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.

Sonneratia caseolaris is a native mangrove species found in China. It is fast growing and highly adaptable for mangrove afforestation, but suffered great damage by chilling event once introduced to high latitude area. To understand the response mechanisms under chilling stress, physiological and transcriptomic analyses were conducted. The relative electrolyte conductivity, malondialdehyde (MDA) content, soluble sugar content and soluble protein content increased significantly under chilling stress. This indicated that S. caseolaris suffered great damage and increased the levels of osmoprotectants in response to the chilling stress. Gene expression comparison analysis of S. caseolaris leaves after 6 h of chilling stress was performed at the transcriptional scale using RNA-Seq. A total of 168,473 unigenes and 3,706 differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analyses showed that the DEGs were mainly involved in carbohydrate metabolism, antioxidant enzyme, plant hormone signal transduction, and transcription factors (TFs). Sixteen genes associated with carbohydrate metabolism, antioxidant enzyme, phytohormones and TFs were selected for qRT-PCR verification, and they indicated that the transcriptome data were reliable. Our work provided a comprehensive review of the chilling response of S. caseolaris at both physiological and transcriptomic levels, which will prove useful for further studies on stress-responses in mangrove plants.

The complete mitochondrial genome of mangrove associated plant: Sesuvium portulacastrum was analyzed in this paper, which is the first for the genus within the family Aizoaceae. The mitogenome sequence is 392,221 bp in length containing six ribosomal RNA genes, 27 transfer RNA genes, and 36 protein-coding genes. Gene nad1, nad2 and nad5 are the trans-splicing genes. One intron is found in gene ccmFc, two introns are found in genes nad4 and rps3, and four introns are found in gene nad7. Phylogenetic analysis using the maximum likelihood method positioned S. portulacastrum within the monophyletic clades of the family Aizoaceae.

The complete mitochondrial genome of an endangered mangrove plant: Scyphiphora hydrophyllacea was analyzed in this paper, which is the first for the genus within the family Rubiaceae. The mitogenome sequence is 354,155 bp in length containing 3 ribosomal RNA genes, 16 transfer RNA genes, and 37 protein-coding genes. Gene ccmFc, ccmFn, rps3, rps13, rps10, rpl12, nad3 and cox1 contain one intron, gene cox2 and atp9 contain three introns and gene nad1, nad4 and nad7 contain four introns. Furthermore, Gene nad2 and nad5 have five introns. Gene nad1, nad2, nad5, nad7and Cox2 are trans-splicing genes. Phylogenetic analysis using the maximum likelihood method positioned S. hydrophyllacea closely with Asclepias syriaca in Gentianales.