Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq

Zhenpu Huang, Fangyuan Qiao, Boming Yang, Jiaqian Liu, Yangqi Liu, Brande B.H. Wulff, Ping Hu, Zengshuai Lv, Ruiqi Zhang, Peidu Chen, Liping Xing*, Aizhong Cao*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Background: 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. Results: 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. Conclusion: 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.

Original languageEnglish (US)
Article number118
JournalBMC genomics
Volume23
Issue number1
DOIs
StatePublished - Dec 2022

Bibliographical note

Funding Information:
This research supported by the high-performance computing platform of Bioinformatics Center, Nanjing Agricultural University. We highly appreciate Dr. Kamil Witek and Prof Jonathan D. G. Jones kind help in the design and performance of SMRT-RenSeq experiment, and Dr. Matthew Moscou (The Sainsbury Laboratory, UK) for sharing the barley baits library.

Funding Information:
This research supported by the high-performance computing platform of Bioinformatics Center, Nanjing Agricultural University. We highly appreciate Dr. Kamil Witek and Prof Jonathan D. G. Jones kind help in the design and performance of SMRT-RenSeq experiment, and Dr. Matthew Moscou (The Sainsbury Laboratory, UK) for sharing the barley baits library.

Publisher Copyright:
© 2022, The Author(s).

Keywords

  • Disease resistance
  • Genomics
  • Haynaldia villosa
  • NLR
  • SMRT-RenSeq

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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