A comparison of 25 complete chloroplast genomes sheds light on
differential energy requirements 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.