the Malay Archipelago and Philippines to Australia and. Its terminal nodes and shoots are distinctively covered by a resinous substance [2]. This species is Forests 2019, 10, 1000; doi:10.3390/f10111000 www.mdpi.com/journal/forests. In China, this species is found only in Hainan Island, and it has been included in a list of key wild plants under provincial protection in Hainan (2006). The incidences of fruit set in this mangrove is high, only a low percentage of seed germination has been reported [1]
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