Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants
Abstract
:1. Introduction
2. Results
2.1. Identification of VHA-H Gene Family Members in the Main Crops
2.2. Protein Sequence Alignments and Phylogenetic and Motif Analyses
2.3. Structures of the VHA-H Genes
2.4. Splice Variants of VHA-H Genes
2.5. Analysis of Cis-acting Elements of VHA-H Promoters
2.6. Tissue-Specific Expression Patterns of VHA-H Genes
3. Discussion
3.1. Identification of V-ATPase Subunit H Genes in the Main Crops
3.2. Protein Sequence Alignments and Phylogenetic and Motif Analyses
3.3. Gene Structural Diversity
3.4. Splice Variants
3.5. Cis-Acting Elements of the VHA-H Promoters
3.6. Tissue-Specific Expression Patterns of VHA-H Genes
4. Materials and Methods
4.1. Identification of VHA-H Genes
4.2. Phylogenetic and Protein Motif Analyses
4.3. Gene Structure of VHA-H Genes
4.4. Splice Variants of VHA-H Genes
4.5. Analysis of cis-acting Elements of VHA-H Promoters
4.6. Tissue-Specific Expression Patterns of VHA-H Genes
5. Conclusions
Author Contributions
Acknowledgments
Conflicts of Interest
Abbreviations
V-ATPase | vacuolar H+-ATPase |
VHA-H | V-ATPase subunit H |
UTRs | Untranslated regions |
ABA | Abscisic acid |
OPR | 12-oxo-phytodienoic acid reductase |
ORF | open reading frame |
aa | amino acid |
GA | gibberellin |
SA | salicylic acid |
MeJA | methyl jasmonate |
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Gene | Species | Ensembl ID | Chromosome: Locations | ORF Length (bp) | No. of Exon | Deduced Polypeptide | ||
---|---|---|---|---|---|---|---|---|
Length (aa) | MW (Da) | PI | ||||||
AtVHA-H | Arabidopsis thaliana | AT3G42050 | 3: 14,229,669−14,233,441 | 1326 | 11 | 441 | 50284.42 | 6.58 |
GrVHA-H1 | Gossypium raimondii | B456_003G056300 | 3: 9,065,281−9,069,803 | 1392 | 11 | 463 | 52652.25 | 7.55 |
GrVHA-H2 | B456_004G256400 | 4: 59,286,789−59,291,565 | 1446 | 12 | 481 | 54453.38 | 6.48 | |
OsiVHA-H | Oryza sativa Indica Group | BGIOSGA025913 | 7: 19,885,495−19,891,284 | 1488 | 12 | 495 | 56165.18 | 9.07 |
BnVHA-H1 | Brassica napus | BnaA01g02950D | A1: 1,436,042−1,439,972 | 1359 | 11 | 452 | 51168.20 | 6.40 |
BnVHA-H2 | BnaA03g50930D | A3: 26,436,023−26,439,323 | 1353 | 11 | 450 | 51179.39 | 6.25 | |
BnVHA-H3 | BnaA08g11340D | A8: 10,300,929−10,304,240 | 1407 | 13 | 468 | 54010.52 | 6.36 | |
BnVHA-H4 | BnaC01g04210D | C1: 2,192,503−2,196,646 | 1359 | 11 | 452 | 51151.19 | 6.58 | |
BnVHA-H5 | BnaC03g77060D | C3: 5,609,855−5,617,966 | 1380 | 14 | 459 | 52350.47 | 7.13 | |
BnVHA-H6 | BnaC07g44770D | C7: 43,161,725−43,165,037 | 1353 | 11 | 450 | 51191.44 | 6.25 | |
BvVHA-H | Beta vulgaris | BVRB_4g074640 | 4: 3,654,561−3,661,113 | 1398 | 11 | 465 | 52980.14 | 7.07 |
GmVHA-H1 | Glycine max | GLYMA_02G059800 | 2: 5,381,068−5,387,111 | 1347 | 11 | 448 | 51058.20 | 6.53 |
GmVHA-H2 | GLYMA_16G142600 | 16: 30,131,160−30,136,817 | 1347 | 11 | 448 | 51004.12 | 6.48 | |
HvVHA-H | Hordeum vulgare | HORVU2Hr1G042700 | 2H: 214,952,610−214,958,367 | 1359 | 11 | 452 | 51420.65 | 7.58 |
StVHA-H1 | Solanum tuberosum | PGSC0003DMG400007911 | 12: 2,431,205−2,438,621 | 1365 | 11 | 454 | 51347.52 | 6.36 |
