The complete chloroplast genome sequences of an endangered orchid species Paphiopedilum parishii (Orchidaceae).

Paphiopedilum parishii (Rchb. f.) Stein is an endangered and rare species with highly ornamental value. In this study, we report the complete chloroplast genome of P. parishii using the Illumina sequencing data. The total genome of P. parishii is 154,689 bp in length and the GC content is 35.9%, with a pair of inverted repeats (IRs) regions of 32,690 bp each, a large single-copy region (LSC) of 86,863 bp and a small single-copy region (SSC) of 2,446 bp. The chloroplast genome encoded 127 genes, including 82 protein-coding genes (CDS), 8 rRNA genes and 37 tRNA genes. The phylogenetic tree showed that P. parishii was clustered with other species in Paphiopedilum with strong support based on the complete chloroplast genome.

Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing.

BACKGROUND: Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants. RESULTS: In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history. CONCLUSIONS: This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.

The complete chloroplast genome sequence of a medicinal orchid species Coelogyne fimbriata (Orchidaceae).

Coelogyne fimbriata is an important orchid species with high medicinal value. Its complete chloroplast genome is 158,935 bp in length, which possesses the typical structure consising of a small single-copy region (SSC) of 18,743 bp, two inverted repeats (IRs) of 26,374 bp, and a large-single copy region (LSC) of 87,444 bp. The genome encodes 137 genes, including 91 protein-coding genes (PCGs), 38 tRNA genes and 8 rRNA genes. And the overall GC content is 37.40%. In addition, our phylogenetic analysis based on cp genome revealed the phylogenetic relationship between C. fimbriata and other 22 species in Orchidaceae.