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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.


Related in: MedlinePlus

Expression profiles of the 39 HbAQP genes in laticifers, barks and leaves. Color scale represents FPKM normalized log2 transformed counts where green indicates low expression and red indicates high expression.
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Figure 5: Expression profiles of the 39 HbAQP genes in laticifers, barks and leaves. Color scale represents FPKM normalized log2 transformed counts where green indicates low expression and red indicates high expression.

Mentions: In the previous study, we reported the identification of 51 AQP genes from rubber tree genome, and focused on their response to ethephon stimulation in the rubber-producing tissue termed laticifer (Zou et al., 2015a) which is not found in physic nut and castor bean. To gain insights into the expression evolution of duplicated HbAQP genes, in the present study, we take advantage of deep transcriptome sequencing data to investigate their expression profiles in two more important tissues, i.e., bark and leaf (all counting about 25 M 100-nt paired-end reads). As shown in Figure 5, 39 out of 51 HbAQP genes representing all five subfamilies were detected in at least one of the examined tissues, though the expression of the XIP subfamily members was not observed in the laticifer. FPKM annotation indicated HbAQP genes were expressed most in barks, exhibiting 1.79 and 11.49 folds more than that in leaves and laticifers, respectively. As observed in castor bean and physic nut, PIPs represented the most abundant subfamily in all examined tissues: in barks, the total expression level of PIP members was 8.77, 95.51, 235.92, and 12,090.95 folds more than the TIP, SIP, NIP, or XIP members, respectively; 1.20, 2.70, 36.52, and 80.52 folds more than the XIP, TIP, NIP, or SIP members in leaves, respectively; and 116.11, 122.84, and 752.87 folds more than the SIP, TIP, or NIP members in laticifers, respectively (Figure 5). Nevertheless, compared with laticiferous cells that are characterized by a high number of polydispersed microvacuoles (Wang X. C. et al., 2013), cells of bark and mature leaf usually contain a large central vacuole and the role of HbPIPs is less important. Instead, the total TIP transcripts in barks and leaves were 147.25 and 135.28 folds more than that in laticifers, respectively. Compared with the PIPs, TIPs, and SIPs expressed more in barks, NIPs and XIPs were shown to be expressed more in leaves (Figure 5). It is worth noting that the expression level of HbXIP2;1 was particularly high in leaves, counting 99.98% of the total XIP transcripts. Similar expression pattern was also observed in physic nut and castor bean, where its orthologs JcXIP2;1 and RcXIP2;1 were shown to be preferentially expressed in leaves (Figure 4; Zou et al., 2015b). Compared with laticifers where three highly abundant PIP members (i.e., HbPIP2;7, HbPIP1;4, and HbPIP2;5) occupied 80.99% of the total PIP transcripts, seven PIPs (i.e., HbPIP1;2, HbPIP1;1, HbPIP2;4, HbPIP1;4, HbPIP2;7, HbPIP1;3, and HbPIP2;2) occupied 89.53% of the total PIP transcripts in barks, and seven abundant PIPs (i.e., HbPIP1;4, HbPIP1;3, HbPIP2;3, HbPIP2;4, HbPIP1;1, HbPIP2;6, and HbPIP1;2) occupied 83.57% of the total PIP transcripts in leaves. In barks, HbTIP1;2, HbTIP2;2, and HbTIP2;1 counted 73.04% of the total TIP transcripts; HbNIP5;1 and HbNIP1;2 counted 67.31% of the total NIP transcripts; HbSIP1;3 counted 56.32% of the total SIP transcripts. In leaves, HbTIP1;2, and HbTIP1;1 counted 81.44% of the total TIP transcripts; HbNIP6;1, HbNIP1;2, and HbNIP5;1 counted 92.39% of the total NIP transcripts; HbSIP1;3 and HbSIP2;1 counted 78.49% of the total SIP transcripts. Among 35 HbAQP genes detected in barks, HbPIP1;2, HbTIP1;2, HbNIP5;1, HbXIP2;1, and HbSIP1;3 represented the most abundant PIP, TIP, NIP, XIP, and SIP subfamily members, respectively. Among 36 HbAQP genes detected in leaves, HbPIP1;4, HbTIP1;2, HbNIP6;1, HbXIP2;1, and HbSIP1;3 represented the most abundant PIP, TIP, NIP, XIP, and SIP subfamily members, respectively (Figure 5).


