Genome-Wide Identification and Analysis of the GRAS Transcription Factor Gene Family in Theobroma cacao
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of GRAS Gene Family in T. cacao
2.2. Physicochemical Properties and Subcellular Localization Analyses of TcGRAS Genes
2.3. Phylogenetic Analysis and Classification of TcGRAS Genes
2.4. Gene Structure and Conserved Motif Analyses of TcGRAS Genes
2.5. Chromosomal Mapping and Cis-Acting Regulatory Analyses of TcGRAS Genes
2.6. Gene Duplication and Synteny Analyses of TcGRAS Genes
2.7. GO Annotation Analyses of T. cacao TcGRAS Genes
3. Results
3.1. Identification of GRAS Members in T. cacao
3.2. Phylogenetic Analysis of TcGRAS and AtGRAS
3.3. Gene Structure, Conserved Motifs, and Domain Analyses of TcGRAS Genes
3.4. Chromosomal Mapping and Cis-Acting Regulatory Analyses of TcGRAS Genes
3.5. Gene Duplication and Syntenic Analysis of TcGRAS Genes
3.6. GO Annotation of T.cacao TcGRAS Proteins
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Subfamily | Function | Species | Classified Subfamilies | Reference |
---|---|---|---|---|---|
HAM | HAM | Maintenance of stems | Petunia hybrida | unclassified | [17] |
LISCL | LISCL | Regulating the transcription process during microsporogenesis | Lilium longiflorum | unclassified | [18] |
Ls | LAS | Initiation of the axillary meristem | tomato | HAM, LAS, SCL4/7, SCR, SCL9, SCL28, DELLA, SHR, PAT1, Os4, Os19, GRAS37, and Pt20 | [19] |
PeSCL7 | SCL4/7 | Enhanced drought tolerance and salt tolerance of transgenic Arabidopsis plants | Populus euphratica | unclassified | [20] |
AtSCR | SCR | Involved in radial root morphology and growth | A. thaliana | HAM, LISCL, LAS, SCL4/7, SCR, DLT, SCL3, DELLA, SHR, and PAT1 | [4] |
AtSHR | SHR | Involved in radial root morphology and growth | A. thaliana | HAM, LISCL, LAS, SCL4/7, SCR, DLT, SCL3, DELLA, SHR, and PAT1 | [21] |
PtSHR1 | SHR | Increased growth rates | Populus tomentosa | Os19, HAM, Os4, Pt20, DLT, AtSCl3, AtSHR, AtPAT1, AtSCR, AtSCL4/7, AtLAS, DELLA, and LISCL | [22] |
DLT | DLT | Involved in brassinoltone signaling | rice | LISCL, SHR, DELLA, SCL3, PAT1, SCR, SCL4/7, LAS, Os19, HAM, Os4, and DLT | [23] |
AtSCL3 | SCL3 | Integrated multiple signals during Arabidopsis root cell elongation | A. thaliana | HAM, LISCL, LAS, SCL4/7, SCR, DLT, SCL3, DELLA, SHR, and PAT1 | [24] |
AtRGA | DELLA | Modulated jasmonate signaling via competitive binding to JAZs | A. thaliana | HAM, LISCL, LAS, SCL4/7, SCR, DLT, SCL3, DELLA, SHR, and PAT1 | [25] |
BdSLR1 BdSLRL1 | DELLA | Play a role in plant growth via the GA signal pathway | Brachypodium distachyon | HAM, PAT1, SHR, DELLA, SCL3, SCL4/7, LAS, SCR, DLT, and LISCL | [12] |
AtPAT1 | PAT1 | Involved in signaling in Arabidopsis photochromes | A. thaliana | HAM, LISCL, LAS, SCL4/7, SCR, DLT, SCL3, DELLA, SHR, and PAT1 | [26] |
