Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China.
BMC Genomics. 2012 Nov 21;13:650. doi: 10.1186/1471-2164-13-650.
Bananas and plantains (Musa spp.) are among the most important crops in the world due to their nutritional and export value. However, banana production has been devastated by fungal infestations caused by Fusarium oxysporum f. sp. cubense (Foc), which cannot be effectively prevented or controlled. Since there is very little known about the molecular mechanism of Foc infections; therefore, we aimed to investigate the transcriptional changes induced by Foc in banana roots.
We generated a cDNA library from total RNA isolated from banana roots infected with Foc Tropical Race 4 (Foc TR 4) at days 0, 2, 4, and 6. We generated over 26 million high-quality reads from the cDNA library using deep sequencing and assembled 25,158 distinct gene sequences by de novo assembly and gap-filling. The average distinct gene sequence length was 1,439 base pairs. A total of 21,622 (85.94%) unique sequences were annotated and 11,611 were assigned to specific metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes database. We used digital gene expression (DGE) profiling to investigate the transcriptional changes in the banana root upon Foc TR4 infection. The expression of genes in the Phenylalanine metabolism, phenylpropanoid biosynthesis and alpha-linolenic acid metabolism pathways was affected by Foc TR4 infection.
The combination of RNA-Seq and DGE analysis provides a powerful method for analyzing the banana root transcriptome and investigating the transcriptional changes during the response of banana genes to Foc TR4 infection. The assembled banana transcriptome provides an important resource for future investigations about the banana crop as well as the diseases that plague this valuable staple food.
香蕉和大蕉（Musa spp.）由于其营养价值和出口价值，是世界上最重要的作物之一。然而，由于由尖孢镰刀菌古巴专化型（Foc）引起的真菌侵染，香蕉生产受到了严重破坏，而这种真菌目前还无法有效预防或控制。由于对 Foc 感染的分子机制知之甚少；因此，我们旨在研究 Foc 感染香蕉根引起的转录变化。
我们从感染 Foc 热带 4 号（Foc TR 4）的香蕉根总 RNA 中生成了 cDNA 文库，在第 0、2、4 和 6 天进行了分析。我们使用深度测序从 cDNA 文库中生成了超过 2600 万个高质量读数，并通过从头组装和缺口填充组装了 25158 个独特的基因序列。平均独特基因序列长度为 1439 个碱基对。共有 21622 个（85.94%）独特序列被注释，11611 个序列被京都基因与基因组百科全书数据库分配到特定的代谢途径。我们使用数字基因表达（DGE）谱分析来研究 Foc TR4 感染对香蕉根的转录变化。苯丙氨酸代谢、苯丙烷生物合成和α-亚麻酸代谢途径中的基因表达受到 Foc TR4 感染的影响。
RNA-Seq 和 DGE 分析的结合为分析香蕉根转录组和研究香蕉基因对 Foc TR4 感染的转录反应提供了一种强大的方法。组装的香蕉转录组为未来研究香蕉作物以及困扰这种有价值主食的疾病提供了重要资源。
