DIVAPRA, University of Torino, Grugliasco, Torino, Italy.
Plant Biotechnol J. 2012 Oct;10(8):956-69. doi: 10.1111/j.1467-7652.2012.00725.x. Epub 2012 Jul 31.
Cynara cardunculus (2n = 2× = 34) is a member of the Asteraceae family that contributes significantly to the agricultural economy of the Mediterranean basin. The species includes two cultivated varieties, globe artichoke and cardoon, which are grown mainly for food. Cynara cardunculus is an orphan crop species whose genome/transcriptome has been relatively unexplored, especially in comparison to other Asteraceae crops. Hence, there is a significant need to improve its genomic resources through the identification of novel genes and sequence-based markers, to design new breeding schemes aimed at increasing quality and crop productivity. We report the outcome of cDNA sequencing and assembly for eleven accessions of C. cardunculus. Sequencing of three mapping parental genotypes using Roche 454-Titanium technology generated 1.7 × 10⁶ reads, which were assembled into 38,726 reference transcripts covering 32 Mbp. Putative enzyme-encoding genes were annotated using the KEGG-database. Transcription factors and candidate resistance genes were surveyed as well. Paired-end sequencing was done for cDNA libraries of eight other representative C. cardunculus accessions on an Illumina Genome Analyzer IIx, generating 46 × 10⁶ reads. Alignment of the IGA and 454 reads to reference transcripts led to the identification of 195,400 SNPs with a Bayesian probability exceeding 95%; a validation rate of 90% was obtained by Sanger-sequencing of a subset of contigs. These results demonstrate that the integration of data from different NGS platforms enables large-scale transcriptome characterization, along with massive SNP discovery. This information will contribute to the dissection of key agricultural traits in C. cardunculus and facilitate the implementation of marker-assisted selection programs.
蓟（2n = 2× = 34）是菊科的一员，对地中海盆地的农业经济有重要贡献。该物种包括两个栽培品种，即朝鲜蓟和刺菜蓟，主要用于食用。蓟是一种孤儿作物种，其基因组/转录组相对来说尚未得到充分探索，特别是与其他菊科作物相比。因此，通过鉴定新基因和基于序列的标记来改善其基因组资源，以设计旨在提高质量和作物生产力的新育种方案，具有重要意义。我们报告了对 11 个蓟属植物品系 cDNA 测序和组装的结果。使用 Roche 454-Titanium 技术对三个作图亲本基因型进行测序，共产生 1.7×10⁶条reads，组装成覆盖 32 Mbp 的 38726 条参考转录本。使用 KEGG 数据库对假定的酶编码基因进行注释。还调查了转录因子和候选抗性基因。对另外 8 个代表性蓟属植物品系的 cDNA 文库进行了 Illumina Genome Analyzer IIx 的配对末端测序，共产生 46×10⁶条reads。将 IGA 和 454 读取与参考转录本进行比对，鉴定出 195400 个具有超过 95%贝叶斯概率的 SNP；通过对一部分 contigs 的 Sanger 测序，验证率达到 90%。这些结果表明，整合来自不同 NGS 平台的数据可实现大规模转录组特征分析和大量 SNP 发现。这些信息将有助于解析蓟属植物的关键农业性状，并促进标记辅助选择计划的实施。
