朱蕉叶绿体基因组特征与系统发育分析  

Genomic Characteristics and Phylogenetic Analysis of Chloroplast of Cordyline fruticosa

作　　者：李卫英 辛静[1,2] 赵文植 董章宏 马路遥 夏茂甜 高洁[3] 辛培尧[1,2] LI Weiying;XIN Jing;ZHAO Wenzhi;DONG Zhanghong;MA Luyao;XIA Maotian;GAO Jie;XIN Peiyao(Southwest Research Center for Engineering Technology of Landscape Architecture(National Forestry and Grassland Administra-tion),Southwest Forestry University,Kunming,Yunnan 650224,China;Key Laboratory of National Forestry and Grassland Ad-ministration on Biodiversity Conservation in Southwest China,Southwest Forestry University,Kunming,Yunnan 650224,China;Center for Integrative Conservation,Xishuangbanna Tropical Botanical Garden,Chinese Academy of Sciences,Mengla,Yunnan 666303,China)

机构地区：[1]西南林业大学国家林业和草原局西南风景园林工程技术研究中心,云南昆明650224 [2]西南林业大学西南地区生物多样性保育国家林业和草原局重点实验室,云南昆明650224 [3]中国科学院西双版纳热带植物园综合保护中心,云南勐腊666303

出　　处：《热带作物学报》2022年第4期653-665,共13页Chinese Journal of Tropical Crops

基　　金：西南林业大学科技创新基金项目(No.KY21035);云南省科技人才与平台计划项目(No.202205AF15002)。

摘　　要：朱蕉(Cordyline fruticosa)是一种常见的园艺植物,广泛分布于亚洲、大洋洲、南美洲等热带地区。为了明确朱蕉叶绿体基因组特征,了解其系统发育地位,利用Illumina测序技术对其叶绿体基因组测序后,进行中线性绘图、ENC-plot、PR2-plot和SSR位点等相关数据的挖掘和分析。结果表明:朱蕉叶绿体基因组全长154488 bp,GC含量为38%,其中大单拷贝区长85279 bp,GC含量为36.1%,小单拷贝区长20325 bp,GC含量为32.6%;双向重复区分别长24442 bp,GC含量分别为43.4%。注释得到131种基因,其中unigenes的有111种,包括了78种蛋白编码基因,rRNA基因4种和tRNA基因29种。以朱蕉与龙舌兰科中19种植物的叶绿体基因组构建系统发育树,结果显示朱蕉与蓝朱蕉(Cordyline indivisa)的亲缘关系最近。朱蕉叶绿体基因组GC_(3)、GC_(1)与GC_(2)的碱基含量分别为29.47%、46.45%和39.14%,GC_(3)的碱基含量低于GC_(1)和GC_(2),说明密码子末尾偏好以A、U结尾;ENC的取值范围为35.48~59.44,表明朱蕉密码子偏好性较弱;ENC-plot分析可知ENC频数比值在-0.05~0.05之间的有20个,表明密码子偏好性主要受自然选择压力的影响;PR2-plot分析中,T>A,G>C,说明朱蕉叶绿体基因组受多种因素的影响;以RSCU值和ENC值作为参考,确定17个密码子为最优密码子。在检测到的91个SSR位点中五核苷酸最少(3个),单核苷酸最多(55个),SSR位点中以A、T(A/T、AT/AT和AAAT/ATTT)为重复单元的占76.92%。说明朱蕉叶绿体基因组SSR位点多以A、T重复单元为主。研究结果可为朱蕉乃至朱蕉属植物分类及系统进化提供理论依据。Cordyline fruticosa is an common horticultural plant, widely distributed in tropical Asia, Oceania and South America. In order to clarify the characteristics of the chloroplast genome of C. fruticosa and understand its phylogenetic status, the chloroplast genome was sequenced by Illumina sequencing technology, and the relevant data of middle linear plot, ENC-plot, PR2-plot and SSR loci were mined and analyzed. The total length of the complete chloroplast genome was 154 488 bp, and the GC content was 38%. The length of large single copy area was 85 279 bp and the GC content was 36.1%. The small single copy area was 20 325 bp, and the GC content was 32.6%. And bidirectional repetition zones were 24 442 bp, respectively, and the GC content was 43.4%. 131 genes were annotated, including 111 unigenes genes, including 78 protein-coding genes, 4 rRNA genes and 29 tRNA genes. Phylogenetic tree was constructed using the chloroplast genomes of 19 plant species in C. fruticosa and Agavaceae family. C. fruticosa was most closely related to C. indivisa. The content of GC_(3) in the chloroplast genome of C. fruticosa was 29.47%, GC_(1) and GC_(2) were 46.45%,39.14%, respectively. The base content of GC_(3) was lower than that of GC_(1) and GC_(2), indicating that codon ends preferred to end with A and U. The ENC values ranged from 35.48 to 59.44, indicating that the codon bias was weak. ENC-plot analysis showed that there were 20 ENC frequency ratios between–0.05 to 0.05, indicating that codon preference was mainly affected by natural selection pressure. PR2-plot analysis revealed T>A, G>C, indicating that the chloroplast genome of C. fruticosa was affected by many factors. Codon preference is mainly influenced by selection. Using RSCU and ENC values as references, 17 codons were determined as optimal codons in the chloroplast genome of C. fruticosa.Among the 91 SSR loci detected, there were 3 pentanucleotides and 55 single nucleotides. 76.92% of the SSR loci took A, T(A/T, AT/AT and AAAT/ATTT) as repeat units. It showed tha

关 键 词：朱蕉 叶绿体基因组 系统发育 密码子 

分 类 号：S687.9[农业科学—观赏园艺]