StVHA-H2 | PGSC0003DMG401011206 | 7: 1,259,585−1,265,564 | 1365 | 11 | 454 | 51545.58 | 6.43 | |
SiVHA-H | Setaria italica | SETIT_029790mg | II: 42,735,808−42,741,948 | 1377 | 12 | 458 | 52115.37 | 6.76 |
SbVHA-H | Sorghum bicolor | SORBI_3004G347600 | 4: 67,696,418−67,701,157 | 1452 | 12 | 483 | 55159.96 | 7.56 |
TaVHA-H1 | Triticum aestivum | TraesCS2A02G212100 | 2A: 196,521,667−196,527,664 | 1359 | 11 | 452 | 51412.63 | 7.57 |
TaVHA-H2 | TraesCS2B02G237200 | 2B: 237,967,455−237,974,014 | 1359 | 11 | 452 | 51382.58 | 7.98 | |
TaVHA-H3 | TraesCS2D02G218000 | 2D: 181,306,271−181,312,853 | 1359 | 11 | 452 | 51426.61 | 7.57 | |
ZmVHA-H1 | Zea mays | Zm00001d006565 | 2: 211,028,576−211,035,348 | 1359 | 11 | 452 | 51428.57 | 7.55 |
ZmVHA-H2 | Zm00001d021721 | 7: 161,424,744−161,430,332 | 1359 | 11 | 452 | 51554.77 | 7.56 |
Number | Motif Logo | E-value | Site Count | Number of aa |
---|---|---|---|---|
Motif 1 | 5.6 × 10−1013 | 23 | 50 | |
Motif 2 | 2.1 × 10−981 | 24 | 50 | |
Motif 3 | 2.8 × 10−889 | 23 | 50 | |
Motif 4 | 4.8 × 10−939 | 24 | 50 | |
Motif 5 | 3.9 × 10−886 | 24 | 50 | |
Motif 6 | 3.7 × 10−823 | 22 | 50 | |
Motif 7 | 3.1 × 10−669 | 22 | 41 | |
Motif 8 | 3.4 × 10−475 | 22 | 29 | |
Motif 9 | 8.6 × 10−260 | 22 | 21 | |
Motif 10 | 5.6 × 10−179 | 23 | 11 | |
Motif 11 | 4.1 × 10−116 | 23 | 11 | |
Motif 12 | 5.3 × 10−105 | 22 | 8 | |
Motif 13 | 2.4 × 10−081 | 24 | 8 | |
Motif 14 | 8.6 × 10−061 | 23 | 8 | |
Motif 15 | 4.9 × 10002 | 2 | 12 |
Gene | Transcript | Ensembl Transcript ID | Predicted Amino Acid Length (aa) | Spliced Exon | Status |
---|---|---|---|---|---|
GrVHA-H2 | GrVHA-H2.1 | KJB26715 | 481 | Wild type | |
GrVHA-H2.2 | KJB26714 | 351 | Exon 1 | Alternative 5′ donor site | |
Exon 3 | Alternative 3′ acceptor site | ||||
Exons 4-7 | Exon skipping | ||||
Exon 12 | Alternative 3′ acceptor site | ||||
HvVHA-H | HvVHA-H.1 | HORVU2Hr1G042700.1 | 452 | Wild type | |
HvVHA-H.2 | HORVU2Hr1G042700.2 | 452 | Exon 1 (5′ UTR) | Alternative 5′ donor site | |
Exon 12 (3′ UTR) | Mutually exclusive exons | ||||
HvVHA-H.3 | HORVU2Hr1G042700.3 | 452 | Exon 1 (5′ UTR) | Alternative 5′ donor site | |
Exon 12 (3′ UTR) | Mutually exclusive exons | ||||
HvVHA-H.4 | HORVU2Hr1G042700.4 | 450 | Exon 1 (5′ UTR) | Alternative 5′ donor site | |
Exon 11 | Mutually exclusive exons | ||||
Exon 12 (3′ UTR) | Exon skipping | ||||
HvVHA-H.5 | HORVU2Hr1G042700.5 | 494 | Exon 1 (5′ UTR) | Alternative 5′ donor site | |
Exon 10 | Alternative 3′ acceptor site | ||||
Exons 11-12 (3′ UTR) | Exon skipping | ||||
HvVHA-H.6 | HORVU2Hr1G042700.6 | 110 | Exon 1 (5′ UTR) | Exon skipping | |
Exons 2-7 | Exon skipping | ||||
Exons 10 | Alternative 3′ acceptor site | ||||
Exons 11-12 (3′ UTR) | Exon skipping | ||||
HvVHA-H.7 | HORVU2Hr1G042700.7 | 109 | Exon 1 (5′ UTR) | Exon skipping | |
Exons 2-7 | Exon skipping | ||||
Exon 11 (3′ UTR) | Mutually exclusive exons | ||||
Exon 12 (3′ UTR) | Exon skipping | ||||
StVHA-H2 | StVHA-H2.1 | PGSC0003DMT400029149 | 454 | Wild type | |
StVHA-H2.2 | PGSC0003DMT400029148 | 454 | Exon 8 | Mutually exclusive exons | |
