Table_3_Reference quality genome sequence of Indian pomegranate cv. ‘Bhagawa’ (Punica granatum L.).XLSX

Pomegranate is an important fruit crop for ensuring livelihood and nutrition security in fragile semi-arid regions of the globe having limited irrigation resources. This is a high-value, nutritionally rich, and export-oriented agri-commodity that ensures high returns on investment to growers across the world. Although it is a valuable fruit crop, it has received only a limited genomics research outcome. To fast-track the pomegranate improvement program, de novo whole-genome sequencing of the main Indian cultivar ‘Bhagawa’ was initiated by the Indian Council of Agricultural Research–National Research Center on Pomegranate (ICAR–NRCP). We have demonstrated that a combination of commercially available technologies from Illumina, PacBio, 10X Genomics, and BioNano Genomics could be used efficiently for sequencing and reference-grade de novo assembly of the pomegranate genome. The research led to a final reference-quality genome assembly for ‘Bhagawa’ of 346.08 Mb in 342 scaffolds and an average N50 of 16.12 Mb and N90 of 1088.62 Kb. This assembly covered more than 98% of the estimated pomegranate genome size, 352.54 Mb. The LTR assembly index (LAI) value of 10 and 93.68% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score over the 1,440 ortholog genes of the completed pomegranate genome indicates the quality of the assembled pomegranate genome. Furthermore, 29,435 gene models were discovered with a mean transcript length of 2,954 bp and a mean coding sequence length 1,090 bp. Four transcript data samples of pomegranate tissues were mapped over the assembled ‘Bhagawa’ genome up to 95% significant matches, indicating the high quality of the assembled genome. We have compared the ‘Bhagawa’ genome with the genomes of the pomegranate cultivars ‘Dabenzi’ and ‘Taishanhong.’ We have also performed whole-genome phylogenetic analysis using Computational Analysis of Gene Family Evolution (CAFE) and found that Eucalyptus grandis and pomegranate diverged 64 (60–70) million years ago. About 1,573 protein-coding resistance genes identified in the ‘Bhagawa’ genome were classified into 32 domains. In all, 314 copies of miRNA belonging to 26 different families were identified in the ‘Bhagawa’ genome. The reference-quality genome assembly of ‘Bhagawa’ is certainly a significant genomic resource for accelerated pomegranate improvement.

石榴是保障全球灌溉资源有限的脆弱半干旱地区民生与营养安全的重要果树作物。该作物兼具高经济价值、丰富营养属性，属于出口导向型农业大宗商品，可为全球种植者带来可观的投资回报。尽管石榴是极具价值的果树作物，但相关基因组学研究成果却较为有限。为加速石榴遗传改良进程，印度农业研究理事会-国家石榴研究中心（ICAR-NRCP）启动了对印度主栽品种‘Bhagawa’的从头全基因组测序（de novo whole-genome sequencing）工作。本研究证实，结合使用Illumina、PacBio、10X Genomics及BioNano Genomics等商业化测序技术，可高效完成石榴基因组的测序与参考级从头组装（reference-grade de novo assembly）。本研究最终获得了‘Bhagawa’品种的参考级基因组组装结果：总长度346.08 Mb，包含342个支架（scaffolds），N50平均值为16.12 Mb，N90平均值为1088.62 Kb。该组装覆盖了预估石榴基因组大小（352.54 Mb）的98%以上。针对该已完成的石榴基因组的1440个单拷贝同源基因集，长末端重复序列组装指数（LTR assembly index, LAI）值为10，通用单拷贝同源基因基准测试（Benchmarking Universal Single-Copy Orthologs, BUSCO）完整度得分为93.68%，上述结果均证实了该组装基因组的质量。本研究共预测得到29435个基因模型（gene models），平均转录本长度为2954 bp，平均编码序列长度为1090 bp。将4份石榴组织的转录组数据（transcript data）比对至组装完成的‘Bhagawa’基因组，比对显著性匹配率可达95%，进一步证实了该组装基因组的高质量。本研究将‘Bhagawa’基因组与石榴栽培品种‘Dabenzi’及‘Taishanhong’的基因组进行了比对分析。本研究还借助基因家族进化计算分析工具（Computational Analysis of Gene Family Evolution, CAFE）开展了全基因组系统发育分析，结果显示巨桉（Eucalyptus grandis）与石榴的分化时间为64（60–70）百万年前。在‘Bhagawa’基因组中共鉴定得到1573个蛋白质编码抗性基因，可分为32个结构域。此外，在‘Bhagawa’基因组中还鉴定得到隶属于26个不同家族的314个微小RNA（miRNA）。该‘Bhagawa’品种的参考级基因组组装，无疑将成为加速石榴遗传改良进程的重要基因组学资源。