Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida

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Plant Biology

Main article text

 

Introduction

Materials & Methods

Identification of NAC transcription factors

Multiple sequence alignment and phylogenetic analysis

Characterization of BjuNAC proteins and BjuNAC genes

Chromosomal distribution cis-element and evolutionary analysis of BjuNAC genes

RNA extraction and qRT-PCR analysis

Results

Genome-wide identification of BjuNAC genes

Phylogenetic analysis of BjuNAC proteins

Analysis of chromosomal distribution and duplication of BjuNAC genes

Exon–intron gene structure and conserved motif analysis

Cis-acting element analysis

Gene expression analysis under temperature stress

Discussion

Conclusions

Supplemental Information

qRT PCR Raw data

DOI: 10.7717/peerj.11212/supp-1

Perl script of getting positions of NAC genes inBrassica juncea var.tumida

DOI: 10.7717/peerj.11212/supp-2

Phylogenetictree among the NAC TFs of Brassica juncea var. tumida, Brassica rapa, Brassica nigra, Oryza sativa L and Arabidopsis thaliana

Multiple sequence alignment of full-length NAC proteins was done using muscle method and the phylogenetic tree was constructed using MEGAX by the neighbor-joining method with bootstrap 1000 replicates.

DOI: 10.7717/peerj.11212/supp-3

Collinear analysis of NACs in Brassica juncea var. tumida

Collinear blocks represented by grey background. 288 BjuNAC duplication pairs are linked with green lines, and 15 tandem duplication pairs are linked with red lines.

DOI: 10.7717/peerj.11212/supp-4

Phylogenetic relationships, gene structure and functional domain analysis of the BjuNACs proteins

(a) A phylogenetic tree using the neighbor-joining method by MEGAX, with bootstrap values of 1,000. (b) The conserved motifs were predicted using Multiple Em for Motif Elicitation (MEME) (http://alternate.meme-suite.org/). (c) The box length indicates the number of amino acids in the motif. The coding sequences (CDS) of exons are represented by purple boxes, the introns are represented by lines.

DOI: 10.7717/peerj.11212/supp-5

Logo representation of the 15 conserved motifs identified for proteins encoded by BjuNAC genes

The height of each amino acid code in the sequence logo of each motif represents the degree of conservation.

DOI: 10.7717/peerj.11212/supp-6

Multiple alignment of NAC domain sequences in Brassica juncea var. tumida using clustalx2.0

All domain sequences of BjuNACs divided into five subdomains A-E.

DOI: 10.7717/peerj.11212/supp-7

Predicted cis regulatory elements in the BjuNAC gene promoters

The promoter sequences (1500 bp) upstream of genes were chosen for cis-regulatory element analysis using the PlantCARE online tool (http://www.dna.affrc.go.jp/PLACE/). Each color indicates a cis-regulatory element.

DOI: 10.7717/peerj.11212/supp-8

Chromosomal distributionof NAC genes on the genetic map in Brassica nigra

Graphical representation of locations for putative BniNAC genes on each chromosome. B1∼B8 represented the chromosome numbers. Other 25 BniNAC genes information belongs to scaffold data were shown in Table S3.

DOI: 10.7717/peerj.11212/supp-9

Primers for NAC members selected for qRT-PCR

DOI: 10.7717/peerj.11212/supp-10

The NAC protein family members in Brassuca. juncea var. tumida

DOI: 10.7717/peerj.11212/supp-11

NAC family members in Brassica nigra

DOI: 10.7717/peerj.11212/supp-12

Blast result of NAC protein sequences of B.juncea var. tumida ,Brassica rapa and Brassica nigra

DOI: 10.7717/peerj.11212/supp-13

Expression analysis of BjuNAC under high and low temperature stresses

DOI: 10.7717/peerj.11212/supp-14

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Longxing Jiang performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Quan Sun conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Yu Wang performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Pingan Chang conceived and designed the experiments, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Haohuan Kong performed the experiments, prepared figures and/or tables, and approved the final draft.

Changshu Luo analyzed the data, authored or reviewed drafts of the paper, and approved the final draft.

Xiaohong He conceived and designed the experiments, prepared figures and/or tables, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The raw measurements are available in the Supplementary Files.

Funding

This work was supported by grants from the Science and Technology Research Program of Chongqing Municipal Education Commission (Grant No. KJQN201800609) and Natural Sciences Foundation of Chongqing (Grant No. cstc2015jcyjA0752). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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