Comparative Genomic And Pedigree Geography Of Chloroplasts In East Asia Across The Sea

Dendrobium moniliforme (L) Sw. is the type species of genus Dendrobium, widely distributed discontinusely in East Asia, such as in mainland China,Taiwan,India,Japan and Korea. This species has important medical and Ornamental value. The over-exploitation of wild resources result in the depredation of this species. To maximise the impact of conservation and management efforts, it is urgent for us to insight into the genomics, phylogeograpy and population genetics. Here, we investigated the comparative chloroplast genomes of orchids; reconstructed the phylogenetic relationships within the subfamily Epidendroideae using four protein-coding regions; identified the genetic structure of the populations of D. moniliforme using microsatelllite markers; examined the phylogeography of D. moniliforme with cpDNA and nrDNA ITS.The major findings are as below:1. Comparative chloroplast genomics of OrchidaceaeHere, we report the complete chloroplast genomes of the medicinal plant D.moniliforme and Dendrobium officinale. These two genomes were colinearity except intergenetic genes and ndh genes. Comparing with other photosynthetic orchid genomes,they showed similarities in structure as well as gene order and content,but differences in the organization of the inverted repeat/small single-copy junction and ndh genes. The organization of the inverted repeat/small single-copy junctions in the chloroplast genomes of these orchids was classified into four types; we propose that inverted repeats flanking the small single-copy underwent expansion or contraction among Orchidaceae.2. A case study of application of comparative chloroplast genomes in phylogeny in the subfamily EpidendroideaeFifteen highly divergent protein-coding genes were identified, which are useful for phylogenetic analyses in orchids. To test the efficiency of these genes serving as markers in phylogenetic analyses, coding regions of four genes of them were used as a case study to construct phylogenetic trees in the subfamily Epidendroideae. High support was obtained for placement of previously unlocated subtribes Collabiinae and Dendrobiinae in the subfamily Epidendroideae. Our findings expand understanding of the diversity of orchid chloroplast genomes and provide a reference for study of the molecular systematics of this family.3. Population genetics of D. moniliforme based on microsatellite markersGenetic diversity and population structure were surveyed using 11 nuclear microsatellite loci in 305 individuals representing 23 populations. Our aim was to determine if recent habit loss and fragmentation have caused genetic bottlenecks. High genetic diversity was identified at population level. Genetic divergence was found among populations. Based on genentic structure, populations located in Yungui Plateau (Yunnan,Sichuan and Guizhou province) formed a clade; while other populations formed another clade. In the later clade,a subclade was formed with east of Nanling Mountains and Taiwan, Korea and Janpan islands. No significant bottleneck was identified within majority populations in East Asia. Moreover, two genetic barriers (Chinese mainland—Taiwan Island, Yungui Plateau—other regions) were identified, which were possibly related with geographic isolation. Our studies will be helpful for the conservation strategies of D. moniliforme.4. Phylogeography of Dendrobium moniliforme based on cpDNA and nrDNAIn this study, some molecular techniques including nrDNA ITS and non-coding region of cpDNA (atpH-atpI and psbK-psbI) were used for defining haplotypes and ribotypes of D. moniliforme and species complex, understanding its geographic distribution and reconstructing phylogenetic trees. The distributions of this species can be devided into two clades: Yungui Pleateau and central and east regions of China-islands of Taiwan-Japan-Korea. Based on neutral test and mismatch analysis, populations did not experience expansion recently and glacial period had limited influence on this species.Gene flow via seed and via pollen flow was discongruent resulting from different historical events during evolutionary processes. The relationships between D. moniliforme and other three D. moniliforme complexes (D. huoshanense, D. henanense and D. funiushanense)were also examined. These four Dendrobium species are sympatric or parapatry. Potential gene introgression was found between D.moniliforme and other three species complex,except for different morphological characters.