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Genome-Wide Identification of Jatropha curcas Aquaporin Genes and the Comparative Analysis Provides Insights into the Gene Family Expansion and Evolution in Hevea brasiliensis.

Zou Z, Yang L, Gong J, Mo Y, Wang J, Cao J, An F, Xie G - Front Plant Sci (2016)

Bottom Line: Arg.).Genome-wide comparative analysis revealed the specific expansion of PIP and TIP subfamilies in rubber tree and the specific gene loss of the XIP subfamily in physic nut.Results obtained from this study not only provide valuable information for future functional analysis and utilization of Jc/HbAQP genes, but also provide a useful reference to survey the gene family expansion and evolution in Euphorbiaceae plants and other plant species.

View Article: PubMed Central - PubMed

Affiliation: Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences Danzhou, China.

ABSTRACT
Aquaporins (AQPs) are channel-forming integral membrane proteins that transport water and other small solutes across biological membranes. Despite the vital role of AQPs, to date, little is known in physic nut (Jatropha curcas L., Euphorbiaceae), an important non-edible oilseed crop with great potential for the production of biodiesel. In this study, 32 AQP genes were identified from the physic nut genome and the family number is relatively small in comparison to 51 in another Euphorbiaceae plant, rubber tree (Hevea brasiliensis Muell. Arg.). Based on the phylogenetic analysis, the JcAQPs were assigned to five subfamilies, i.e., nine plasma membrane intrinsic proteins (PIPs), nine tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and four small basic intrinsic proteins (SIPs). Like rubber tree and other plant species, functional prediction based on the aromatic/arginine selectivity filter, Froger's positions, and specificity-determining positions showed a remarkable difference in substrate specificity among subfamilies of JcAQPs. Genome-wide comparative analysis revealed the specific expansion of PIP and TIP subfamilies in rubber tree and the specific gene loss of the XIP subfamily in physic nut. Furthermore, by analyzing deep transcriptome sequencing data, the expression evolution especially the expression divergence of duplicated HbAQP genes was also investigated and discussed. Results obtained from this study not only provide valuable information for future functional analysis and utilization of Jc/HbAQP genes, but also provide a useful reference to survey the gene family expansion and evolution in Euphorbiaceae plants and other plant species.

No MeSH data available.


Exon-intron structures of the 32 JcAQP genes. The graphic representation of the gene models is displayed using GSDS.
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Figure 3: Exon-intron structures of the 32 JcAQP genes. The graphic representation of the gene models is displayed using GSDS.

Mentions: The exon-intron structures of 32 JcAQPs were analyzed based on the optimized gene models. Although the ORF (open reading frame) length of each gene is consistent (639–924 bp, similar to 627–830 bp in castor bean, and 684–927 bp in rubber tree), the gene size (from start to stop codons) is distinct (729–6716 bp, longer than 705–4934 bp in castor bean and shorter than 720–13,833 bp in rubber tree) (Table 2 and Figure 3; Zou et al., 2015a,b). The JcAQP introns have an average length of about 380 bp (same as that in castor bean but relatively shorter than 404 bp in rubber tree), with the minimum of 63 bp in JcNIP4;1 (corresponding to 46 bp in RcPIP2;5 and 71 bp in HbNIP2;1) and the maximum of 5879 bp in JcSIP2;1 (corresponding to 3360 bp in RcNIP5;1 and 13,000 bp in HbSIP2;1) (Figure 3; Zou et al., 2015a,b). Like observed in rubber tree and castor bean (Zou et al., 2015a,b), AQP genes in different subfamilies harbor distinct exon-intron structures. Except for JcPIP1;3 that contains four introns, other JcPIP subfamily members feature three introns (83–481, 90–1751, and 87–487 bp, respectively). It is worth noting that JcPIP1;3 is more likely to be a pseudogene, because no evidence is available for its expression and a C deletion at the 82th position and an A/T mutation at the 456th position were observed when compared with other JcPIP1 genes. Most JcTIPs contain two introns (75–302 bp and 77–372 bp, respectively), while JcTIP1;1 and JcTIP1;4 contain only one intron. Most JcNIPs harbor four introns (70–1063, 72–957, 79–980, and 88–262 bp, respectively), whereas JcNIP5;1 contain three introns instead. Two out of three JcSIP1s don't contain introns, in contrast, JcSIP1;3 and the only JcSIP2 subgroup member JcSIP2;1 harbor two introns. The two identified JcXIP subfamily members JcXIP1;1 and JcXIP2;1 contain one or two introns, respectively (Figure 3).


