红花龙胆叶绿体基因组特征及适应性进化分析

Characteristics and adaptive evolution analysis of the chloroplast genome of Gentiana rhodantha

红花龙胆(Gentiana rhodantha)为特色苗族药材,在治疗湿热黄疸、小便不利、肺热咳嗽等方面具有显著疗效,但在物种进化关系及分类鉴定方面存在争议。本研究对红花龙胆叶绿体基因组进行了二代、三代测序,并分析其结构特点及适应性进化分析。结果表明,红花龙胆叶绿体基因组全长148844 bp,大单拷贝区(LSC)80076 bp、小单拷贝区(SSC)17596 bp和反向重复区(IR)25586 bp,GC含量37.75%。共注释到124个基因,包括80个蛋白编码基因(CDS)、36个tRNA基因和8个rRNA基因;红花龙胆叶绿体基因组密码子偏好性较弱,影响因素主要是自然选择,最优密码子为CUU、UCU、UCA、CCA、ACU;MISA共发现169个SSR,其中单核苷酸重复最多(114个,67.50%),其次是二核苷酸重复(43个,25.44%);与同组及同属其他物种相比,红花龙胆叶绿体基因的Ka/Ks值基本小于1,表明在长期的进化过程中受到了较强的纯化选择,存在进化事件的光合作用基因psaI和表达相关基因rpl22、rps11出现组间差异,且系统发育分析结果支持红花龙胆与龙胆属狭蕊组聚为一支,并与其他组能够明显区别开,支持了狭蕊组独立成属的观点。本研究将为今后开展红花龙胆叶绿体基因工程、分子育种等研究提供参考依据。

Gentiana rhodantha is a characteristic medicinal material of Miao Ethnomedicine.It has significant curative effect in the treatment of acute jaundice hepatitis,dysentery,pediatric pneumonia and bronchitis,etc.However,the evolutionary relationship and taxonomic identification of G.rhodantha are controversial.In this study,we sequenced the chloroplast genome of G.rhodantha using the second and third generation sequencing technology.Then,the structural characteristics and suitability evolution characteristics were analyzed.The results showed that the G.rhodantha chloroplast genome was 148844 bp in length with 37.75%GC content,consisting of a large single copy region(LSC)of 80076 bp,a small single copy region(SSC)of 17596 bp and an inverted repeat region(IR)of 25586 bp.A total of 124 genes were annotated,including 80 protein-coding genes,36 tRNA genes,and 8 rRNA genes;the chloroplast genome of G.rhodantha has a weak codon preference,and the influencing factors are mainly natural selection.The optimal codons are CUU,UCU,UCA,CCA,and ACU.A total of 169SSRs were found in MISA,of which the single nucleotide repeats were the most(114,67.50%),followed by dinucleotide repeats(43,25.44%).The phylogenetic analysis support that G.rhodantha belong to Sect.Stenogyne which can be clearly distinguished from other groups.Compared with other species,the Ka/Ks value of chloroplast genes of G.rhodantha is basically less than 1 except for psaI,rpl22 and rps11,indicating that they have been subjected to strong purification selection in the long-term evolutionary process.The photosynthesis gene psaI and the expression-related genes rpl22 and rps11 showed differences between groups,which supported the view that Sect.Stenogyne was an independent genus.This study will provide a reference for future researches on chloroplast genetic engineering and molecular breeding of G.rhodantha.