Exon 12 (3′ UTR) | Exon skipping | ||||
StVHA-H2.3 | PGSC0003DMT400029147 | 454 | Exon 12 (3′ UTR) | Exon skipping | |
StVHA-H2.4 | PGSC0003DMT400029150 | 369 | Exon 9 (3′ UTR) | Mutually exclusive exons | |
Exons 10-11 | Exon skipping | ||||
Exons 12-13 (3′ UTR) | Exon skipping | ||||
StVHA-H2.5 | PGSC0003DMT400029145 | 144 | Exons 1 (5′ UTR) | Exon skipping | |
Exons 2-7 | Exon skipping | ||||
Exon 8 | Alternative 5′ donor site | ||||
Retained one exon between exons 8 and 9 | Exon skipping | ||||
Exon 11 (3′ UTR) | Alternative 3′ acceptor site | ||||
Exon 12, 13 (3′ UTR) | Exon skipping | ||||
SiVHA-H | SiVHA-H.1 | KQL26169 | 458 | Wild type | |
SiVHA-H.2 | KQL26168 | 404 | Exon 1 (5′ UTR) | Alternative 5′ donor site | |
Exon 12 (3′ UTR) | Mutually exclusive exons | ||||
TaVHA-H1 | TaVHA-H1.1 | TraesCS2A02G212100.2 | 452 | Wild type | |
TaVHA-H1.2 | TraesCS2A02G212100.1 | 455 | Exon 12 | Mutually exclusive exons | |
Exon 13 (3′ UTR) | Exon skipping | ||||
ZmVHA-H1 | ZmVHA-H1.1 | Zm00001d006565_T002 | 452 | Wild type | |
ZmVHA-H1.2 | Zm00001d006565_T001 | 379 | Exons 4-6 | Exon skipping | |
Exon 7 | Alternative 5′ donor site | ||||
ZmVHA-H1.3 | Zm00001d006565_T003 | 431 | Exons 1-2 (5′ UTR) | Exon skipping | |
ZmVHA-H2 | ZmVHA-H2.1 | Zm00001d021721_T003 | 452 | Wild type | |
ZmVHA-H2.2 | Zm00001d021721_T001 | 464 | Retained two exons between exons 3 and 4 | Exon skipping | |
Exon 5 | Exon skipping | ||||
ZmVHA-H2.3 | Zm00001d021721_T002 | 461 | Retained two exons between exons 3 and 4 | Exon skipping | |
Exon 5 | Exon skipping | ||||
Exon 6 | Alternative 3′ acceptor site | ||||
Exon 7 | Alternative 5′ donor site | ||||
ZmVHA-H2.4 | Zm00001d021721_T004 | 199 | Exons 1-2 (5′ UTR) | Exon skipping | |
Retained exon between exons 2 and 3 (5′ UTR) | Exon skipping | ||||
Introns 3-5 (5′ UTR) | Intron retention | ||||
ZmVHA-H2.5 | Zm00001d021721_T005 | 431 | Exons 1-2 (5′ UTR) | Exon skipping |
Species | VHA-H1 | VHA-H2 | VHA-H3 | VHA-H4 | VHA-H5 | VHA-H6 |
---|---|---|---|---|---|---|
Gossypium raimondii | 1 | 2 | ||||
Oryza sativa (Indica Group) | 1 | |||||
Brassica napus | 1 | 1 | 1 | 1 | 1 | 1 |
Beta vulgaris | 1 | |||||
Glycine max | 1 | 1 | ||||
Hordeum vulgare | 6 | |||||
Solanum tuberosum | 1 | 4 | ||||
Setaria italica | 2 | |||||
Sorghum bicolor | 1 | |||||
Triticum aestivum | 2 | 1 | 1 | |||
Zea mays | 3 | 5 |
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Kang, C.; Sun, F.; Yan, L.; Li, R.; Bai, J.; Caetano-Anollés, G. Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants. Int. J. Mol. Sci. 2019, 20, 5125. https://doi.org/10.3390/ijms20205125
Kang C, Sun F, Yan L, Li R, Bai J, Caetano-Anollés G. Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants. International Journal of Molecular Sciences. 2019; 20(20):5125. https://doi.org/10.3390/ijms20205125
Chicago/Turabian StyleKang, Chen, Fengjie Sun, Lei Yan, Rui Li, Jianrong Bai, and Gustavo Caetano-Anollés. 2019. "Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants" International Journal of Molecular Sciences 20, no. 20: 5125. https://doi.org/10.3390/ijms20205125