| 青藏高原4种葱属叶绿体基因组比较及系统发育分析 |
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| 引用本文：蔡相楠，王宏霞.青藏高原4种葱属叶绿体基因组比较及系统发育分析[J].西北农业学报,2026,(3):457~465 |
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| 基金项目:青海省昆仑英才“中青年科技人才”托举项目 (2024QHSKXRCTJ05)。 |
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| 中文摘要:为探究青藏高原4种葱属植物叶绿体基因组特征及其系统发育关系，以镰叶韭（Allium carolinianu）、细叶韭（A.tenuissimum）、唐古韭（A.tanguticum）和碱韭（A.polyrhizum）为材料，利用Illumina NovaSeq 6000 平台对其进行高通量测序，并利用生物信息学工具对基因组进行序列特征、密码子偏性及系统发育分析。结果表明，4种葱属植物叶绿体基因组长度为152 916~153 766 bp，各基因组均编码132个基因，GC含量为36.71%~36.85%；镰叶韭、细叶韭和碱韭叶绿体高频密码子有30个，唐古韭有32个，密码子偏好以A/U结尾；共检测到SSRs位点83~97个，其中单碱基位点最多，镰叶韭和唐古韭各有1个六碱基位点；4种葱属叶绿体基因组的LSC和SSC区变异性较高，共发现9个高频变异区，其中rpl32-trnL(pi值0.061 )区段变异最高，可作为DNA条形码；系统发育分析表明，细叶韭、碱韭和山韭（Allium senescens）聚为一小支，唐古韭、镰叶韭、西川韭（A xichuanense）、野葱（Allium chrysanthum）、折被韭（Achrysocephalum）、洋葱（A.cepa） 和阿尔泰葱（A.altaicum）亲缘关系较近。 |
| 中文关键词:葱属 叶绿体基因组 序列特征 密码子偏性 系统发育分析 |
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| Comparative Genomics and Phylogenetic Analysis of Four Allium Species from Qinghai-Tibet Plateau Based on Chloroplast Genomes |
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| Abstract:To investigate the chloroplast genome characteristics and phylogenetic relationships of four Allium species from the Qinghai-Tibet Plateau, high-throughput Illumina NovaSeq 6000 reads were sequenced for A.carolinianum, A.tenuissimum, A.tanguticum,and A.polyrhizum.Comprehensive bioinformatic analyses were subsequently conducted to explore sequence features, codon usage bias, and phylogenetic relationships.The chloroplast genomes of the four Alliumspecies ranged from 152 916 to 153 766 bp, each encoding 132 genes with a GC content of 36.71%-36.85%.Thirty high-frequency codons were identified in A.carolinianum, A.tenuissimum, and A.polyrhizum, while A.tanguticum exhibited 32.All four species displayed a pronounced A/U bias at the third codon position.A total of 83-97 SSR loci were detected, with mononucleotide motifs predominant.Both A.carolinianum and A.tanguticum harbored a single hexanucleotide SSR locus.Comparative analyses revealed elevated divergence within the LSC and SSC regions, yielding nine hypervariable loci, among which rpl32-trnL (pi=0.061) exhibited the highest variability and was proposed as a candidate DNA barcode.Phylogenetic analysis indicated that A.tenuissimum, A.polyrhizum, and A.senescens formed a small clade, while A.tanguticum, A.carolinianum, A.xichuanense, A.chrysanthum, A.chrysocephalum, A.cepa and A.altaicum constituted a separate, closely related lineage. |
| keywords:Allium Chloroplast genome Sequence characteristics Codon usage bias Phylogenetic analysis |
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