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Genome-Wide Analysis of the NAC Gene Family in Physic Nut (Jatropha curcas L.).

Wu Z, Xu X, Xiong W, Wu P, Chen Y, Li M, Wu G, Jiang H - PLoS ONE (2015)

Bottom Line: Physic nut has a single intron-containing NAC gene subfamily that has been lost in many plants.Digital gene expression analysis indicates that some of the JcNAC genes have tissue-specific expression profiles (e.g. in leaves, roots, stem cortex or seeds), and 29 genes differentially respond to abiotic stresses (drought, salinity, phosphorus deficiency and nitrogen deficiency).Our results will be helpful for further functional analysis of the NAC genes in physic nut.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.

ABSTRACT
The NAC proteins (NAM, ATAF1/2 and CUC2) are plant-specific transcriptional regulators that have a conserved NAM domain in the N-terminus. They are involved in various biological processes, including both biotic and abiotic stress responses. In the present study, a total of 100 NAC genes (JcNAC) were identified in physic nut (Jatropha curcas L.). Based on phylogenetic analysis and gene structures, 83 JcNAC genes were classified as members of, or proposed to be diverged from, 39 previously predicted orthologous groups (OGs) of NAC sequences. Physic nut has a single intron-containing NAC gene subfamily that has been lost in many plants. The JcNAC genes are non-randomly distributed across the 11 linkage groups of the physic nut genome, and appear to be preferentially retained duplicates that arose from both ancient and recent duplication events. Digital gene expression analysis indicates that some of the JcNAC genes have tissue-specific expression profiles (e.g. in leaves, roots, stem cortex or seeds), and 29 genes differentially respond to abiotic stresses (drought, salinity, phosphorus deficiency and nitrogen deficiency). Our results will be helpful for further functional analysis of the NAC genes in physic nut.

No MeSH data available.


Chromosomal localization of physic nut NAC genes.Chromosomal localization of JcNAC genes based on the linkage map. In total, 98 JcNAC genes were mapped to the 11 linkage groups (LGs). The scale is in centimorgan. T, tandem duplication; A, ancient segmental duplication based on the genome synteny [26].
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pone.0131890.g002: Chromosomal localization of physic nut NAC genes.Chromosomal localization of JcNAC genes based on the linkage map. In total, 98 JcNAC genes were mapped to the 11 linkage groups (LGs). The scale is in centimorgan. T, tandem duplication; A, ancient segmental duplication based on the genome synteny [26].

Mentions: A total of 98 JcNAC genes were mapped to 11 chromosomes according to the linkage map we constructed [26], while the other two genes (JcNAC024 and 064) located on unmapped scaffolds (S2 Table). The distribution and density of the JcNAC genes on chromosomes were not uniform (Fig 2). Chromosome 8 contained the highest frequency (21%) of JcNAC genes, while chromosome 1, 3 and 5 contained the lowest frequencies (4%). Evidence of both segmental and tandem duplication events of NAC genes in plants has been previously reported [14–16, 40]. To determine the possible relationships between the NAC genes and potential segmental duplications, we mapped the JcNAC genes to the duplicated blocks established in the recent study [26]. As a result, five blocks of pairs (A1-A5) of JcNAC genes were observed that may have arisen from the corresponding duplicate genomic blocks (Fig 2). In addition, a total of 30 JcNAC genes (30% of the total number) were observed to be in tandem repeats genes, which we designated them as T1-T11 (Fig 2). Nine direct tandem repeats (JcNAC065-069 and 071–074) (T7) were observed on chromosome 8, which has the highest number of tandem repeats of JcNAC genes. Their orthologs in castor bean were also clustered on a genomic sequence of scaffold 30076 (Fig 3). According to the phylogenetic tree, T4, T8, T9, and T11 genes duplicated after separation of lineages of the analyzed species; T6 genes (JcNAC003 and 026, originating from OGs1g and 3c) on chromosome 6 arose from ancient tandem repeats, predating the divergence between monocots and dicots [20]; and T1 genes on chromosome 6 (JcNAC021 and 028, originating from OGs 3e and 3d) predate the divergence of dicots because homologous repeats are present in genomes of grape (VvNAC17/GSVIVT01014403001 and VvNAC17/GSVIVT01014405001) and Arabidospis (ANAC018/AT1G52880 and ANAC019/AT1G52890).


