Xianggang Shi

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

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.

Development of microsatellite markers for Carallia brachiata (Rhizophoraceae).

Premise of the study: Microsatellite markers were developed for Carallia brachiata to assess the genetic diversity and structure of this terrestrial species of the Rhizophoraceae. Methods and Results: Based on transcriptome data for C. brachiata, 40 primer pairs were initially designed and tested, of which 18 were successfully amplified and 11 were polymorphic. For these microsatellites, one to three alleles per locus were identified. The observed and expected heterozygosities ranged from 0 to 0.727 and 0 to 0.520, respectively. In addition, all primers were successfully amplified in two congeners: C. pectinifolia and C. garciniifolia. Conclusions: The microsatellite markers described here will be useful in population genetic studies of C. brachiata and related species, suggesting that developing microsatellite markers from next-generation sequencing data can be efficient for genetic studies across this genus.

The complete chloroplast genome sequence of Camellia ptilophylla (Theaceae): a natural caffeine-free tea plant endemic to China

Abstract Camellia ptilophylla is a natural caffeine-free tea plant endemic to China with high commercial and therapeutic values. Here, we report the complete chloroplast genome assembled using Illumina pair-end sequencing data. The chloroplast genome was 157,097 bp in length, with a large single copy (LSC) region of 86,631 bp, a small single copy (SSC) region of 18,286 bp, separated by two inverted repeat (IR) regions of 26,090 bp each. It contains a total of 132 genes, with an overall GC content of 37.3%. The phylogenetic analysis showed that C. ptilophylla is sister to a congeneric species, C. reticulata.

Chloroplast phylogeography of a widely distributed mangrove species, Excoecaria agallocha , in the Indo-West Pacific region

Excoecaria agallocha is one of the predominant mangrove species in the Indo-West Pacific (IWP) region with an extensive range of distribution. To infer the current geographical patterns of genetic variation and provide new insights on the historical population dynamics of mangrove species in the IWP region, we sampled E. agallocha across its distribution range and investigated the phylogeography of this species using four chloroplast DNA (cpDNA) fragments. Our results showed that E. agallocha possessed a high degree of species-level genetic diversity, while the average genetic diversity within populations was much lower. The presence of population genetic structure was supported by the estimates of genetic differentiation and the analysis of molecular variance (AMOVA). Of the ten haplotypes identified, no haplotypes were shared between the East Indian Ocean (EIO), the West Pacific Ocean (WPO), and the North Australian (NA) regions. Genealogy analysis, haplotype distribution patterns, and the principal coordinate analysis (PCoA) consistently suggested the existence of three haplotype groups distributed in distinct geographical locations. The genealogical breaks observed and further analysis of geographic/genetic barriers indicated that both land barriers and oceanic currents may have played important roles in the divergence and demography of E. agallocha.

Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion

BackgroundMikania micrantha H.B.K. (Asteraceae) is one of the world’s most invasive weeds which has been rapidly expanding in tropical Asia, including China, while its close relative M. cordata, the only Mikania species native to China, shows no harm to the local ecosystems. These two species are very similar in morphology but differ remarkably in several ecological and physiological traits, representing an ideal system for comparative analysis to investigate the genetic basis underlying invasion success. In this study, we performed RNA-sequencing on the invader M. micrantha and its native congener M. cordata in China, to unravel the genetic basis underlying the strong invasiveness of M. micrantha. For a more robust comparison, another non-invasive congener M. cordifolia was also sequenced and compared.ResultsA total of 52,179, 55,835, and 52,983 unigenes were obtained for M. micrantha, M. cordata, and M. cordifolia, respectively. Phylogenetic analyses and divergence time dating revealed a relatively recent split between M. micrantha and M. cordata, i.e., approximately 4.81 million years ago (MYA), after their divergence with M. cordifolia (8.70 MYA). Gene ontology classifications, pathway assignments and differential expression analysis revealed higher representation or significant up-regulation of genes associated with photosynthesis, energy metabolism, protein modification and stress response in M. micrantha than in M. cordata or M. cordifolia. Analysis of accelerated evolution and positive selection also suggested the importance of these related genes and processes to the adaptability and invasiveness of M. micrantha. Particularly, most (77 out of 112, i.e. 68.75%) positively selected genes found in M. micrantha could be classified into four groups, i.e., energy acquisition and utilization (10 genes), growth and reproduction (13 genes), protection and repair (34 genes), and signal transduction and expression regulation (20 genes), which may have contributed to the high adaptability of M. micrantha to various new environments and the capability to occupy a wider niche, reflected in its high invasiveness.ConclusionsWe characterized the transcriptomes of the invasive species M. micrantha and its non-invasive congeners, M. cordata and M. cordifolia. A comparison of their transcriptomes provided insights into the genetic basis of the high invasiveness of M. micrantha.

Development of polymorphic EST-SSR markers in Itea chinensis (Iteaceae) and cross-amplification in related species

Premise of the Study We isolated and characterized 16 expressed sequence tag–simple sequence repeat (EST‐SSR) markers in Itea chinensis (Iteaceae), a common evergreen broadleaf tree, for future studies on the genetic diversity and spatial genetic structure of the species. Methods and Results Based on transcriptome data of I. chinensis, a total of 36 primer pairs were initially designed and tested. Of these, 16 were successfully amplified and showed clear polymorphism. For these markers, the number of alleles per locus varied from two to 15. The observed and expected heterozygosity ranged from 0 to 0.600 and 0.072 to 0.554, respectively. Furthermore, all loci were successfully cross‐amplified in two congeneric species, I. oblonga and I. yangchunensis. Conclusions The EST‐SSR markers described here can be used to study the genetic diversity and phylogeographic patterns of I. chinensis and other related species in Itea.

Development of Microsatellite Markers for Eurya acuminatissima (Theaceae)

Premise of the study: Sixteen microsatellite markers were developed to study the fine-scale spatial genetic structure of Eurya acuminatissima, a dioecious tree species of Theaceae endemic to southern China. Methods and Results: A total of 30 primer pairs were initially designed and tested on the basis of the transcriptome data of E. acuminatissima, of which 16 were successfully amplified and showed clear polymorphism. For these microsatellites, one to 17 alleles per locus were identified. The observed and expected heterozygosities ranged from 0 to 1.000 and 0 to 0.903, respectively. Conclusions: The microsatellite markers described here can be used to study genetic diversity and spatial genetic structure of E. acuminatissima. Furthermore, all loci were successfully cross-amplified in a related species, E. auriformis.

Eurya pilosa (Theaceae), a New Species from Yunnan, China

Eurya pilosa C.X. Ye & X.G. Shi sp. nova (Theaceae) from Yunnan Province, China, is described and illustrated. It is morphologically most similar to E. loquaiana, from which it differs by having inconspicuously 2-ribbed branches; densely pubescent branchlets, bracteoles and sepals; sparsely pubescent petals, ovaries and fruits; and leaves that do not turn purplish when dry.