2021年9月28日，中国农业科学院蔬菜花卉研究所甘蓝青花菜研究团队在期刊International Journal of Molecular Sciences上发表了题为”Global Survey of the Full-Length Cabbage T ranscriptome (Brassica oleracea V ar. capitata L.) Reveals Key Alternative Splicing Events Involved in Growth and Disease Response“的研究论文。论文第一作者为王勇博士和季家磊博士，通讯作者为张扬勇研究员和吕红豪研究员。

甘蓝是在世界各地广泛栽培的重要蔬菜作物。以往的甘蓝基因转录本的研究主要以二代测序技术（Next Generation Sequencing，NGS）为主，无法提供有关转录本组装和结构分析的准确信息。因此，作者用PacBio RS Ⅱ Single-Molecule Real- Time（SMRT）测序技术对甘蓝的五个组织部位（根、茎、叶、花、长角果（我觉得应该是种荚））进行了全长转录组测序分析。

从SMRT产生的数据中，共获得了77048个同工异构体，捕获了18183个注释基因。对其中的可变剪切（ alternative splicing，AS）和可变聚腺苷化（alternative polyadenylation，APA）进行分析。总共检测到13468个含有APA位点的异构体基因和8978个发生了可变剪切的基因。此外，还发现5272个长链非编码RNAs，而且大多都表现出组织特异性表达。共检测到3147个转录因子，鉴定出10个有意义的基因共表达网络模块。此外，还发现枯萎病、黑腐病、根肿病的侵染显著影响抗病甘蓝的可变剪切。

Figure 1. Statistics and annotations of the isoforms obtained by SMRT sequencing. (A) Venn diagram illustrating unique and common isoforms in different tissues. (B) Statistics of the isoforms in different tissues. (C) GO annotations of the tissue-specific genes. (D) KEGG annotations of the tissue-specific genes.

Figure 2. Characterization of genes with alternative splicing (AS). (A) V enn diagram illustrating unique and common AS genes in different tissues. (B) Number of AS genes in different tissues. (C) Percent of each AS type in different tissues. (D) Verification of AS events by RT-PCR.

Figure 3. Statistics for long noncoding RNAs (lncRNAs) and genes with alternative polyadenylation (APA). (A) Venn diagram illustrating unique and common lncRNAs in different tissues. (B) V enn diagram illustrating unique and common APA genes in different tissues. (C) Number of the genes with different poly(A) sites in five tissues.

Figure 4. Weighted correlation network analysis of transcription factors (TFs). (A) Cluster dendrogram of the expressed TFs. (B) Heat map of module–trait relationships. (C) TF types in different co-expression modules.

Figure 5. Analysis of the cabbage splicing variants in response to Fusarium wilt (FW). (A) V enn diagram illustrating unique and common AS genes at different times after Fusarium oxysporum f. sp. conglutinans (Foc) inoculation. (B) Number of differential AS events at different times after Foc inoculation. (C) The splicing variant of Boc03g06003 in response to FW. R0, R3, R6, and R9 represent resistant plants at 0, 3, 6, and 9 dpi, respectively . S0, S3, S6, and S9 represent susceptible plants at 0, 3, 6, and 9 dpi, respectively . (D) V enn diagram illustrating unique and common AS genes in response to black rot (BR), clubroot (CR) and Fusarium wilt (FW).