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)

Expression profiles of the 39 HbAQP genes in laticifers, barks and leaves. Color scale represents FPKM normalized log2 transformed counts where green indicates low expression and red indicates high expression.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Expression profiles of the 39 HbAQP genes in laticifers, barks and leaves. Color scale represents FPKM normalized log2 transformed counts where green indicates low expression and red indicates high expression.
Mentions: In the previous study, we reported the identification of 51 AQP genes from rubber tree genome, and focused on their response to ethephon stimulation in the rubber-producing tissue termed laticifer (Zou et al., 2015a) which is not found in physic nut and castor bean. To gain insights into the expression evolution of duplicated HbAQP genes, in the present study, we take advantage of deep transcriptome sequencing data to investigate their expression profiles in two more important tissues, i.e., bark and leaf (all counting about 25 M 100-nt paired-end reads). As shown in Figure 5, 39 out of 51 HbAQP genes representing all five subfamilies were detected in at least one of the examined tissues, though the expression of the XIP subfamily members was not observed in the laticifer. FPKM annotation indicated HbAQP genes were expressed most in barks, exhibiting 1.79 and 11.49 folds more than that in leaves and laticifers, respectively. As observed in castor bean and physic nut, PIPs represented the most abundant subfamily in all examined tissues: in barks, the total expression level of PIP members was 8.77, 95.51, 235.92, and 12,090.95 folds more than the TIP, SIP, NIP, or XIP members, respectively; 1.20, 2.70, 36.52, and 80.52 folds more than the XIP, TIP, NIP, or SIP members in leaves, respectively; and 116.11, 122.84, and 752.87 folds more than the SIP, TIP, or NIP members in laticifers, respectively (Figure 5). Nevertheless, compared with laticiferous cells that are characterized by a high number of polydispersed microvacuoles (Wang X. C. et al., 2013), cells of bark and mature leaf usually contain a large central vacuole and the role of HbPIPs is less important. Instead, the total TIP transcripts in barks and leaves were 147.25 and 135.28 folds more than that in laticifers, respectively. Compared with the PIPs, TIPs, and SIPs expressed more in barks, NIPs and XIPs were shown to be expressed more in leaves (Figure 5). It is worth noting that the expression level of HbXIP2;1 was particularly high in leaves, counting 99.98% of the total XIP transcripts. Similar expression pattern was also observed in physic nut and castor bean, where its orthologs JcXIP2;1 and RcXIP2;1 were shown to be preferentially expressed in leaves (Figure 4; Zou et al., 2015b). Compared with laticifers where three highly abundant PIP members (i.e., HbPIP2;7, HbPIP1;4, and HbPIP2;5) occupied 80.99% of the total PIP transcripts, seven PIPs (i.e., HbPIP1;2, HbPIP1;1, HbPIP2;4, HbPIP1;4, HbPIP2;7, HbPIP1;3, and HbPIP2;2) occupied 89.53% of the total PIP transcripts in barks, and seven abundant PIPs (i.e., HbPIP1;4, HbPIP1;3, HbPIP2;3, HbPIP2;4, HbPIP1;1, HbPIP2;6, and HbPIP1;2) occupied 83.57% of the total PIP transcripts in leaves. In barks, HbTIP1;2, HbTIP2;2, and HbTIP2;1 counted 73.04% of the total TIP transcripts; HbNIP5;1 and HbNIP1;2 counted 67.31% of the total NIP transcripts; HbSIP1;3 counted 56.32% of the total SIP transcripts. In leaves, HbTIP1;2, and HbTIP1;1 counted 81.44% of the total TIP transcripts; HbNIP6;1, HbNIP1;2, and HbNIP5;1 counted 92.39% of the total NIP transcripts; HbSIP1;3 and HbSIP2;1 counted 78.49% of the total SIP transcripts. Among 35 HbAQP genes detected in barks, HbPIP1;2, HbTIP1;2, HbNIP5;1, HbXIP2;1, and HbSIP1;3 represented the most abundant PIP, TIP, NIP, XIP, and SIP subfamily members, respectively. Among 36 HbAQP genes detected in leaves, HbPIP1;4, HbTIP1;2, HbNIP6;1, HbXIP2;1, and HbSIP1;3 represented the most abundant PIP, TIP, NIP, XIP, and SIP subfamily members, respectively (Figure 5).

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.


Related in: MedlinePlus