Open Access
ARTICLE
Comparative Analyses and Phylogenetic Relationships between Cryptomeria fortunei and Related Species Based on Complete Chloroplast Genomes
Yingting Zhang1,2,3, Junjie Yang1,2,3, Zhenhao Guo1,2,3, Jiaxing Mo1,2,3, Jiebing Cui1,2,3, Hailiang Hu1,2,3, Jin Xu1,2,3,*
1 Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China
2 Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
3 College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
* Corresponding Author: Jin Xu. Email:
Phyton-International Journal of Experimental Botany 2020, 89(4), 957-986. https://doi.org/10.32604/phyton.2020.011211
Received 27 April 2020; Accepted 22 June 2020; Issue published 09 November 2020
Abstract
Cryptomeria fortunei (Chinese cedar) is a highly adaptable woody species and one of the main forest plantation trees in subtropical high-altitude areas in
China. However, there are few studies on its chloroplast (cp) genome. In this
study, the complete cp genome of
C. fortunei was sequenced and evaluated via
comparative analyses with those of related species (formerly the Taxodiaceae)
in Cupressaceae. The
C. fortunei cp genome was 131,580 bp in length, and the
GC content of the whole genome was 35.38%. It lost one relevant large inverted
repeat and contained 114 unique genes, including 82 protein-coding genes, 28
tRNAs and 4 rRNAs. The relative synonymous codon usage (RSCU) of codons
ending with A/U was more than twice that of codons ending with G/C. Thirty
long repeat structures (LRSs) and 213 simple sequence repeat (SSR) loci were
detected in the
C. fortunei cp genome. Comparative analyses of 10 cp genomes
revealed that substantial rearrangements occurred in the gene organization. Additionally, 6 cp hotspot regions (
trnS-GGA,
ycf1, trnP-GGG,
trnC-GCA,
psbZ and
accD) were identified, and 4 genes (
petL,
psbM,
rpl22 and
psaM) had likely
underwent positive selection. Phylogenetic analysis showed that Cupressaceae,
Taxaceae and Cephalotaxaceae clustered to form a clade and that
C. fortunei
was most closely related to
C. japonica (Japanese cedar),
C. japonica cv. Wogon
Hort and
Taxodium distichum (baldcypress). These results provide references for
future studies of population genetics, phylogenetic status and molecular markers
among Cupressaceae species and for the cultivation of improved varieties.
Keywords
Cite This Article
APA Style
Zhang, Y., Yang, J., Guo, Z., Mo, J., Cui, J. et al. (2020). Comparative analyses and phylogenetic relationships between cryptomeria fortunei and related species based on complete chloroplast genomes. Phyton-International Journal of Experimental Botany, 89(4), 957-986. https://doi.org/10.32604/phyton.2020.011211
Vancouver Style
Zhang Y, Yang J, Guo Z, Mo J, Cui J, Hu H, et al. Comparative analyses and phylogenetic relationships between cryptomeria fortunei and related species based on complete chloroplast genomes. Phyton-Int J Exp Bot. 2020;89(4):957-986 https://doi.org/10.32604/phyton.2020.011211
IEEE Style
Y. Zhang et al., "Comparative Analyses and Phylogenetic Relationships between Cryptomeria fortunei and Related Species Based on Complete Chloroplast Genomes," Phyton-Int. J. Exp. Bot., vol. 89, no. 4, pp. 957-986. 2020. https://doi.org/10.32604/phyton.2020.011211