Seong Kyungyong, Seo Eunyoung, Witek Kamil, Li Meng, Staskawicz Brian
Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA.
New Phytol. 2020 Sep;227(5):1530-1543. doi: 10.1111/nph.16628. Epub 2020 May 23.
Nucleotide-binding and leucine-rich repeat immune receptors (NLRs) provide resistance against diverse pathogens. To create comparative NLR resources, we conducted resistance gene enrichment sequencing (RenSeq) with single-molecule real-time sequencing of PacBio for 18 accessions in Solanaceae, including 15 accessions of five wild tomato species. We investigated the evolution of a class of NLRs, CNLs with extended N-terminal sequences previously named Solanaceae Domain. Through comparative genomic analysis, we revealed that the extended CNLs (exCNLs) anciently emerged in the most recent common ancestor between Asterids and Amaranthaceae, far predating the Solanaceae family. In tomatoes, the exCNLs display exceptional modes of evolution in a clade-specific manner. In the clade G3, exCNLs have substantially elongated their N-termini through tandem duplications of exon segments. In the clade G1, exCNLs have evolved through recent proliferation and sequence diversification. In the clade G6, an ancestral exCNL has lost its N-terminal domains in the course of evolution. Our study provides high-quality NLR gene models for close relatives of domesticated tomatoes that can serve as a useful resource for breeding and molecular engineering for disease resistance. Our findings regarding the exCNLs offer unique backgrounds and insights for future functional studies of the NLRs.
核苷酸结合和富含亮氨酸重复序列的免疫受体（NLRs）提供了对多种病原体的抗性。为了创建比较性的NLR资源，我们对茄科的18个种质进行了抗性基因富集测序（RenSeq），并使用PacBio的单分子实时测序技术，其中包括五个野生番茄物种的15个种质。我们研究了一类NLRs的进化，即具有先前命名为茄科结构域的延长N端序列的CNLs。通过比较基因组分析，我们发现延长的CNLs（exCNLs）在菊类植物和苋科的最近共同祖先中古老地出现，远远早于茄科家族。在番茄中，exCNLs以进化枝特异性的方式表现出特殊的进化模式。在进化枝G3中，exCNLs通过外显子片段的串联重复大幅延长了它们的N端。在进化枝G1中，exCNLs通过最近的增殖和序列多样化而进化。在进化枝G6中，一个祖先exCNL在进化过程中失去了其N端结构域。我们的研究为驯化番茄的近缘种提供了高质量的NLR基因模型，可作为抗病育种和分子工程的有用资源。我们关于exCNLs的发现为未来NLRs的功能研究提供了独特的背景和见解。
