西北农业学报2026，Vol.35Issue(3)：457-465,9.DOI:10.7606/j.issn.1004-1389.2026.03.006
青藏高原4种葱属叶绿体基因组比较及系统发育分析
Comparative Genomics and Phylogenetic Analysis of Four Allium Species from Qinghai-Tibet Plateau Based on Chloroplast Genomes
摘要
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 posi-tion.A total of 83-97 SSR loci were detected,with mononucleotide motifs predominant.Both A.car-olinianum and A.tanguticum harbored a single hexanucleotide SSR locus.Comparative analyses re-vealed 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.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Key words
Allium/Chloroplast genome/Sequence characteristics/Codon usage bias/Phylogenetic analysis引用本文复制引用
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,2026,35(3):457-465,9.基金项目
青海省昆仑英才"中青年科技人才"托举项目(2024QHSKXRCTJ05).Qinghai Province"Kunlun Talents·Science and Technology Leaders"Support Program for Mid-Career and Young Researchers(No.2024QHSKXRCTJ05). （2024QHSKXRCTJ05）
