Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
Sci Rep. 2023 Nov 22;13(1):20503. doi: 10.1038/s41598-023-45982-8.
Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.
黄檀（Shisham）是一种生产木材的物种，在印度次大陆具有经济、文化和药用重要性。在过去的几十年中，由真菌 Botryodiplodia theobromae 引起的 Shisham 衰退病已成为该地区的一个正在发展的问题，危及到其生存。为了深入了解这一问题，我们采用了标准转录组组装技术，在受 B. theobromae 感染的胁迫下，从转录组水平评估 D. sissoo 的反应。为了进行 RNA 分离，从温室中生长的 1 年生 D. sissoo 植物的茎基部孢子接种后 20 天的对照和感染叶片组织中采集了样本。从这些新分离的 RNA 样本中进行 cDNA 合成，然后进行测序。使用 BGISEQ-500 测序平台生成了约 18.14 Gb（吉字节）的数据。在 Unigenes 方面，对所有样本进行联合组装并过滤丰度后，鉴定出 513821 个 Unigenes。Unigenes 的总长度、平均长度、N50 和 GC 含量分别为 310523693bp、604bp、1101bp 和 39.95%。使用 7 个功能数据库对 Unigenes 进行注释，即 200355 个（NR：38.99%）、164973 个（NT：32.11%）、123733 个（Swissprot：24.08%）、142580 个（KOG：27.75%）、139588 个（KEGG：27.17%）、99752 个（GO：19.41%）和 137281 个（InterPro：26.72%）。此外，Transdecoder 检测到 115762 个 CDS。在 SSR（简单序列重复）标记方面，其中 62863 个分布在 51508 个 Unigenes和预测的 4673 个 TF（转录因子）编码 Unigenes上。还鉴定了 16018 个上调和 19530 个下调的差异表达基因（DEGs）。此外，植物抗性基因（PRGs）的数量为 9230。我们希望在未来，这些鉴定出的 Unigenes、SSR 标记、DEGs 和 PRGs 将为管理 Shisham 衰退病、其育种以及树木改良计划提供前提条件。
