小檗属植物叶绿体基因组序列结构及系统发育分析

Chloroplast genome sequences and phylogenetic analysis of Berberis genus

目的了解小檗属植物叶绿体基因组成及结构特征,为小檗属的系统发育及基因组进化研究提供参考。方法获取小檗属9个物种的叶绿体基因组,利用生物信息学方法比较叶绿体基因组间的结构特征与变异程度,并以小檗科的桃儿七属3个物种的叶绿体基因组为外类群分析了小檗属的系统发育关系。结果小檗属9个种的叶绿体基因组均为双链环形结构,均包含1个大单拷贝区(large single-copy,LSC)、1个小单拷贝区(small single-copy,SSC)以及2个反向重复区(IRa和IRb)。叶绿体基因组大小差异较小,最大差异为1984 bp。基因排列顺序基本一致,各基因数量相对保守,其中核糖体RNA(rRNA)数量最为保守,均为8个。此外,小檗属叶绿体基因组在序列长度、基因组成以及GC含量等方面相对保守,但4个边界存在明显的多样性。小檗属叶绿体基因组中非基因编码区存在较大差异,变异程度较高,而基因编码区差异较小,具有较高的保守性。在叶绿体基因组4个部分中,SSC区的变异程度最高,IRa区的变异程度最低。小檗属叶绿体基因组中包括rps12、rps16、rpl2、rpl16、rpo C1、pet B、pet D、ndh B、ndh A、atp F、clp P和ycf312个含内含子的蛋白编码基因。大部分基因的编码区长度较为保守,但在内含子长度或编码区长度均存在少量改变。十大功劳组Berberis amurensis是最先从小檗属中分离出来,是小檗属的原始组。在十大功劳组中阿里山十大功劳B.oiwakensis和安坪十大功劳B.ganpinensis与其他小檗属物种存在较远的亲缘关系。而其余小檗属物种可分为2支,威宁小檗B.weiningensis为1支;黄芦木B.amurensis和朝鲜小檗B.koreana为1支。结论小檗属叶绿体基因组具有较高的保守性,其基因排列顺序基本一致,未检测到大规模的倒位或基因重排,但其IR区与单拷贝区(single-copy,SC)边界存在明显的多样性。基于叶绿体基因组构建的系统发育树在一定程度上可以揭示小檗属物种的系统发育关系。

Objective To understand the chloroplast gene composition and structural characteristics of Berberis,so as to provide reference for the phylogeny and genome evolution of Berberis.Methods The chloroplast genomes of nine species of Berberis were obtained.The structural characteristics and variation degree of chloroplast genomes were compared by bioinformatics methods.The phylogenetic relationship of Berberis was analyzed by taking the chloroplast genomes of three species of Sinopodophyllum as an outgroup.Results The chloroplast genomes of nine species of Berberis had a double stranded ring structure,including a long single copy region(LSC),a short single copy region(SSC)and two reverse repeats(IRa and IRb).The difference of chloroplast genome size was small,and the maximum difference was 1984 bp.The sequence of genes was basically the same,and the number of genes was relatively conservative,among which the number of ribosomal RNA(rRNA)was the most conservative,with eight genes each.In addition,the chloroplast genome of Berberis was relatively conservative in sequence length,gene composition and GC content,but there was obvious diversity in the four boundaries.The non gene coding regions in the chloroplast genome of Berberis had great differences and high degree of variation,while the gene coding regions had small differences and high conservatism.Among the four parts of chloroplast genome,the variation degree of SSC region was the highest and that of IRA region was the lowest.The chloroplast genome of Berberis included 12 protein coding genes containing intron such as rps12,rps16,rpl2,rpl16,rpoC1,petB,petD,ndhB,ndhA,atpF,clpP and ycf3.The length of coding region of most genes was conservative,but there were a few changes in intron length or coding region length.B.amurensis group was the first isolated from Berberis,which was the original group of Berberis.In the B.amurensis formation,B.oiwakensis and B.ganpinensis were far related to other Berberis species.The other species of Berberis can be divided into two branches,and B.weiningensis was one branch;B.amurensis and B.koreana were one branch.Conclusion The chloroplast genome of Berberis is highly conservative,and its gene sequence is basically the same.No large-scale inversion or gene rearrangement is detected,but there is obvious diversity at the boundary between IR region and single copy region(SC).The phylogenetic tree based on chloroplast genome can reveal the phylogenetic relationship of Berberis species to a certain extent.