title: Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae.
abstract: Sciadopitys verticillata is an evergreen conifer and an economically valuable tree used in construction, which is the only member of the family Sciadopityaceae. Acquisition of the S. verticillata chloroplast (cp) genome will be useful for understanding the evolutionary mechanism of conifers and phylogenetic relationships among gymnosperm. In this study, we have first reported the complete chloroplast genome of S. verticillata. The total genome is 138,284 bp in length, consisting of 118 unique genes. The S. verticillata cp genome has lost one copy of the canonical inverted repeats and shown distinctive genomic structure comparing with other cupressophytes. Fifty-three simple sequence repeat loci and 18 forward tandem repeats were identified in the S. verticillata cp genome. According to the rearrangement of cupressophyte cp genome, we proposed one mechanism for the formation of inverted repeat: tandem repeat occured first, then rearrangement divided the tandem repeat into inverted repeats located at different regions. Phylogenetic estimates inferred from 59-gene sequences and cpDNA organizations have both shown that S. verticillata was sister to the clade consisting of Cupressaceae, Taxaceae, and Cephalotaxaceae. Moreover, accD gene was found to be lost in the S. verticillata cp genome, and a nucleus copy was identified from two transcriptome data.
authors: CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Jia
authors: J
authors: Li
authors: CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
authors: Lei
authors: L
authors: Gao
authors: CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Shanshan
authors: S
authors: Chen
authors: CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.|University of Chinese Academy of Sciences, Beijing, China.
authors: Ke
authors: K
authors: Tao
authors: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.|Institute for Technology Research and Innovation of Sun Yat-sen University, Zhuhai, Guangdong, China.
authors: Yingjuan
authors: Y
authors: Su
authors: CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.|College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, China.
authors: Ting
authors: T
authors: Wang
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D005075:Biological Evolution; D002467:Cell Nucleus / Q000235:genetics; D002736:Chloroplasts / Q000235:genetics; D029779:Cupressaceae / Q000145:classification / Q000235:genetics*; D017343:Genes, Plant; D059646:Genome Size; D054628:Genome, Chloroplast; D055029:Inverted Repeat Sequences; D010802:Phylogeny; D059828:Plant Cells / Q000378:metabolism; D016415:Sequence Alignment; D059467:Transcriptome