Genome-Wide Identification, Characterization, and Transcriptional Profile of the HECT E3 Ubiquitin Ligase Gene Family in the Hard-Shelled Mussel Mytilus coruscus Gould
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of HECTs in M. coruscus
2.2. Bioinformatics Analysis of HECT Genes
2.3. Construction of Phylogenetic Tree
2.4. Collinearity Analysis
2.5. Subcellular Localization and Protein Structure Prediction
2.6. Characterization of HECT Gene Expression
3. Results
3.1. Identification and Characterization of HECT Gene Family Members in Mussel
3.2. Phylogenetic Analysis of the HECT Gene Family among Species
3.3. Analysis of Conserved Domains, Motif Discovery, and Gene Structures
3.4. Chromosomal Localization of the HECT Gene Family
3.5. Secondary Homology Modeling of HECT Protein Structures and Subcellular Localization
3.6. HECT Gene Colinearity Analysis
3.7. Analysis of HECT Gene Expression Patterns
3.8. Gene Ontology Analysis of the HECT Gene
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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No | Gene Name | Gene ID | CDSa Length | Protein Length | HECT Domain | Molecular Weight | Theoretical | Chromosome | Location |
---|---|---|---|---|---|---|---|---|---|
(bp) | (aa) | Location (aa) | (kDa) | pI | |||||
1 | Mco_NEDD4 | Maker00024065 | 1545 | 514 | 264–510 | 59,629.23 | 8.25 | chr8 | 11,448,585–11,509,784 |
2 | Mco_EDD1 | Maker00026964 | 6696 | 2231 | 1935–2228 | 245,120.18 | 5.43 | chr12 | 18,904,970–19,014,437 |
3 | Mco_UPL3 | Maker00035072 | 1608 | 535 | 450–532 | 60,513.88 | 4.62 | chr5 | 45,075,511–45,107,379 |
4 | Mco_HERC4 | Maker00002539 | 384 | 127 | 11–106 | 15,283.79 | 5.63 | chr10 | 81,621,876–81,717,176 |
5 | Mco_HERC1 | Maker00017428 | 9186 | 3061 | 2936–3022 | 338,818.36 | 5.84 | chr8 | 30,444,670–30,540,646 |
6 | Mco_AREL1 | Maker00023631 | 1536 | 511 | 183–509 | 58,122.03 | 5.58 | chr3 | 31,450,908–31,484,837 |
7 | Mco_UBE3A | Maker00027142 | 2118 | 705 | 556–675 | 79,286.27 | 5.69 | chr4 | 93,795,246–93,823,387 |
8 | Mco_HACE1 | Maker00030301 | 1266 | 421 | 194–414 | 47,852.62 | 5.63 | chr9 | 115,378,105–115,430,703 |
9 | Mco_SMURF2 | Maker00031130 | 2328 | 775 | 516–772 | 86,570.70 | 6.24 | chr10 | 2,742,196–2,791,928 |
10 | Mco_UPL1 | Maker00034862 | 1332 | 443 | 350–428 | 50,020.41 | 4.6 | chr1 | 56,026,608–56,033,160 |
11 | Mco_HUWE1 | Maker00035590 | 11,616 | 3871 | 3613–3868 | 427,315.87 | 5.16 | chr1 | 109,925,874–110,051,336 |
12 | Mco_UPL2 | Maker00001812 | 2172 | 723 | 578–653 | 82,200.81 | 5.26 | chr6 | 99,678,904–99,683,847 |
13 | Mco_UBE3C | Maker00001502 | 1821 | 606 | 350–604 | 69,595.05 | 5.36 | chr1 | 53,415,654–53,447,223 |
14 | Mco_HECTD1 | Maker00005002 | 2991 | 996 | 487–994 | 112,627.93 | 5.02 | chr3 | 99,488,382–99,510,834 |
15 | Mco_HECDT2 | Maker00005191 | 1056 | 351 | 139–348 | 39,778.40 | 9.29 | chr8 | 111,081,717–11,114,3368 |
16 | Mco_TRIP12 | Maker00005211 | 4692 | 1563 | 1254–1562 | 171,572.52 | 8.14 | chr3 | 135,995,715–136,168,882 |
17 | Mco_HECW1 | Maker00007292 | 1494 | 497 | 208–491 | 58,686.15 | 8.3 | chr2 | 109,062,131–109,097,211 |
18 | Mco_HECW2 | Maker00007303 | 4050 | 1349 | 992–1347 | 151,476.02 | 6.19 | chr2 | 108,953,278–108,963,278 |
19 | Mco_UBE3B | Maker00008133 | 1485 | 494 | 144–492 | 56,659.97 | 6.49 | chr7 | 102,429,555–102,469,658 |
20 | Mco_HECTD3 | Maker00011666 | 2274 | 757 | 511–715 | 87,274.83 | 5.54 | chr1 | 5,886,440–5,977,704 |
21 | Mco_WWP1 | Maker00013008 | 1371 | 456 | 137–454 | 54,119.19 | 6.37 | chr5 | 125,313,868–125,339,147 |
22 | Mco_HERC2 | Maker00015302 | 11,241 | 3746 | 3603–3722 | 412,033.61 | 5.92 | chr4 | 33,350,025–33,456,457 |
HECT Subfamily | Gene Name | Acc. No. | Presence in Bivalvia Species * |
---|---|---|---|
NEDD4 | Mco_NEDD4 | Maker00024065 | M. coruscus(5), M. galloprovincialis(4), C. gigas(4), R. philippinarum(1), M. yessoensis(4) |
Mco_SMURF2 | Maker00031130 | ||
Mco_WWP1 | Maker00013008 | ||
Mco_HECW1 | Maker00007292 | ||
Mco_HECW2 | Maker00007303 | ||
UPL1-3 | Mco_UPL1 | Maker00035072 | M. coruscus(3), M. galloprovincialis(0), C. gigas(0), R. philippinarum(2), M. yessoensis(0) |
