@Article{phyton.2020.011211,
AUTHOR = {Yingting Zhang, Junjie Yang, Zhenhao Guo, Jiaxing Mo, Jiebing Cui, Hailiang Hu, Jin Xu},
TITLE = {Comparative Analyses and Phylogenetic Relationships between <i>Cryptomeria fortunei</i> and Related Species Based on Complete Chloroplast Genomes},
JOURNAL = {Phyton-International Journal of Experimental Botany},
VOLUME = {89},
YEAR = {2020},
NUMBER = {4},
PAGES = {957--986},
URL = {http://www.techscience.com/phyton/v89n4/40529},
ISSN = {1851-5657},
ABSTRACT = {<i>Cryptomeria fortunei</i> (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 <i>C. fortunei</i> was sequenced and evaluated via
comparative analyses with those of related species (formerly the Taxodiaceae)
in Cupressaceae. The <i>C. fortunei</i> 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 <i>C. fortunei</i> cp genome. Comparative analyses of 10 cp genomes
revealed that substantial rearrangements occurred in the gene organization. Additionally, 6 cp hotspot regions (<i>trnS-GGA</i>, <i>ycf1</i>, trnP-GGG</i>, <i>trnC-GCA</i>, <i>psbZ</i> and
<i>accD</i>) were identified, and 4 genes (<i>petL</i>, <i>psbM</i>, <i>rpl22</i> and <i>psaM</i>) had likely
underwent positive selection. Phylogenetic analysis showed that Cupressaceae,
Taxaceae and Cephalotaxaceae clustered to form a clade and that <i>C. fortunei</i>
was most closely related to <i>C. japonica</i> (Japanese cedar), <i>C. japonica</i> cv. Wogon
Hort and <i>Taxodium distichum</i> (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.},
DOI = {10.32604/phyton.2020.011211}
}