Version 1
: Received: 25 October 2018 / Approved: 26 October 2018 / Online: 26 October 2018 (15:40:04 CEST)
How to cite:
Wang, L.; Wang, J.; He, C.; Zhang, J.; Zeng, Y. Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae). Preprints2018, 2018100638. https://doi.org/10.20944/preprints201810.0638.v1
Wang, L.; Wang, J.; He, C.; Zhang, J.; Zeng, Y. Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae). Preprints 2018, 2018100638. https://doi.org/10.20944/preprints201810.0638.v1
Wang, L.; Wang, J.; He, C.; Zhang, J.; Zeng, Y. Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae). Preprints2018, 2018100638. https://doi.org/10.20944/preprints201810.0638.v1
APA Style
Wang, L., Wang, J., He, C., Zhang, J., & Zeng, Y. (2018). Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus <em>Hippophae</em> (Elaeagnaceae). Preprints. https://doi.org/10.20944/preprints201810.0638.v1
Chicago/Turabian Style
Wang, L., Jianguo Zhang and Yanfei Zeng. 2018 "Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus <em>Hippophae</em> (Elaeagnaceae)" Preprints. https://doi.org/10.20944/preprints201810.0638.v1
Abstract
Hippophae is a tree species with ecological, economic and social benefits. In this study, we assembled and annotated chloroplast genomes of sympatric Hippophae gyantsensis and H. rhamnoides subsp. yunnanensis. Their full-length are 155260 and 156415 bp, respectively. Each of them has 131 genes, comprising 85 protein-coding genes, 8 ribosomal RNA genes and 38 transfer RNA genes. After comparing the chloroplast genomes, we found 1302 base difference loci, and 63.29% are located in the intergenic region or intron sequences and 36.71% are located in the coding sequences. The SSC region has the highest mutation rate, followed by the LSC region; the IR regions have the lowest mutation rate. Among the protein-coding genes, three had a ratio of nonsynonymous to synonymous substitutions (Ka/Ks) >1 (but P values were non-significant) and 66 had Ka/Ks <1 (46 were significant). In general, the chloroplast protein-coding genes may be subject to purification selection. Among H. gyantsensis and H. rhamnoides subsp. yunnanensis chloroplast protein-coding genes, there are 20 and 16 optimal codons, respectively. Most of the optimal codons were ending with A or U, which indicates significant AT preference. It is an important reference for studies on the general characteristics and evolution of the Hippophae chloroplast genome.
Keywords
Chloroplast genome; H. gyantsensis; H. rhamnoides subsp. yunnanensis; Ka/ks; Optimal codons
Subject
Biology and Life Sciences, Plant Sciences
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.