A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea

Abstract

In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.

Keywords: Kandelia; chloroplast genome; environment adaptation; gene diversity; mangrove; protein dynamics simulation.

Figure 1

Geographic distribution of 25 Kandelia samples collected from 4 different countries including 11 sampling sites for sequencing and assembly the whole chloroplast genomes. The blue solid circle represented Kandelia candel species and the red tangle represented Kandelia obovata species.

Figure 2

Phylogenetic tree. (A) The Kandelia tree constructed using the UPGMA model based on the 76 single-copy genes in the 25 whole cp genomes. (B) The tree constructed using the UPGMA model based on 38 homologous pair genes in 13 mangrove species including 40 samples.

Figure 3

Gene maps of the chloroplast genomes of Kandelia. Genes shown outside the outer circle are transcribed clockwise, and genes shown inside the circle are transcribed counterclockwise. Genes belonging to different functional groups are color coded. The dashed area in the inner circle indicates the GC content of the chloroplast, and the light gray area corresponds to AT content of the chloroplast. Point mutations of atpA and ndpD gene were shown between K. obovata and K. candel.

Figure 4

Analyses of indels in the chloroplast genomes. (A) Frequency of different indels types and locations. (B) Number and size of non-SSR-related indels in the K. obovata genomes. (C) The PCA result of SNPs. (D) The phylogenetic tree based on SNPs data.

Figure 5

Gene map comparison between K.candel and K.obovata chloroplast genomes aligned using Mauve, showing a big ‘gap’ of 1,149bp with rich A and T in LSC regions in K. obovata.

Figure 6

The Pi value in sliding-window analysis of the whole chloroplast genomes. The genes highlighted in blue color showcase the SNPs between K. candel and K. obovata. The genes highlighted in orange color were SNPs within K. candel species. The purple color highlighted genes were SNPs within K. obovata species.

Figure 7

The predicated 3D structural modeling and molecular dimnamics simulation of the NDH-D protein. By setting different colors (gray to blue to yellow to orange to red) according to the b-factor values, the color in the structure is closer to red, the more flexible the structure. (A) The 3D model of NDH-D protein for K. candel. (B) The 3D model of NDH-D protein for K. obovata. (C) The mutation sites of protein sequence compared between K. candel and K. obovata. Molecular dynamics simulations showed with RMSD (D) and RMS fluctuation (E).

Figure 8

The predicated 3D structural modeling and molecular dimnamics simulation of the ATP-A protein. By setting different colors (gray to blue to yellow to orange to red) according to the b-factor values, the color in the structure is closer to red, the more flexible the structure. (A) The conformational variations of protein amino acid residues during the molecular dynamics simulation process showing the distinct difference in the region from 26aa to 96aa. (B) The 3D model of ATP-A protein for K. candel. (C) The 3D model of ATP-A protein for K. obovata. (D) The mutation at the site of the 89 aa of ATP-A protein between K. candel and K. obovata. (E) Molecular dimnamics simulation of ATP-A protein and ligand ADP docking exhibuted by binding affinity for K. candel (E) and K. obovata (F).