Genome-wide analysis of lectin receptor-like kinases in Populus

Yongil Yang; Jessy Labbé; Wellington Muchero; Xiaohan Yang; Sara S. Jawdy; Megan Kennedy; Jenifer Johnson; Avinash Sreedasyam; Jeremy Schmutz; Gerald A. Tuskan; Jin Gui Chen

doi:10.1186/s12864-016-3026-2

Genome-wide analysis of lectin receptor-like kinases in Populus

Yongil Yang, Jessy Labbé, Wellington Muchero, Xiaohan Yang, Sara S. Jawdy, Megan Kennedy, Jenifer Johnson, Avinash Sreedasyam, Jeremy Schmutz, Gerald A. Tuskan, Jin Gui Chen

Research output: Contribution to journal › Article › peer-review

49 Scopus citations

Abstract

Background: Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a characteristic extracellular carbohydrate-binding lectin domain and play important roles in plant development and innate immunity. There are 75 and 173 LecRLKs in Arabidopsis and rice, respectively. However, little is known about LecRLKs in perennial woody plants. Results: Here we report the genome-wide analysis of classification, domain architecture and expression of LecRLKs in the perennial woody model plant Populus. We found that the LecRLK family has expanded in Populus to a total of 231, including 180 G-type, 50 L-type and 1 C-type LecRLKs. Expansion of the Populus LecRLKs (PtLecRLKs) occurred partially through tandem duplication. Based on domain architecture and orientation features, we classified PtLecRLKs into eight different classes. RNA-seq-based transcriptomics analysis revealed diverse expression patterns of PtLecRLK genes among leaves, stems, roots, buds and reproductive tissues and organs. Conclusions: This study offers a comprehensive view of LecRLKs in the perennial woody model plant Populus and provides a foundation for functional characterization of this important family of receptor-like kinases.

Original language	English
Article number	699
Journal	BMC Genomics
Volume	17
Issue number	1
DOIs	https://doi.org/10.1186/s12864-016-3026-2
State	Published - Sep 1 2016

Funding

This work was supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research in the U.S. Department of Energy Office of Science. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. The work conducted by the U.S. Department of Energy Joint Genome Institute was supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231.

Funders	Funder number
Plant-Microbe Interfaces Scientific Focus Area
U.S. Department of Energy	DE-AC05-00OR22725, DE-AC02-05CH11231
Office of Science
Biological and Environmental Research
Oak Ridge National Laboratory

Keywords

Lectin domain
Lectin receptor-like kinase (LecRLK)
Perennial woody plant
Populus
Receptor like-kinase (RLK)
Transmembrane kinase

Access to Document

10.1186/s12864-016-3026-2

Cite this

@article{b719ce9604a047c284ed841d10f068ae,

title = "Genome-wide analysis of lectin receptor-like kinases in Populus",

abstract = "Background: Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a characteristic extracellular carbohydrate-binding lectin domain and play important roles in plant development and innate immunity. There are 75 and 173 LecRLKs in Arabidopsis and rice, respectively. However, little is known about LecRLKs in perennial woody plants. Results: Here we report the genome-wide analysis of classification, domain architecture and expression of LecRLKs in the perennial woody model plant Populus. We found that the LecRLK family has expanded in Populus to a total of 231, including 180 G-type, 50 L-type and 1 C-type LecRLKs. Expansion of the Populus LecRLKs (PtLecRLKs) occurred partially through tandem duplication. Based on domain architecture and orientation features, we classified PtLecRLKs into eight different classes. RNA-seq-based transcriptomics analysis revealed diverse expression patterns of PtLecRLK genes among leaves, stems, roots, buds and reproductive tissues and organs. Conclusions: This study offers a comprehensive view of LecRLKs in the perennial woody model plant Populus and provides a foundation for functional characterization of this important family of receptor-like kinases.",

