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Genome-wide identification and expression analysis of ClLAX , ClPIN and ClABCB genes families in Citrullus lanatus under various abiotic stresses and grafting

View Article: PubMed Central - PubMed

ABSTRACT

Background: Auxin plays an important role in regulating plant growth and development as well as in the response of plants to abiotic stresses. Auxin is transported by three kinds of major protein families, including the AUXIN RESISTANT 1/LIKE AUX1 (AUX⁄LAX) influx carriers, the PIN-FORMED (PIN) efflux carriers and the ATP binding cassette B/P-glycoprotein/Multidrug-resistance (ABCB/MDR/PGP) efflux/condition carriers. The biological function of several auxin transporter genes has been well characterized in Arabidopsis thaliana. However, their function in response to exogenous auxin and abiotic stresses in watermelon (Citrullus lanatus. L) remained unknown.

Results: Here, the latest updated watermelon genome was used to characterise the ClLAX, ClPIN and ClABCB family genes from watermelon. The genome-wide analysis of the ClLAX, ClPIN and ClABCB family genes, including chromosome localisation, gene structure, and phylogenic relationships, was carried out. Seven ClLAXs, 11 ClPINs and 15 ClABCBs were mapped on 10 watermelon chromosomes. The expression profiles of the ClLAX, ClPIN and ClABCB genes under exogenous indole-3-acetic acid and various abiotic stresses (salt, drought, and cold stresses) treatments were performed by quantitative real-time PCR (qRT-PCR). The transcriptional level of majority ClLAX, ClPIN and ClABCB genes were changed by abiotic stresses in both shoots and roots. We also analysed the expression levels of ClLAX, ClPIN and ClABCB genes in graft response.

Conclusion: Analysis of the expression patterns of ClLAX, ClPIN and ClABCB genes under salt, drought, cold treatment and grafting response helps us to understand the possible roles of auxin transporter genes in watermelon adaptation to environmental stresses.

Electronic supplementary material: The online version of this article (doi:10.1186/s12863-017-0500-z) contains supplementary material, which is available to authorized users.

No MeSH data available.


Chromosomal distributionsand expansion patterns of ClLAX, ClPIN and ClABCB family genes in watermelon. a The genome visualization tool SyMAP Synteny Browser was employed to analyze the watermelon genome. Watermelon chromosomes were arranged in blocks. Seven ClLAX genes, 11 ClPIN genes and 15 ClABCB genes were mapped by locus. Red boxes presented the gene clusters. b Tandem duplicate ClABCB2/ClABCB3 and Four pairs of segmental duplicates ClABCB4/ClABCB13, ClABCB6/ClABCB8, ClABCB11/ClABCB14 were showed with dotted arrows. Scale bar represents 10 Mb
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Fig1: Chromosomal distributionsand expansion patterns of ClLAX, ClPIN and ClABCB family genes in watermelon. a The genome visualization tool SyMAP Synteny Browser was employed to analyze the watermelon genome. Watermelon chromosomes were arranged in blocks. Seven ClLAX genes, 11 ClPIN genes and 15 ClABCB genes were mapped by locus. Red boxes presented the gene clusters. b Tandem duplicate ClABCB2/ClABCB3 and Four pairs of segmental duplicates ClABCB4/ClABCB13, ClABCB6/ClABCB8, ClABCB11/ClABCB14 were showed with dotted arrows. Scale bar represents 10 Mb

Mentions: Based on position of ClLAX, ClPIN and ClABCB genes on the watermelon chromosomes, we mapped all 33 genes of ClLAX, ClPIN and ClABCB family on chromosomes (Fig. 1a, Table 1). The 33 genes were unevenly distributed on 10 out of the 11 watermelon chromosomes. Among 33 genes, not a single gene was located on chromosome 8. Chromosome 3 only contained one gene. Two genes were located on chromosome 1, 6 and 11, respectively. Three genes were distributed on each of chromosomes 4 and 7. Seven genes were located on chromosome 2 (Fig. 1a). In many plants, including S.bicolor, Arabidopsis, G.max, O.sativa, some of the auxin transporter genes were clustered. Three small gene clusters were identified in accord with the definition of gene clusters [55]. Two gene clusters were distributed on chromosome 2 (Fig. 1a). The other one was distributed on chromosome 7. The first gene cluster contained two ClABCB genes (ClABCB2 and ClABCB3). The second gene cluster contained two ClPIN genes (ClPIN2 and ClPIN3). The third gene cluster contained two ClPIN genes (ClPIN8 and ClPIN9).Fig. 1


