Shaanxi Engineering Research Center for Conservation and Utilization of Botanical Resources

Xi’an, China

Shaanxi Engineering Research Center for Conservation and Utilization of Botanical Resources

Xi’an, China
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Zhou T.,Northwest University, China | Yang Y.,Northwest University, China | Hu Y.,Northwest University, China | Zhang X.,Northwest University, China | And 3 more authors.
Conservation Genetics Resources | Year: 2017

Lepidium meyenii (Maca), is an important medical plant, only located in a rather restricted ecological zone in the Andes at a high altitude. Here, the complete chloroplast (cp) genome of L. meyenii (Brassicaceae) was assembled based on the Illumina sequencing reads. The complete cp genome of L. meyenii was 154,624 bp in length and contained two short inverted repeat (IRa and IRb) regions (26,330 bp) which were separated by a small single copy (SSC) region (17,963 bp) and a large single copy (LSC) region (83,998 bp). The L. meyenii chloroplast encoded 130 genes including 85 protein-coding genes (80 PCG species), 37 tRNAs (30 tRNA species), eight rRNA operons (four rRNA species). The overall GC content of L. meyenii chloroplast genome is 36.4% and the corresponding values in LSC, SSC and IR regions are 34.2%, 29.3% and 42.4%, respectively. The maximum likelihood (ML) phylogenetic analysis based on 18 chloroplast genomes demonstrated a close phylogenetic relationship between L. meyenii and L. virginicum. © 2017, Springer Science+Business Media Dordrecht.


Zhou T.,Northwest University, China | Chen C.,Northwest University, China | Wei Y.,Northwest University, China | Chang Y.,Northwest University, China | And 5 more authors.
Frontiers in Plant Science | Year: 2016

Dipteronia (order Sapindales) is an endangered genus endemic to China and has two living species, D.sinensis and D. dyeriana. The plants are closely related to the genus Acer, which is also classified in the order Sapindales. Evolutionary studies on Dipteronia have been hindered by the paucity of information on their genomes and plastids. Here, we used next generation sequencing to characterize the transcriptomes and complete chloroplast genomes of both Dipteronia species. A comparison of the transcriptomes of both species identified a total of 7814 orthologs. Estimation of selection pressures using Ka/Ks ratios showed that only 30 of 5435 orthologous pairs had a ratio significantly >1, i.e., showing positive selection. However, 4041 orthologs had a Ka/Ks < 0.5 (p < 0.05), suggesting that most genes had likely undergone purifying selection. Based on orthologous unigenes, 314 single copy nuclear genes (SCNGs) were identified. Through a combination of de novo and reference guided assembly, plastid genomes were obtained; that of D. sinensis was 157,080 bp and that of D. dyeriana was 157,071 bp. Both plastid genomes encoded 87 protein coding genes, 40 tRNAs, and 8 rRNAs; no significant differences were detected in the size, gene content, and organization of the two plastomes. We used the whole chloroplast genomes to determine the phylogeny of D. sinensis and D. dyeriana and confirmed that the two species were highly divergent. Overall, our study provides comprehensive transcriptomic and chloroplast genomic resources, which will be valuable for future evolutionary studies of Dipteronia. © 2016 Zhou, Chen, Wei, Chang, Bai, Li, Kanwal and Zhao.


Bai G.-Q.,Shaanxi Engineering Research Center for Conservation and Utilization of Botanical Resources | Bai G.-Q.,Northwest University, China | Zhou T.,Northwest University, China | Zhao J.-X.,Northwest University, China | And 3 more authors.
Mitochondrial DNA | Year: 2015

The complete chloroplast genome of Kolkwitzia amabilis (Caprifoliaceae) is first presented in the current study. The cp genome of K. amabilis was 156 875 bp in length and composed of two short inverted repeat (IRa and IRb) regions of 23 946 bp which were separated by a small single copy (SSC) region of 18 846 bp and a large single copy (LSC) region of 90 137 bp. The genome encoded 130 genes contained 81 coding genes, 39 tRNA genes, and 8 rRNA genes. The overall AT content of K. amabilis is 61.6% and the corresponding values of the SSC, LSC and IR regions are 66.8%, 64.1%, and 57.3%, respectively. The phylogenetic analysis based on the maximum parsimony tree revealed that K. amabilis was closely related to Lonicera japonica. © 2015 Taylor & Francis

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