The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species
The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species
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DOI：
10.1534/g3.119.400529
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发表时间：
2019-12-01
影响因子：
2.6
通讯作者：
Tellier, Aurelien
中科院分区：
文献类型：
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作者：
Stam, Remco;Nosenko, Tetyana;Tellier, Aurelien
辣椒等野生番茄是番茄育种中提高生物和非生物抗逆性的重要种质资源。也可以作为研究植物对干旱的适应和种子库进化的模型。在这个物种多样性很强的强制异交中，缺乏一个注释良好的参考基因组，这限制了对所涉及基因的深入研究。我们为S辣椒产生了类似134GBDNA和157GBRNA序列数据，产生了一个估计长度为914Mb的基因组草稿，编码25,885个高置信度预测基因模型，显示出与其他番茄物种已知的蛋白质编码基因的同源性。这些基因模型中约有71%得到了来自叶片组织样本的RNA-SEQ数据的支持。用通用单拷贝同源序列(BUSCO)对预测基因模型进行分析，检索到93.3%的BUSCO基因。为了进一步验证基因组注释的完整性和准确性，我们人工检查了NLR抗性基因家族并评估了其组装质量。我们发现了少年儿童所特有的NLR亚家族。Synteny分析表明，辣椒、番茄和番茄基因组之间的基因序列具有显著的保守性。我们首次构建了野生番茄品种辣椒茄子的基因组和转录组序列组合，并证明了它们在比较基因组学分析中的价值。这些数据为研究茄科植物对生物和非生物胁迫的适应性、自交不亲和性的进化和番茄育种提供了重要的资源。
Wild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. S. chilense also serves as a model to study adaptation of plants to drought and the evolution of seed banks. The absence of a well-annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved.We generated similar to 134 Gb of DNA and 157 Gb of RNA sequence data for S chilense, which yielded a draft genome with an estimated length of 914 Mb, encoding 25,885 high-confidence predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% of these gene models are supported by RNA-seq data derived from leaf tissue samples. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% of BUSCO genes. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We find subfamilies of NLRs unique to S. chilense. Synteny analysis suggests significant degree of the gene order conservation between the S. chilense, S. lycopersicum and S. pennellii genomes.We generated the first genome and transcriptome sequence assemblies for the wild tomato species Solanum chilense and demonstrated their value in comparative genomics analyses. These data are an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, on evolution of self-incompatibility and for tomato breeding.