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Plastome characteristics and species identification of Chinese medicinal wintergreens(Gaultheria,Ericaceae)

Plant Diversity 2022年第6期44卷 519-529页

作者： Yan-Ling Xu Hao-Hua Shen Xin-Yu Du Lu Lu School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products Kunming Medical UniversityKunmingYunnanChina Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina

Wintergreen oil is a folk medicine widely used in foods,pesticides,cosmetics and drugs.In China,nine out of 47 species within Gaultheria(Ericaceae)are traditionally used as Chinese medicinal wintergreens;however,phylogenetic approaches currently used to discriminating these species remain unsatisfactory.In this study,we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria.Each Gaultheria plastome contained 110 unique genes(76 protein-coding,30 tRNA,and four rRNA genes).Duplication of trnfM,rps14,and rpl23 genes were detected,while all plastomes lacked ycf1 and ycf2 genes.Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene.Moreover,plastomes of Gaultheria leucocarpa var.yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene.Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales.Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species.Additionally,seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens.Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria.In addition,our findings provide important resources for identification of Chinese medicinal wintergreens.

关键词： DNA barcodes Gene duplication Plastome repeat sequences Structural variation

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Structural characterization of four Rhododendron spp.chloroplast genomes and comparative analyses with other azaleas

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BIOCELL 2023年第3期47卷 657-668页

作者： XIAOJUN ZHOU MENGXUE LIU LINLIN SONG Life Science College Luoyang Normal UniversityLuoyang471934China College of Life Science and Technology Henan Institute of Science and TechnologyXinxiang453003China

Azalea is a general designation of Rhododendron in the Ericaceae family.Rhododendron not only has high ornamental value but also has application value in ecological protection,medicine,and scientific research.In this study,we used Illumina and PacBio sequencing to assemble and annotate the entire chloroplast genomes(cp genomes)of four Rhododendron species.The chloroplast genomes of R.concinnum,R.henanense subsp.lingbaoense,R.micranthum,and R.simsii were assembled into 207,236,208,015,207,233,and 206,912 bp,respectively.All chloroplast genomes contain eight rRNA genes,with either 88 or 89 protein-coding genes.The four cp genomes were compared and analyzed by bioinformatics,and the phylogenetic analysis based on chloroplast genomes of 26 species of Ericaceae,Actinidiaceae,and Primulaceae under Ericales was conducted.A comparison of the linear structure of cp genomes of four Rhododendron showed that there were substantial sequence similarities in coding regions,but high differences in non-coding regions.A phylogenetic analysis,based on chloroplast whole genome sequences,showed that all Rhododendron species are in the clade Ericaceae.This study provides valuable genetic information for the study of population genetics and evolutionary relationships in Rhododendron and other azalea species.

关键词： Rhododendron Comparative analysis repeat sequences Phylogeny

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BAC-end sequencing and analysis of Zhikong scallop （Chlamys farreri） genome

BAC-end sequencing and analysis of Zhikong scallop （Chlamys...

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中国海洋湖沼学会第十次全国会员代表大会暨学术研讨会

作者： Zhang Xiaojun Zhao Cui Zhang Xiuying Liu Chengzhang Huan Pin Yu Yang Duan Hu Li Fuhua Xiang Jianhai Key Laboratory of Experimental Marine Biology Institute of Oceanology Chinese Academy of Sciences Graduate University of Chinese Academy of Sciences

Zhikong scallop （Chlamys farreri） is one of most economically important species to aquaculture industry in China. To further understand scallop genome, a total of 10,237 BAC clones were randomly selected and sequenced both ends with ABI 3130xl Genetic Analyzer. After trimming and quality filtering, 17,447 BAC end sequences （BESs） including 7,314 paired-ends were obtained, with an average length of 446 bp. A total of 7,773,272 bp were generated, representing approximately 0.63% of the scallop genome. Based on this survey, the scallop genome was found to be highly AT-rich, with 63.45% AT and 36.55% GC. Approximately 23.95% of the scallop genome consisted of repetitive elements, of which tandem repeats sequences amounted to 14.92% and interspersed repeats amounted to 9.03% of the scallop genome. A total of 8,550 simple sequence repeats （SSR） were detected from 5,473 BESs. AT-rich SSR motifs, especially poly （A/T） and poly （AT/TA）, were the most abundant tandem repeats units. LTR/Gypsy and LINE/CR1 were the main retrotransposons elements, accounted for 1.87% and 1.22% of the genome respectively. After annotation with Nr, Nt and EST database, 1,610 protein-coding sequences were recognized from 4,006 BESs. These BESs were identified as a major genome resource for scallop and mollusc genomic research.

关键词： Chlamys farreri BAC end sequence repeat sequences gene annotation genome survey

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