Genome-Wide Analysis of the NAC Gene Family in Physic Nut (Jatropha curcas L.).

Wu Z, Xu X, Xiong W, Wu P, Chen Y, Li M, Wu G, Jiang H - PLoS ONE (2015)

Chromosomal localization of physic nut NAC genes.Chromosomal localization of JcNAC genes based on the linkage map. In total, 98 JcNAC genes were mapped to the 11 linkage groups (LGs). The scale is in centimorgan. T, tandem duplication; A, ancient segmental duplication based on the genome synteny [26].
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4488383&req=5

pone.0131890.g002: Chromosomal localization of physic nut NAC genes.Chromosomal localization of JcNAC genes based on the linkage map. In total, 98 JcNAC genes were mapped to the 11 linkage groups (LGs). The scale is in centimorgan. T, tandem duplication; A, ancient segmental duplication based on the genome synteny [26].
Mentions: A total of 98 JcNAC genes were mapped to 11 chromosomes according to the linkage map we constructed [26], while the other two genes (JcNAC024 and 064) located on unmapped scaffolds (S2 Table). The distribution and density of the JcNAC genes on chromosomes were not uniform (Fig 2). Chromosome 8 contained the highest frequency (21%) of JcNAC genes, while chromosome 1, 3 and 5 contained the lowest frequencies (4%). Evidence of both segmental and tandem duplication events of NAC genes in plants has been previously reported [14–16, 40]. To determine the possible relationships between the NAC genes and potential segmental duplications, we mapped the JcNAC genes to the duplicated blocks established in the recent study [26]. As a result, five blocks of pairs (A1-A5) of JcNAC genes were observed that may have arisen from the corresponding duplicate genomic blocks (Fig 2). In addition, a total of 30 JcNAC genes (30% of the total number) were observed to be in tandem repeats genes, which we designated them as T1-T11 (Fig 2). Nine direct tandem repeats (JcNAC065-069 and 071–074) (T7) were observed on chromosome 8, which has the highest number of tandem repeats of JcNAC genes. Their orthologs in castor bean were also clustered on a genomic sequence of scaffold 30076 (Fig 3). According to the phylogenetic tree, T4, T8, T9, and T11 genes duplicated after separation of lineages of the analyzed species; T6 genes (JcNAC003 and 026, originating from OGs1g and 3c) on chromosome 6 arose from ancient tandem repeats, predating the divergence between monocots and dicots [20]; and T1 genes on chromosome 6 (JcNAC021 and 028, originating from OGs 3e and 3d) predate the divergence of dicots because homologous repeats are present in genomes of grape (VvNAC17/GSVIVT01014403001 and VvNAC17/GSVIVT01014405001) and Arabidospis (ANAC018/AT1G52880 and ANAC019/AT1G52890).

Bottom Line: Physic nut has a single intron-containing NAC gene subfamily that has been lost in many plants.Digital gene expression analysis indicates that some of the JcNAC genes have tissue-specific expression profiles (e.g. in leaves, roots, stem cortex or seeds), and 29 genes differentially respond to abiotic stresses (drought, salinity, phosphorus deficiency and nitrogen deficiency).Our results will be helpful for further functional analysis of the NAC genes in physic nut.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.

ABSTRACT
The NAC proteins (NAM, ATAF1/2 and CUC2) are plant-specific transcriptional regulators that have a conserved NAM domain in the N-terminus. They are involved in various biological processes, including both biotic and abiotic stress responses. In the present study, a total of 100 NAC genes (JcNAC) were identified in physic nut (Jatropha curcas L.). Based on phylogenetic analysis and gene structures, 83 JcNAC genes were classified as members of, or proposed to be diverged from, 39 previously predicted orthologous groups (OGs) of NAC sequences. Physic nut has a single intron-containing NAC gene subfamily that has been lost in many plants. The JcNAC genes are non-randomly distributed across the 11 linkage groups of the physic nut genome, and appear to be preferentially retained duplicates that arose from both ancient and recent duplication events. Digital gene expression analysis indicates that some of the JcNAC genes have tissue-specific expression profiles (e.g. in leaves, roots, stem cortex or seeds), and 29 genes differentially respond to abiotic stresses (drought, salinity, phosphorus deficiency and nitrogen deficiency). Our results will be helpful for further functional analysis of the NAC genes in physic nut.

No MeSH data available.