Tussipkan Dilnur, Shevtsov Vladislav, Ramazanova Malika, Rakhimzhanova Aizhan, Shevtsov Alexandr, Manabayeva Shuga
Plant Genetic Engineering Laboratory, National Center for Biotechnology, Astana, Kazakhstan.
Plant Genomics and Bioinformatics Laboratory, National Center for Biotechnology, Astana, Kazakhstan.
Front Plant Sci. 2024 Nov 12;15:1433253. doi: 10.3389/fpls.2024.1433253. eCollection 2024.
Species of are important ornamental plants used for horticultural purposes in various countries, across Asia, Europe, and North Africa. The present study is the first report on typical features of the complete chloroplast genome sequence of four local and endangered species including , and from Kazakhstan using Illumina sequencing technology. The comparative analyses revealed that the complete genomes of four species were highly conserved in terms of total genome size (152. 006 bp - 152. 382 bp), including a pair of inverted repeat regions (26. 330 bp - 26. 371 bp), separated by a large single copy region (82.169 bp - 82,378 bp) and a small copy region (17.172 bp -17.260 bp). Total GC content (36.58-36.62 %), gene number (131), and intron length (540 bp - 2620 bp) of 28 genes. The complete genomes of four species showed nucleotide diversity (π =0,003257). The total number of SSR loci was 159 in , 158 in , 174 in , and 163 in . The result indicated that ten CDS genes, namely , and , with effective polymorphic simple sequence repeats (SSRs), high sequence variability (SV) ranging from 2.581 to 6.102, and high nucleotide diversity (Pi) of these loci ranging from 0,004 to 0,010. For all intergenic regions longer than 150 bp, twenty one most variable regions were found with high sequence variability (SV) ranging from 4,848 to 11,862 and high nucleotide diversity (Pi) ranging from 0,01599 to 0,01839. Relative synonymous codon usage (RSCU) analysis was used to identify overrepresented and underrepresented codons for each amino acid. Based on the phylogenic analysis, the sequences clustered into four major groups, reflecting distinct evolutionary lineages corresponding to the subgenera , and . Notably, was distinctively grouped with species from and rather than with other species, suggesting a unique evolutionary history potentially shaped by geographical isolation or specific ecological pressures. The complete chloroplast genome of the four Tulipa species provides fundamental information for future research studies, even for designing the high number of available molecular markers.
[此处原文缺失物种名称]属的物种是重要的观赏植物，在亚洲、欧洲和北非的各个国家用于园艺目的。本研究是首次使用Illumina测序技术对来自哈萨克斯坦的包括[此处原文缺失物种名称]、[此处原文缺失物种名称]、[此处原文缺失物种名称]和[此处原文缺失物种名称]在内的四个本地濒危物种的完整叶绿体基因组序列的典型特征进行的报道。比较分析表明，这四个物种的完整基因组在总基因组大小（152,006 bp - 152,382 bp）方面高度保守，包括一对反向重复区域（26,330 bp - 26,371 bp），由一个大单拷贝区域（82,169 bp - 82,378 bp）和一个小单拷贝区域（17,172 bp - 17,260 bp）分隔。28个基因的总GC含量（36.58 - 36.62%）、基因数量（131个）和内含子长度（540 bp - 2,620 bp）。这四个物种的完整基因组显示出核苷酸多样性（π = 0.003257）。SSR位点总数在[此处原文缺失物种名称]中为159个，在[此处原文缺失物种名称]中为158个，在[此处原文缺失物种名称]中为174个，在[此处原文缺失物种名称]中为163个。结果表明，十个CDS基因，即[此处原文缺失基因名称]、[此处原文缺失基因名称]和[此处原文缺失基因名称]，具有有效的多态性简单序列重复（SSR），高序列变异性（SV）范围为2.581至6.102，这些位点的高核苷酸多样性（Pi）范围为0.004至0.010。对于所有长度超过150 bp的基因间隔区，发现了21个最可变区域，其高序列变异性（SV）范围为4.848至11.862，高核苷酸多样性（Pi）范围为0.01599至0.01839。相对同义密码子使用（RSCU）分析用于确定每个氨基酸的过表达和低表达密码子。基于系统发育分析，序列聚类为四个主要组，反映了与亚属[此处原文缺失亚属名称]、[此处原文缺失亚属名称]和[此处原文缺失亚属名称]相对应的不同进化谱系。值得注意的是，[此处原文缺失物种名称]与来自[此处原文缺失属名称]和[此处原文缺失属名称]的物种明显聚类在一起，而不是与其他[此处原文缺失属名称]物种聚类在一起，这表明其独特的进化历史可能是由地理隔离或特定生态压力形成的。这四个郁金香物种的完整叶绿体基因组为未来的研究提供了基础信息，甚至为设计大量可用的分子标记提供了基础信息。
