In-silico identification of simple sequence repeat (SSR) markers and phylogenetic analysis from chloroplast genomes of the genus Bambusa

IF 1 Q4 GENETICS & HEREDITY Gene Reports Pub Date : 2024-09-28 DOI:10.1016/j.genrep.2024.102048

Swati Pandey, Atul Bhargava

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Abstract

Microsatellites or simple sequence repeats (SSRs), are short DNA sequences composed of repetitive units typically 1 to 6 base pairs long. These highly variable sequences are found in both protein-coding and noncoding DNA regions and exhibit a high degree of polymorphism. In the present study, chloroplast genomes of five species of Bambusa viz. B. bambos, B. multiplex, B. teres, B. vulgaris, and B. tulda, along with three outgroup species viz. Sorghum timorense, Hordeum vulgare, and Triticum aestivum were retrieved from NCBI in FASTA and GenBank formats and screened for chloroplast SSRs (cpSSRs) using MISA Perl script. The sequence analysis of the chloroplast genomes of different species of Bambusa confirmed the presence of 144 cpSSRs. The number of cpSSRs varied among the five bamboo species, with B. vulgaris exhibiting the highest count (31) and B. multiplex showing the lowest (27). Tetranucleotides were the most observed repeats in Bambusa, followed by mono-, di- and trinucleotides. Of the 144 SSR markers identified, only 16 (11.11 %) were suitable for primer design since the remaining sequences failed to produce acceptable primer pairs. An unweighted pair-group method with an arithmetic mean (UPGMA) dendrogram was constructed to analyze the genetic relationships among the genotypes. This analysis revealed three distinct clusters among the genotypes. SSR markers were found to be informative in differentiating the species of Bambusa and were likely to find potential applications in genetic fingerprinting, population genetics, conservation, and phylogenetics.

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簕杜鹃属叶绿体基因组中简单序列重复（SSR）标记的内部鉴定和系统发育分析

微卫星或简单序列重复序列（SSR）是由重复单元组成的短 DNA 序列，长度一般为 1 到 6 个碱基对。这些高度可变的序列存在于蛋白质编码和非编码 DNA 区域，并表现出高度的多态性。本研究以 FASTA 和 GenBank 格式从 NCBI 检索了五个簕杜鹃物种（B. bambos、B. multiplex、B. teres、B. vulgaris 和 B. tulda）以及三个外群物种（Sorghum timorense、Hordeum vulgare 和 Triticum aestivum）的叶绿体基因组，并使用 MISA Perl 脚本筛选了叶绿体 SSR（cpSSR）。对不同种类簕杜鹃叶绿体基因组的序列分析证实了 144 个 cpSSR 的存在。五种竹子的 cpSSR 数量各不相同，其中粗竹子的 cpSSR 数量最多（31 个），多节竹子的 cpSSR 数量最少（27 个）。在簕竹中观察到最多的重复序列是四核苷酸，其次是单核苷酸、二核苷酸和三核苷酸。在鉴定出的 144 个 SSR 标记中，只有 16 个（11.11%）适合设计引物，因为其余序列未能产生可接受的引物对。为分析基因型之间的遗传关系，构建了一个算术平均的非加权成对分组法（UPGMA）树枝图。该分析表明基因型之间存在三个不同的聚类。研究发现，SSR 标记在区分簕杜鹃物种方面具有参考价值，有望在遗传指纹学、种群遗传学、物种保护和系统发育学中得到应用。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.