Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq.
Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq.
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DOI：
10.1186/s12864-022-08334-w
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发表时间：
2022-02-10
期刊：
影响因子：
4.4
通讯作者：
Cao A
中科院分区：
文献类型：
--
作者：
Huang Z;Qiao F;Yang B;Liu J;Liu Y;Wulff BBH;Hu P;Lv Z;Zhang R;Chen P;Xing L;Cao A
核苷酸结合和富含亮氨酸重复序列（NLR）基因因其在保护植物免受病原菌侵害方面的重要作用而受到广泛关注。SMRT-RenSeq结合了抗性基因富集测序（RenSeq）后的PacBio测序，是一种选择性捕获和测序全长NLR的强大方法。簇毛麦是一种具有改良小麦潜力的野生禾本科植物，对多种病害具有抗性。因此，利用SMRT-RenSeq对簇毛麦NLR基因家族进行全基因组鉴定，有助于抗病基因的发掘。在这项研究中，SMRT-RenSeq被用于鉴定H.绒毛。总共在1169个重叠群中注释了1320个NLR，包括772个完整的NLR。对所有完整的NLR进行了系统进化分析，得到了11个具有特征的主要分支。当与克隆的R基因比对时，可以高效地捕获NLR，并且在一些特定基因位点观察到簇扩展。NLR在H. villosa与小麦族第1、2、3、5、6类群的近缘种关系较好，而位于4VL上的近缘种主要位于近缘种第7类群。在52个NLR中整合了15种类型的整合结构域（ID），其中Kelch和B3 NLR ID在H.而DUF 948、NAM-associated和PRT_C被检测为唯一整合结构域，这意味着继H. villosa之后新出现的NLR-ID。villosa从其它种分化出来。SMRT-RenSeq是一种利用进化相关物种的诱饵和参考序列从野生物种中鉴定NLR基因的有力工具。从H. villosa为抗病基因的挖掘和抗病基因的导入提供了有价值的文库。在线版本包含补充材料，可通过10.1186/s12864-022-08334-w获得。
Nucleotide-binding and leucine-rich repeat (NLR) genes have attracted wide attention due to their crucial role in protecting plants from pathogens. SMRT-RenSeq, combining PacBio sequencing after resistance gene enrichment sequencing (RenSeq), is a powerful method for selectively capturing and sequencing full-length NLRs. Haynaldia villosa, a wild grass species with a proven potential for wheat improvement, confers resistance to multiple diseases. So, genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq can facilitate disease resistance genes exploration. In this study, SMRT-RenSeq was performed to identify the genome-wide NLR complement of H. villosa. In total, 1320 NLRs were annotated in 1169 contigs, including 772 complete NLRs. All the complete NLRs were phylogenetically analyzed and 11 main clades with special characteristics were derived. NLRs could be captured with high efficiency when aligned with cloned R genes, and cluster expansion in some specific gene loci was observed. The physical location of NLRs to individual chromosomes in H. villosa showed a perfect homoeologous relationship with group 1, 2, 3, 5 and 6 of other Triticeae species, however, NLRs physically located on 4VL were largely in silico predicted to be located on the homoeologous group 7. Fifteen types of integrated domains (IDs) were integrated in 52 NLRs, and Kelch and B3 NLR-IDs were found to have expanded in H. villosa, while DUF948, NAM-associated and PRT_C were detected as unique integrated domains implying the new emergence of NLR-IDs after H. villosa diverged from other species. SMRT-RenSeq is a powerful tool to identify NLR genes from wild species using the baits of the evolutionary related species with reference sequences. The availability of the NLRs from H. villosa provide a valuable library for R gene mining and transfer of disease resistance into wheat. The online version contains supplementary material available at 10.1186/s12864-022-08334-w.