Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments

Abstract

Mangroves are woody plants that grow at the interface between land and sea in tropical and subtropical latitudes, where they exist in conditions of high salinity, extreme tides, strong winds, high temperatures, and muddy, anaerobic soils. Rhizophoraceae is a key mangrove family, with highly developed morphological and physiological adaptations to extreme conditions. It is an ideal system for the study of the origin and adaptive evolution of mangrove plants. In this study, we characterized and comprehensively compared the transcriptomes of four mangrove species, from all four mangrove genera, as well as their closest terrestrial relative in Rhizophoraceae, using RNA-Seq. We obtained 41,936-48,845 unigenes with N50 values of 982-1,185 bp and 61.42-69.48% annotated for the five species in Rhizophoraceae. Orthology annotations of Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Clusters of Orthologous Groups revealed overall similarities in the transcriptome profiles among the five species, whereas enrichment analysis identified remarkable genomic characteristics that are conserved across the four mangrove species but differ from their terrestrial relative. Based on 1,816 identified orthologs, phylogeny analysis and divergence time estimation revealed a single origin for mangrove species in Rhizophoraceae, which diverged from the terrestrial lineage ~56.4 million years ago (Mya), suggesting that the transgression during the Paleocene-Eocene Thermal Maximum may have been responsible for the entry of the mangrove lineage of Rhizophoraceae into intertidal environments. Evidence showed that the ancestor of Rhizophoraceae may have experienced a whole genome duplication event ~74.6 Mya, which may have increased the adaptability and survival chances of Rhizophoraceae during and following the Cretaceous-Tertiary extinction. The analysis of positive selection identified 10 positively selected genes from the ancestor branch of Rhizophoraceae mangroves, which were mainly associated with stress response, embryo development, and regulation of gene expression. Positive selection of these genes may be crucial for increasing the capability of stress tolerance (i.e., defense against salt and oxidative stress) and development of adaptive traits (i.e., vivipary) of Rhizophoraceae mangroves, and thus plays an important role in their adaptation to the stressful intertidal environments.

Keywords: abiotic stress; adaptive evolution; extreme environment; mangrove; positive selection; transcriptome.

Figure 1

Divergence time and whole-genome duplication in Rhizophoraceae. (A) Phylogenetic relationships and divergence time of the five Rhizophoraceae species. (B) Histograms of gene duplication ages using the mixture model (above) and SiZer (below) analysis for the mangrove R. apiculata and terrestrial Ca. brachiata. (C) The relative placement of two inferred whole-genome duplications (WGDs) in Rhizophoraceae. (D) Gene Ontology (GO) annotations of paleologs from each Rhizophoraceae species examined. The red dot in the phylogenetic tree in (A) indicates the time when the inferred WGD shared by Rhizophoraceae occurred. Plots of normal distributions in (B) were fitted from mixture model analysis; red lines represent the younger WGDs shared in Rhizophoraceae, while green lines probably correspond to the older triplication shared by all angiosperms. Red and blue areas in SiZer maps indicate significantly decreasing and increasing slopes, respectively; purple represents no significant slope change; and gray indicates not enough data for the test. In (C), histograms represent K_S distributions of ortholog genes between Ca. brachiata and B. gymnorrhiza (black), and between Ca. brachiata and P. trichocarpa (gray); red and green lines refer to (B). In (D), colors represent the percentage of paleologs that a particular GO category composes; Bgy, Kob, Rap, Cta, and Cbr represent B. gymnorrhiza, K. obovata, R. apiculata, Ce. tagal, and Ca. brachiata, respectively.

Figure 2

Positively selected genes and stress resistance in the four Rhizophoraceae mangroves. Positively selected genes are marked in red.