| 引用本文: | 阎 侃, 周雪琼, 赵润东, 王悠悠, 马哲学, 冉 娟, 孙 超.老虎刺叶绿体基因组解析及其对豆科新分类系统的验证[J].广西植物,2026,(9):1441-1458.[点击复制] |
| YAN Kan, ZHOU Xueqiong, ZHAO Rundong, WANG Youyou,
MA Zhexue, RAN Juan, SUN Chao.Chloroplast genome analysis of Pterolobiumpunctatum and its validation of the new Fabaceae classification system[J].Guihaia,2026,(9):1441-1458.[点击复制] |
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| 老虎刺叶绿体基因组解析及其对豆科新分类系统的验证 |
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阎 侃1*, 周雪琼1, 赵润东1, 王悠悠1, 马哲学1, 冉 娟2, 孙 超3
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1. 兰州交通大学 生物与制药工程学院, 兰州 730070;2. 重庆工贸职业技术学院,
重庆 408000;3. 甘肃农业大学 农学院, 兰州 730070
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| 摘要: |
| 豆科系统分类的最新修订将含羞草亚科并入广义云实亚科,但其可靠性仍需多遗传系统的独立验证。为了阐明云实亚科代表类群老虎刺(Pterolobium punctatum)的叶绿体基因组特征及其系统发育位置,该研究利用Illumina测序技术组装并注释了老虎刺叶绿体基因组,分析了其密码子偏好性; 同时,联合19个近缘物种进行比较基因组学研究,并整合云实亚科代表物种的基因组数据进行系统发育重建及分化时间估算。结果表明:(1)老虎刺叶绿体基因组全长159 063 bp,编码128个基因,呈现典型的环状四分体结构,反向重复(IR)区GC含量(42.61%)显著高于单拷贝区。(2)比较基因组学分析显示,老虎刺及其近缘物种IR/SC边界呈现动态演变,以A/T碱基为主导的单核苷酸简单重复序列是最常见的SSR类型。(3)密码子偏好性分析显示,自然选择是主要驱动力,并筛选出 ycf1 等高变区作为潜在DNA条形码。(4)系统发育分析强烈支持老虎刺与阿拉伯金合欢印度亚种(Vachellia nilotica subsp. indica)互为姐妹群,从叶绿体基因组层面为豆科新分类系统提供了关键验证; 分化时间估算表明老虎刺属分化于渐新世-中新世过渡期(约24.09百万年前)。该研究系统解析了老虎刺叶绿体基因组特征,确证了其在广义云实亚科中的系统位置,为理解叶绿体基因组结构进化及云实亚科资源的保护利用提供了重要的科学依据。 |
| 关键词: 老虎刺, 叶绿体基因组, 系统发育, 密码子偏好性, 序列变异 |
| DOI：10.11931/guihaia.gxzw202510009 |
| 分类号:Q949 |
| 文章编号:1000-3142(2026)09-1441-18 |
| 基金项目:干旱生境作物学国家重点实验室开放基金项目(GSCS-2024-08); 甘肃省高等教育教学改革研究项目(GJJGB140); 兰州交通大学实验教学研究与改革项目(2025008); 兰州市人才创新创业项目(2017-RC-39); 甘肃农业大学伏羲人才资助项目(Gaufx-05Y03)。 |
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| Chloroplast genome analysis of Pterolobiumpunctatum and its validation of the new Fabaceae classification system |
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YAN Kan1*, ZHOU Xueqiong1, ZHAO Rundong1, WANG Youyou1,
MA Zhexue1, RAN Juan2, SUN Chao3
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1. School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;2. Chongqing
Vocational and Technical College of Industry and Trade, Chongqing 408000, China;3. College
of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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| Abstract: |
| The recent revision of the Fabaceae classification system merged the Mimosoideae into a broadly defined Caesalpinioideae, but its reliability still requires independent validation across multiple genetic systems. To clarify the chloroplast genome characteristics and phylogenetic position of Pterolobium punctatum, a representative species within the Caesalpinioideae, the complete chloroplast genome of P. punctatum was assembled and annotated using Illumina sequencing technology. This study analyzed codon usage bias and performed comparative genomics with 19 related species. Furthermore, phylogenetic reconstruction and divergence time estimation were conducted by integrating genomic data from representative species of Caesalpinioideae. The results were as follows:(1)The chloroplast genome of P. punctatum was 159 063 bp in length, encoding 128 genes, and exhibited a typical circular quadripartite structure, with significantly higher GC content in the inverted repeat(IR)regions(42.61%)than in the single-copy regions.(2)Comparative genomic analysis revealed dynamic evolution at the IR/SC boundaries among P. punctatum and its close relatives, and mono-nucleotide repeats dominated by A/T bases were the most frequent SSR type.(3)Analysis of codon usage bias indicated that natural selection was the primary driving force, and we identified highly variable regions such as ycf1 as potential DNA barcodes.(4)Phylogenetic analysis strongly supported P. punctatum as a sister group to Vachellia nilotica subsp. indica, providing critical chloroplast genomic validation for the new classification system of Fabaceae; divergence time estimation suggested that the genus Pterolobium diverged during the Oligocene-Miocene transition(approx. 24.09 million years ago). This study systematically elucidates the chloroplast genome characteristics of P. punctatum and confirms its phylogenetic position, providing a significant scientific basis for understanding the structural evolution of the chloroplast genome as well as for the conservation and utilization of Caesalpinioideae resources. |
| Key words: Pterolobium punctatum, chloroplast genome, phylogeny, codon usage bias, sequence variation |
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