Mco_UPL2 | Maker00034862 | ||
Mco_UPL3 | Maker00001812 | ||
HACE1 | Mco_HACE1 | Maker00030301 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
HUWE1 | Mco_HUWE1 | Maker00035590 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
KIAA0317 | Mco_AREL1 | Maker00023631 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
UBE3A/E6-AP | Mco_UBE3A | Maker00027142 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
SMALL HERCs | Mco_HERC4 | Maker00002539 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
UBE3B/3C | Mco_UBE3B | Maker00008133 | M. coruscus(2), M. galloprovincialis(1), C. gigas(2), R. philippinarum(1), M. yessoensis(2) |
Mco_UBE3C | Maker00001502 | ||
TRIP12 | Mco_TRIP12 | Maker00005211 | M. coruscus(1), M. galloprovincialis(0), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
HECTD1 | Mco_HECTD1 | Maker00005002 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
HECTD2 | Mco_HECDT2 | Maker00005191 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(0), M. yessoensis(1) |
HECTD3 | Mco_HECTD3 | Maker00011666 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
EDD/UBR5 | Mco_EDD1 | Maker00026964 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
G2E3 | Not found | Not found | M. coruscus(0), M. galloprovincialis(0), C. gigas(1), R. philippinarum(0), M. yessoensis(1) |
LARGE HERCs | Mco_HERC1 | Maker00017428 | M. coruscus(1), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
LARGE HERCs | Mco_HERC2 | Maker00015302 | M. coruscus(1), M. galloprovincialis(0), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
Not in any subfamily | M. coruscus(0), M. galloprovincialis(1), C. gigas(1), R. philippinarum(1), M. yessoensis(1) |
Proteins | Alpha | Beta | Random | Extended | Subcellular |
---|---|---|---|---|---|
Helix | Turn | Coil | Stand | Location Prediction | |
Mco_NEDD4 | 34.82% | 6.03% | 48.83% | 10.31% | Nucleus |
Mco_EDD1 | 34.02% | 6.28% | 42.94% | 16.76% | Cytoplasm |
Mco_UPL3 | 50.47% | 5.05% | 35.70% | 8.79% | Nucleus |
Mco_HERC4 | 53.54% | 5.51% | 25.98% | 14.96% | Cytoplasm |
Mco_HERC1 | 36.92% | 8.95% | 35.41% | 18.72% | Nucleus |
Mco_AREL1 | 40.90% | 4.89% | 34.44% | 19.77% | Cytoplasm |
Mco_UBE3A | 42.55% | 4.82% | 40.43% | 12.20% | Cytoplasm |
Mco_HACE1 | 44.66% | 4.51% | 35.87% | 14.96% | Cytoplasm |
Mco_SMURF2 | 19.23% | 8.26% | 51.35% | 21.16% | Nucleus |
Mco_UPL1 | 38.83% | 6.77% | 42.44% | 11.96% | Nucleus |
Mco_HUWE1 | 44.33% | 4.55% | 40.02% | 11.11% | Nucleus |
Mco_UPL2 | 41.63% | 4.98% | 40.39% | 13.00% | Plasma membrane |
Mco_UBE3C | 48.68% | 7.10% | 28.88% | 15.35% | Plasma membrane |
Mco_HECTD1 | 36.55% | 4.62% | 44.08% | 14.76% | Cytoplasm |
Mco_HECDT2 | 40.17% | 6.55% | 35.90% | 17.38% | Cytoplasm |
Mco_TRIP12 | 39.60% | 7.49% | 38.20% | 14.72% | Nucleus |
Mco_HECW1 | 50.30% | 5.43% | 33.60% | 10.66% | Mitochondria |
Mco_HECW2 | 28.54% | 5.86% | 51.22% | 14.38% | Nucleus |
Mco_UBE3B | 48.38% | 5.26% | 33.00% | 13.36% | Cytoplasm |
Mco_HECTD3 | 35.40% | 4.10% | 43.73% | 16.78% | Nucleus |
Mco_WWP1 | 37.28% | 6.80% | 41.01% | 14.91% | Cytoplasm |
Mco_HERC2 | 38.49% | 6.19% | 38.60% | 16.71% | Nucleus |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Guo, F.; Xin, Z.; Dong, Z.; Ye, Y. Genome-Wide Identification, Characterization, and Transcriptional Profile of the HECT E3 Ubiquitin Ligase Gene Family in the Hard-Shelled Mussel Mytilus coruscus Gould. Genes 2024, 15, 1085. https://doi.org/10.3390/genes15081085
Guo F, Xin Z, Dong Z, Ye Y. Genome-Wide Identification, Characterization, and Transcriptional Profile of the HECT E3 Ubiquitin Ligase Gene Family in the Hard-Shelled Mussel Mytilus coruscus Gould. Genes. 2024; 15(8):1085. https://doi.org/10.3390/genes15081085
Chicago/Turabian StyleGuo, Feng, Zhenqi Xin, Zhenyu Dong, and Yingying Ye. 2024. "Genome-Wide Identification, Characterization, and Transcriptional Profile of the HECT E3 Ubiquitin Ligase Gene Family in the Hard-Shelled Mussel Mytilus coruscus Gould" Genes 15, no. 8: 1085. https://doi.org/10.3390/genes15081085