Genome-Wide Identification of Jatropha curcas Aquaporin Genes and the Comparative Analysis Provides Insights into the Gene Family Expansion and Evolution in Hevea brasiliensis.

Zou Z, Yang L, Gong J, Mo Y, Wang J, Cao J, An F, Xie G - Front Plant Sci (2016)

Exon-intron structures of the 32 JcAQP genes. The graphic representation of the gene models is displayed using GSDS.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814485&req=5

Figure 3: Exon-intron structures of the 32 JcAQP genes. The graphic representation of the gene models is displayed using GSDS.
Mentions: The exon-intron structures of 32 JcAQPs were analyzed based on the optimized gene models. Although the ORF (open reading frame) length of each gene is consistent (639–924 bp, similar to 627–830 bp in castor bean, and 684–927 bp in rubber tree), the gene size (from start to stop codons) is distinct (729–6716 bp, longer than 705–4934 bp in castor bean and shorter than 720–13,833 bp in rubber tree) (Table 2 and Figure 3; Zou et al., 2015a,b). The JcAQP introns have an average length of about 380 bp (same as that in castor bean but relatively shorter than 404 bp in rubber tree), with the minimum of 63 bp in JcNIP4;1 (corresponding to 46 bp in RcPIP2;5 and 71 bp in HbNIP2;1) and the maximum of 5879 bp in JcSIP2;1 (corresponding to 3360 bp in RcNIP5;1 and 13,000 bp in HbSIP2;1) (Figure 3; Zou et al., 2015a,b). Like observed in rubber tree and castor bean (Zou et al., 2015a,b), AQP genes in different subfamilies harbor distinct exon-intron structures. Except for JcPIP1;3 that contains four introns, other JcPIP subfamily members feature three introns (83–481, 90–1751, and 87–487 bp, respectively). It is worth noting that JcPIP1;3 is more likely to be a pseudogene, because no evidence is available for its expression and a C deletion at the 82th position and an A/T mutation at the 456th position were observed when compared with other JcPIP1 genes. Most JcTIPs contain two introns (75–302 bp and 77–372 bp, respectively), while JcTIP1;1 and JcTIP1;4 contain only one intron. Most JcNIPs harbor four introns (70–1063, 72–957, 79–980, and 88–262 bp, respectively), whereas JcNIP5;1 contain three introns instead. Two out of three JcSIP1s don't contain introns, in contrast, JcSIP1;3 and the only JcSIP2 subgroup member JcSIP2;1 harbor two introns. The two identified JcXIP subfamily members JcXIP1;1 and JcXIP2;1 contain one or two introns, respectively (Figure 3).

Bottom Line: Arg.).Genome-wide comparative analysis revealed the specific expansion of PIP and TIP subfamilies in rubber tree and the specific gene loss of the XIP subfamily in physic nut.Results obtained from this study not only provide valuable information for future functional analysis and utilization of Jc/HbAQP genes, but also provide a useful reference to survey the gene family expansion and evolution in Euphorbiaceae plants and other plant species.

View Article: PubMed Central - PubMed

Affiliation: Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences Danzhou, China.

ABSTRACT
Aquaporins (AQPs) are channel-forming integral membrane proteins that transport water and other small solutes across biological membranes. Despite the vital role of AQPs, to date, little is known in physic nut (Jatropha curcas L., Euphorbiaceae), an important non-edible oilseed crop with great potential for the production of biodiesel. In this study, 32 AQP genes were identified from the physic nut genome and the family number is relatively small in comparison to 51 in another Euphorbiaceae plant, rubber tree (Hevea brasiliensis Muell. Arg.). Based on the phylogenetic analysis, the JcAQPs were assigned to five subfamilies, i.e., nine plasma membrane intrinsic proteins (PIPs), nine tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and four small basic intrinsic proteins (SIPs). Like rubber tree and other plant species, functional prediction based on the aromatic/arginine selectivity filter, Froger's positions, and specificity-determining positions showed a remarkable difference in substrate specificity among subfamilies of JcAQPs. Genome-wide comparative analysis revealed the specific expansion of PIP and TIP subfamilies in rubber tree and the specific gene loss of the XIP subfamily in physic nut. Furthermore, by analyzing deep transcriptome sequencing data, the expression evolution especially the expression divergence of duplicated HbAQP genes was also investigated and discussed. Results obtained from this study not only provide valuable information for future functional analysis and utilization of Jc/HbAQP genes, but also provide a useful reference to survey the gene family expansion and evolution in Euphorbiaceae plants and other plant species.

No MeSH data available.