黄丹木姜子叶绿体基因组特征分析

Characteristics of chloroplast genome of Litsea elongata(Wall.ex Nees)Benth.et Hook.f.

【目的】分析黄丹木姜子(Litsea elongata)叶绿体基因组特征,为木姜子属物种鉴定、遗传多样性分析和资源保护提供理论参考。【方法】基于Illumina HiSeq 2000高通量测序平台对黄丹木姜子叶绿体基因组进行测序,利用GeSeq在线工具对叶绿体基因组进行注释,并利用REPuter、MISA、CodonW和IQ-TREE等生物信息学软件对其基因组结构、基因数目、序列重复、密码子使用偏性和系统发育进行分析。【结果】黄丹木姜子叶绿体基因组全长为154028 bp,具有典型的四分结构,编码126个基因,其中蛋白编码基因82个,rRNA基因8个,tRNA基因36个。叶绿体基因组的注释基因中,有9个基因含1个内含子,有3个基因含有2个内含子,其余基因均不含内含子;44个基因编码蛋白参与光合作用信号途径,21个基因编码蛋白构成了核糖体大小亚基。黄丹木姜子叶绿体基因组含有32对长序列重复和90个SSR位点,其中,正向重复和回文重复最多,均为12对,反向重复和互补重复分别为6和2对;95.56%的SSR位点位于单拷贝区[大单拷贝区(LSC)和小单拷贝区(SSC)],仅4.44%的SSR位点位于反向重复区(IR)。黄丹木姜子叶绿体蛋白编码基因GC含量为39.14%,GC3s为27.95%,平均有效密码子数(ENC)为49.04,说明其密码子偏性弱;相对同义密码子使用度(RSCU)大于1.00的密码子31个,其中13个以A结尾,16个以U(T)结尾。系统发育进化树分析结果显示,木姜子属的14个物种聚为两组,其中黄丹木姜子和10种木姜子属植物聚在一个组,与日本木姜子的亲缘关系最近。【结论】黄丹木姜子叶绿体基因组结构保守,偏好A或U(T)结尾的密码子,鉴定的SSR位点可用于物种鉴定和群体遗传学研究。

【Objective】Research of Litsea elongata(Wall.ex Nees)Benth.et Hook.f.chloroplast genome possessed essential theoretical and practical significance for species identification,analysis of genetic diversity,and resource protection of Litsea.【Method】The chloroplast genome of L.elongata was sequenced and annotated based on Illumina HiSeq 2000 high-throughput sequencing platform.The chloroplast genome was annotated using GeSeq.The genome structure,gene number,repeats,codon usage bias,phylogenetic development were analyzed by using the bioinformatics softwares such as REPuter,MISA,codonW and IQ-TREE.【Result】The size of chloroplast genome of L.elongata was 154028 bp,with a typical quadripartite structure.The genome contained 126 genes,including 82 protein coding genes,8 rRNA genes,and 36 tRNA genes.Among the annotated genes of chloroplast genome,nine genes contained one intron,three genes contained two introns.None of the remaining genes contained introns.Forty-four proteins were involved in the photosynthetic signal pathway,and 21 proteins constituted large/small subunit ribosome.The chloroplast genome of L.elongata contained 32 long repeats,and 90 simple sequence repeats(SSR).Among them,the forward repeats(12)and palindrome repeats(12)were the most,followed by the reverse repeats(6)and complementary repeats(2).95.56%of the SSR loci were located in the single copy regions[large single copy region(LSC)and small single copy region(SSC)],and only 4.44%of SSR loci were located in the reverse repeat regions(IR).The guanine and cytosine(GC)content and synonymous third codons positions(GC3s)of chloroplast protein coding genes of L.elongata were 39.14%and 27.95%,respectively.And the average effective codon number(ENC)was 49.04,indicating that the codon bias of the chloroplast genome was weak.There were 31 codons with relative synonymous codon usage(RSCU)was greater than 1.00,of which 13 ended with A and 16 ended with U(T).Phylogenetic analysis showed that 14 Litseas pecies were clustered into two clades,and L.elongata gathered together with other ten Litsea species and shared the closest genetic relationship with L.japonica.【Conclusion】The chloroplast genome structure of L.elongata is conservative and prefers codons ending in A or U(T).The identified SSR loci can be used for species identification and population genetics.