Rui Liao’s research while affiliated with South-Central University For Nationalities and other places

Achimenes Pers. is well known for its floral diversity and widely used in horticulture, but its phylogenetic position is still poorly understood. And most research about the complete chloroplast genome sequence focused on the Old World species; therefore, we think it is necessary to examine taxa of the New World in more detail. This study determined the complete chloroplast genome of Achimenes cettoana H.E. Moore. The cp genome was 153,011 bp in a total length containing two inverted repeats (IRs) of 25,162 bp separated by a large single-copy (LSC) region of 84,669 bp and a small single-copy (SSC) region of 18,018 bp. The whole cp genome of A. cettoana contains 112 genes, including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. This plastid genome is firstly reported in the New World Gesneriaceae, which will be a valuable resource for future studies on breeding, conservation genetics, and phylogeny of Gesneriaceae.

Background: Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated. Results: To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection. Conclusion: This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.

Chrysosplenium zhouzhiense Hong Liu, a new species from Shaanxi, northwestern China, is described and photographed. The new species belongs to Subgen. Gamosplenium Sect. Nephrophylloides Ser. Macrophylla and is most similar to C. macrophyllum and C. zhangjiajieense from which it differs by having a shorter stem, rhizome absent, basal leaf absent, sterile branch arising from the flowering stem and a light yellow flower with longer stamen. A global conservation assessment is performed and classifies C. zhouzhiense as Endangered (EN).

The complete chloroplast genome of Chrysosplenium ramosum Maxim. and Chrysosplenium alternifolium L. were reported in this study. The chloroplast genomes were 153,460 bp for C. ramosum and 152,619 bp for C. alternifolium. LSC and SSC of 83,670 bp and 17,342 bp were separated by two IRs of 26,224 bp each in C. ramosum. While C. alternifolium contained IRs of 25,992 bp, LSC of 83,524 bp and SSC of 17,111 bp. The chloroplast genome of C. ramosum contains 112 unique genes, including 79 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. And the chloroplast genome of C. alternifolium contains 112 unique genes, including 79 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. In addition, the rps12 gene was recognized as a trans-spliced gene and 17 intron-containing genes were also detected.

Populus pruinosa Schrenk plays an important role on ecological services in desert areas. The complete chloroplast genome was reported in this study using the PacBio Sequel II Platform. The chloroplast genome with a total size of 157,856 bp consists of two inverted repeats (IR, 27,673 bp) separated by a large single-copy region (LSC, 85,867 bp) and a small single-copy region (SSC, 16,645 bp). Further annotation revealed the chloroplast genome contains 111 genes, including 78 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. A total of 151 simple sequence repeats (SSRs) were identified in the chloroplast genome. This information will be useful for study on the evolution and genetic diversity of P. pruinosa in the future.

The complete chloroplast genome of Chrysosplenium macrophyllum Oliv. and Chrysosplenium flagelliferum Fr. Schmidt. were reported in this study. The chloroplast genomes were 152,837 bp for C. macrophyllum and 151,679 bp for C. flagelliferum. LSC and SSC of 83,584 bp and 17,265 bp were separated by two IRs of 25,994 bp each in C. macrophyllum. While C. flagelliferum contained IRs of 25,973 bp, LSC of 82,772 bp and SSC of 16,961 bp, for a total 151,679 bp length. The chloroplast genome of Chrysosplenium macrophyllum contains 130 genes, including 85 protein-coding genes (78 PCG species), 8 ribosomal RNA genes (4 rRNA species), 37 transfer RNA genes (30 tRNA species). And the chloroplast genome of Chrysosplenium flagelliferum contains 130 genes, including 85 protein-coding genes (78 PCG species), 8 ribosomal RNA genes (4 rRNA species), 37 transfer RNA genes (30 tRNA species).

Background Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in China and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low-light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated. Results To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka)/synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The pair-wise Ka/Ks ratios of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to relatively relaxed selection. Conclusion This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low-light conditions. The lower average GC content and the lacking gene of rpl32 indicating selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.

Background: Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low-light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium , its chloroplast genome evolution remains to be investigated. Results: To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium . Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection. Conclusion: This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low-light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2 ) were under positive selection at sites in the coding region.

Background: Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low-light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated. Results: To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection. Conclusion: This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low-light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.

Background: Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated. Results: To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection. Conclusion: This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.