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Genome-Wide Identification and Expression Analysis of the CrRLK1L Gene Family in Apple (Malus domestica)

  • Cunwu Zuo
  • Weina Zhang
  • Zonghuan Ma
  • Mingyu Chu
  • Juan Mao
  • Zeshan An
  • Baihong Chen
Original Paper
  • 25 Downloads

Abstract

It has been reported that members of the Catharanthus roseus receptor-like kinase1-like kinase (CrRLK1L) gene family detect cell wall integrity, cell-to-cell communication, and biotic and abiotic stress. We performed a comprehensive study including the genome-wide identification, characterization, and gene expression analysis of CrRLK1Ls in apple (Malus domestica). Sixty-seven M. domestica CrRLK1Ls (MdCrRLK1Ls) were identified based on their domain structure. Molecular weight and pI ranged from 52.36–141 kDa and 5.05–8.9, respectively. They were distributed across 16 of the 18 chromosomes and classified into five phylogenetic branches. Exon-intron structural analysis indicated a wide range of exon numbers. Collinearity analysis showed that both segmental-and tandem-duplication contributed to the expansion of this family. Cis-elements in the MdCrRLK1L promoter region responded mainly to light, circadian rhythm, phytohormones, and biotic or abiotic stress. Many members exhibited tissue-specific expression patterns and differentially expressed under biotic stresses, which may contribute to the different functional roles of MdCrRLK1Ls under physiological stress and/or pathological conditions. This study provides new insights into the CrRLK1Ls in Malus spp.

Keywords

CrRLK1L Malus domestica Bioinformatic analysis Expression pattern 

Abbreviations

RLK

receptor-like kinase

CrRLK1L

Catharanthus roseus receptor-like kinase1-like kinase

MdCrRLK1L

Malus domestica CrRLK1L

GDR

Genome database of Rosaceae species

GEF

guanine nucleotide exchange factor

RAC/ROP

GEF-regulated Rho GTPase

ROS

reactive oxygen species

RT-qPCR

quantitative real-time PCR

FLS2

Flagellin sensing2

EFR

Ef-Tu receptor

CERK1

chitin elicitor receptor kinase 1

PRR

pattern recognition receptor

PTI

pattern-triggered immunity

Notes

Authors’ Contributions

ZC, CB, and ZW conceived and designed the study; ZC, MZ, CM, MJ, and AZ performed the experiments, analyzed the data, and wrote the manuscript. All the authors agreed on the content of this manuscript.

Funding

This work was supported by the horticultural innovation fund of Gansu Agricultural University (GAU-XKJS-2018-217), the National Natural Science Foundation of China (31860549; 31501728), the Science and Technology Major Project of Gansu Province (18ZD2NA006), and the Fund for higher education of Gansu province (2018B-034).

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

Data Archiving Statement

All identified amino acid and/or CDS of MdCrRLK1L gene sequences were deposited into the GDR (https://www.rosaceae.org/species/malus/all) and/or NCBI database (http://www.ncbi.nlm.nih.gov/). The accession numbers are listed in Table 1.

Supplementary material

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Supplementary Table 1 (DOCX 13 kb)
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Supplementary Table 2 (DOCX 13 kb)
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Supplementary Table 3 (DOCX 14 kb)
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Supplementary Table 4 (DOCX 24 kb)
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Supplementary Table 5 (DOCX 24 kb)
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Supplementary Table 6 (XLSX 15 kb)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Cunwu Zuo
    • 1
  • Weina Zhang
    • 1
  • Zonghuan Ma
    • 1
  • Mingyu Chu
    • 1
  • Juan Mao
    • 1
  • Zeshan An
    • 1
  • Baihong Chen
    • 1
  1. 1.College of HorticultureGansu Agricultural UniversityLanzhouPeople’s Republic of China

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