Mahajan Ritu, Gupta Suruchi, Tanoj Nipunta, Sagar Tania, Kaur Sandeep, Hussain Shajaat, Kapoor Nisha
Plant Molecular Biology Lab, School of Biotechnology, University of Jammu, Jammu, (J&K), 180006, India.
Plant Science and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, (J&K), 180001, India.
Protoplasma. 2025 May;262(3):501-514. doi: 10.1007/s00709-024-02012-2. Epub 2024 Dec 2.
Wild pomegranate is a potent medicinal plant known for its medicinal and nutritional attributes. Despite its healing and curative properties, the genome of this wild species remains elusive, thus limiting our understanding on the genetic processes involved in the biosynthesis of functional molecules. This study presents the annotation of a de novo genome assembly of wild pomegranate, with a genome size of 279.0 Mb. From the assembly, 34.8 GB of the data was retained, encompassing 72,055 scaffolds. A total of 49,178 genes were predicted, with an average of 5.36 exons per gene and a GC content of 49%. About 14,400 genes were annotated in biological, cellular and molecular processes related mostly to carbohydrate metabolism, intracellular signal transduction, mRNA binding and DNA helicase activity. KEGG enrichment analysis revealed maximum number of genes associated with biosynthesis of secondary metabolites mainly phenypropanoid pathway, followed by ribosome and plant hormone signal transduction. From the identified functional genes, 230 genes scaffolds encoded for transcription factors belonging to 25 families with highest recorded for MYB gene family. Study of annotated transposable elements unveiled the existence of long terminal repeats and retrotransposons. Additionally, our investigation involves the comparative analysis and identification of orthologous genes among the genomes of wild and cultivated species of Punica granatum and also across selected five plant species Eucalyptus grandis, Vitis vinifera, Jatropha curcas, Theobroma cacao and Gossypium raimondii, revealing the functional and evolutionary dynamics across species. To the best of our knowledge, this is the first report on the genome assembly, annotation and gene prediction in wild pomegranate. Also, information regarding the terpenoid pathway genes has been unravelled for the first time in the present study. Inclusively, the current study offers thorough details on important aspects of the wild pomegranate genome that would be useful in comprehending its genetics and will facilitate discovery of genes against various biotic and abiotic stresses.
野生石榴是一种具有强大药用价值的植物，以其药用和营养特性而闻名。尽管它具有治疗功效，但其基因组仍然未知，这限制了我们对其功能分子生物合成所涉及的遗传过程的理解。本研究展示了野生石榴从头基因组组装的注释，其基因组大小为279.0 Mb。从组装结果中，保留了34.8 GB的数据，包含72,055个支架。总共预测了49,178个基因，每个基因平均有5.36个外显子，GC含量为49%。大约14,400个基因在主要与碳水化合物代谢、细胞内信号转导、mRNA结合和DNA解旋酶活性相关的生物学、细胞和分子过程中得到注释。KEGG富集分析显示，与次生代谢物生物合成相关的基因数量最多，主要是苯丙烷途径，其次是核糖体和植物激素信号转导。在鉴定出的功能基因中，有230个基因支架编码属于25个家族的转录因子，其中MYB基因家族记录最多。对注释的转座元件的研究揭示了长末端重复序列和逆转座子的存在。此外，我们的研究还涉及石榴野生种和栽培种基因组之间以及与选定的五个植物物种（巨桉、葡萄、麻疯树、可可和雷蒙德氏棉）之间直系同源基因的比较分析和鉴定，揭示了物种间的功能和进化动态。据我们所知，这是关于野生石榴基因组组装、注释和基因预测的第一份报告。此外，本研究首次揭示了萜类途径基因的信息。总体而言，当前研究提供了野生石榴基因组重要方面的详细信息，这将有助于理解其遗传学，并促进针对各种生物和非生物胁迫的基因发现。