keywords = "Lectin domain, Lectin receptor-like kinase (LecRLK), Perennial woody plant, Populus, Receptor like-kinase (RLK), Transmembrane kinase",

author = "Yongil Yang and Jessy Labb{\'e} and Wellington Muchero and Xiaohan Yang and Jawdy, {Sara S.} and Megan Kennedy and Jenifer Johnson and Avinash Sreedasyam and Jeremy Schmutz and Tuskan, {Gerald A.} and Chen, {Jin Gui}",

note = "Publisher Copyright: {\textcopyright} 2016 The Author(s).",

year = "2016",

month = sep,

day = "1",

doi = "10.1186/s12864-016-3026-2",

language = "English",

volume = "17",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central",

number = "1",

}

TY - JOUR

T1 - Genome-wide analysis of lectin receptor-like kinases in Populus

AU - Yang, Yongil

AU - Labbé, Jessy

AU - Muchero, Wellington

AU - Yang, Xiaohan

AU - Jawdy, Sara S.

AU - Kennedy, Megan

AU - Johnson, Jenifer

AU - Sreedasyam, Avinash

AU - Schmutz, Jeremy

AU - Tuskan, Gerald A.

AU - Chen, Jin Gui

PY - 2016/9/1

Y1 - 2016/9/1

N2 - Background: Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a characteristic extracellular carbohydrate-binding lectin domain and play important roles in plant development and innate immunity. There are 75 and 173 LecRLKs in Arabidopsis and rice, respectively. However, little is known about LecRLKs in perennial woody plants. Results: Here we report the genome-wide analysis of classification, domain architecture and expression of LecRLKs in the perennial woody model plant Populus. We found that the LecRLK family has expanded in Populus to a total of 231, including 180 G-type, 50 L-type and 1 C-type LecRLKs. Expansion of the Populus LecRLKs (PtLecRLKs) occurred partially through tandem duplication. Based on domain architecture and orientation features, we classified PtLecRLKs into eight different classes. RNA-seq-based transcriptomics analysis revealed diverse expression patterns of PtLecRLK genes among leaves, stems, roots, buds and reproductive tissues and organs. Conclusions: This study offers a comprehensive view of LecRLKs in the perennial woody model plant Populus and provides a foundation for functional characterization of this important family of receptor-like kinases.

AB - Background: Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a characteristic extracellular carbohydrate-binding lectin domain and play important roles in plant development and innate immunity. There are 75 and 173 LecRLKs in Arabidopsis and rice, respectively. However, little is known about LecRLKs in perennial woody plants. Results: Here we report the genome-wide analysis of classification, domain architecture and expression of LecRLKs in the perennial woody model plant Populus. We found that the LecRLK family has expanded in Populus to a total of 231, including 180 G-type, 50 L-type and 1 C-type LecRLKs. Expansion of the Populus LecRLKs (PtLecRLKs) occurred partially through tandem duplication. Based on domain architecture and orientation features, we classified PtLecRLKs into eight different classes. RNA-seq-based transcriptomics analysis revealed diverse expression patterns of PtLecRLK genes among leaves, stems, roots, buds and reproductive tissues and organs. Conclusions: This study offers a comprehensive view of LecRLKs in the perennial woody model plant Populus and provides a foundation for functional characterization of this important family of receptor-like kinases.

KW - Lectin domain

KW - Lectin receptor-like kinase (LecRLK)

KW - Perennial woody plant

KW - Populus

KW - Receptor like-kinase (RLK)

KW - Transmembrane kinase

UR - http://www.scopus.com/inward/record.url?scp=84984669543&partnerID=8YFLogxK

U2 - 10.1186/s12864-016-3026-2

DO - 10.1186/s12864-016-3026-2

M3 - Article

C2 - 27580945

AN - SCOPUS:84984669543

SN - 1471-2164

VL - 17

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 699

ER -

Genome-wide analysis of lectin receptor-like kinases in Populus

Abstract

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this