Genome-wide identification and expression analysis of ClLAX , ClPIN and ClABCB genes families in Citrullus lanatus under various abiotic stresses and grafting
Chromosomal distributionsand expansion patterns of ClLAX, ClPIN and ClABCB family genes in watermelon. a The genome visualization tool SyMAP Synteny Browser was employed to analyze the watermelon genome. Watermelon chromosomes were arranged in blocks. Seven ClLAX genes, 11 ClPIN genes and 15 ClABCB genes were mapped by locus. Red boxes presented the gene clusters. b Tandem duplicate ClABCB2/ClABCB3 and Four pairs of segmental duplicates ClABCB4/ClABCB13, ClABCB6/ClABCB8, ClABCB11/ClABCB14 were showed with dotted arrows. Scale bar represents 10 Mb
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5384148&req=5

Fig1: Chromosomal distributionsand expansion patterns of ClLAX, ClPIN and ClABCB family genes in watermelon. a The genome visualization tool SyMAP Synteny Browser was employed to analyze the watermelon genome. Watermelon chromosomes were arranged in blocks. Seven ClLAX genes, 11 ClPIN genes and 15 ClABCB genes were mapped by locus. Red boxes presented the gene clusters. b Tandem duplicate ClABCB2/ClABCB3 and Four pairs of segmental duplicates ClABCB4/ClABCB13, ClABCB6/ClABCB8, ClABCB11/ClABCB14 were showed with dotted arrows. Scale bar represents 10 Mb
Mentions: Based on position of ClLAX, ClPIN and ClABCB genes on the watermelon chromosomes, we mapped all 33 genes of ClLAX, ClPIN and ClABCB family on chromosomes (Fig. 1a, Table 1). The 33 genes were unevenly distributed on 10 out of the 11 watermelon chromosomes. Among 33 genes, not a single gene was located on chromosome 8. Chromosome 3 only contained one gene. Two genes were located on chromosome 1, 6 and 11, respectively. Three genes were distributed on each of chromosomes 4 and 7. Seven genes were located on chromosome 2 (Fig. 1a). In many plants, including S.bicolor, Arabidopsis, G.max, O.sativa, some of the auxin transporter genes were clustered. Three small gene clusters were identified in accord with the definition of gene clusters [55]. Two gene clusters were distributed on chromosome 2 (Fig. 1a). The other one was distributed on chromosome 7. The first gene cluster contained two ClABCB genes (ClABCB2 and ClABCB3). The second gene cluster contained two ClPIN genes (ClPIN2 and ClPIN3). The third gene cluster contained two ClPIN genes (ClPIN8 and ClPIN9).Fig. 1

View Article: PubMed Central - PubMed

ABSTRACT

Background: Auxin plays an important role in regulating plant growth and development as well as in the response of plants to abiotic stresses. Auxin is transported by three kinds of major protein families, including the AUXIN RESISTANT 1/LIKE AUX1 (AUX⁄LAX) influx carriers, the PIN-FORMED (PIN) efflux carriers and the ATP binding cassette B/P-glycoprotein/Multidrug-resistance (ABCB/MDR/PGP) efflux/condition carriers. The biological function of several auxin transporter genes has been well characterized in Arabidopsis thaliana. However, their function in response to exogenous auxin and abiotic stresses in watermelon (Citrullus lanatus. L) remained unknown.

Results: Here, the latest updated watermelon genome was used to characterise the ClLAX, ClPIN and ClABCB family genes from watermelon. The genome-wide analysis of the ClLAX, ClPIN and ClABCB family genes, including chromosome localisation, gene structure, and phylogenic relationships, was carried out. Seven ClLAXs, 11 ClPINs and 15 ClABCBs were mapped on 10 watermelon chromosomes. The expression profiles of the ClLAX, ClPIN and ClABCB genes under exogenous indole-3-acetic acid and various abiotic stresses (salt, drought, and cold stresses) treatments were performed by quantitative real-time PCR (qRT-PCR). The transcriptional level of majority ClLAX, ClPIN and ClABCB genes were changed by abiotic stresses in both shoots and roots. We also analysed the expression levels of ClLAX, ClPIN and ClABCB genes in graft response.

Conclusion: Analysis of the expression patterns of ClLAX, ClPIN and ClABCB genes under salt, drought, cold treatment and grafting response helps us to understand the possible roles of auxin transporter genes in watermelon adaptation to environmental stresses.

Electronic supplementary material: The online version of this article (doi:10.1186/s12863-017-0500-z) contains supplementary material, which is available to authorized users.

No MeSH data available.