GmGRAS37 | PAT1 | Improved resistance to drought and salt stresses | soybean | AtSCL4/7, Os19, Os4, HAM, DELLA, DLT, AtPAT1, LISCL, AtSCR, AtSCL3, and AtSHR | [10] |
StGRAS9 | PAT1 | Responded to plant hormones IAA, ABA, and GA3 treatment | potato | DELLA, LAS, HAM, PATI, SCR, LISCL, SHR, and SCL3 | [13] |
Gene Name | Gene ID | Physicochemical Characteristics | SL | ORF | ||||
---|---|---|---|---|---|---|---|---|
PI | MW (Da) | Length (aa) | Instability Index | Aliphatic Index | ||||
TcGRAS1 | TCM_000399 | 5.00 | 67,286.55 | 608 | 54.24 | 81.73 | endomembrane system | 1827 |
TcGRAS2 | TCM_000435 | 6.80 | 77,476.49 | 684 | 50.67 | 84.71 | nucleus | 2055 |
TcGRAS3 | TCM_000764 | 5.46 | 50,905.28 | 456 | 41.68 | 92.43 | chloroplast | 1371 |
TcGRAS4 | TCM_000801 | 5.59 | 57,001.87 | 505 | 52.26 | 70.32 | chloroplast | 1518 |
TcGRAS5 | TCM_002021 | 5.42 | 48,046.37 | 441 | 56.70 | 91.54 | nucleus | 1326 |
TcGRAS6 | TCM_002319 | 5.57 | 63,858.30 | 569 | 55.85 | 79.17 | nucleus | 1710 |
TcGRAS7 | TCM_003984 | 5.84 | 57,336.13 | 511 | 44.83 | 83.99 | nucleus | 1536 |
TcGRAS8 | TCM_004818 | 6.15 | 63,796.67 | 565 | 31.39 | 85.91 | nucleus | 1698 |
TcGRAS9 | TCM_005571 | 5.41 | 79,449.91 | 730 | 62.24 | 84.47 | nucleus | 2193 |
TcGRAS10 | TCM_007806 | 5.31 | 49,737.63 | 445 | 43.06 | 88.97 | chloroplast | 1338 |
TcGRAS11 | TCM_010708 | 6.38 | 56,277.83 | 499 | 47.40 | 92.06 | nucleus | 1500 |
TcGRAS12 | TCM_010965 | 5.66 | 67,186.67 | 615 | 39.21 | 80.93 | nucleus | 1848 |
TcGRAS13 | TCM_014574 | 6.04 | 57,510.78 | 519 | 52.58 | 90.02 | nucleus | 1560 |
TcGRAS14 | TCM_015228 | 5.76 | 67,975.59 | 628 | 45.58 | 77.82 | nucleus | 1887 |
TcGRAS15 | TCM_015991 | 5.69 | 87,113.44 | 795 | 55.54 | 80.34 | nucleus | 2388 |
TcGRAS16 | TCM_016186 | 5.68 | 74,493.64 | 671 | 52.33 | 79.79 | nucleus | 2016 |
TcGRAS17 | TCM_017269 | 5.67 | 72,460.97 | 654 | 53.85 | 78.35 | nucleus | 1965 |
TcGRAS18 | TCM_017746 | 5.88 | 86,321.23 | 795 | 53.09 | 81.66 | nucleus | 2388 |
TcGRAS19 | TCM_018964 | 6.92 | 46,686.93 | 418 | 44.25 | 94.07 | nucleus | 1257 |
TcGRAS20 | TCM_019165 | 5.27 | 71,951.43 | 655 | 49.47 | 81.62 | nucleus | 1968 |
TcGRAS21 | TCM_019414 | 5.43 | 39,709.90 | 347 | 49.00 | 94.96 | nucleus | 1044 |
TcGRAS22 | TCM_019956 | 6.08 | 191,183.51 | 1659 | 47.01 | 80.49 | nucleus | 4980 |
TcGRAS23 | TCM_019978 | 5.82 | 51,125.89 | 457 | 46.55 | 79.63 | chloroplast | 1374 |
TcGRAS24 | TCM_021350 | 5.67 | 50,849.34 | 457 | 33.62 | 93.09 | nucleus | 1374 |
TcGRAS25 | TCM_021351 | 5.08 | 67,410.79 | 600 | 47.40 | 83.42 | nucleus | 1803 |
TcGRAS26 | TCM_021618 | 4.86 | 61,003.74 | 538 | 49.81 | 70.91 | nucleus | 1617 |
TcGRAS27 | TCM_021920 | 6.17 | 85,337.10 | 755 | 52.92 | 73.09 | nucleus | 2268 |
TcGRAS28 | TCM_029136 | 6.30 | 64,717.65 | 582 | 46.26 | 74.60 | nucleus | 1749 |
TcGRAS29 | TCM_030393 | 5.89 | 61,290.47 | 548 | 52.83 | 79.00 | nucleus | 1647 |
TcGRAS30 | TCM_030498 | 6.19 | 49,455.27 | 438 | 55.76 | 96.74 | nucleus | 1317 |
TcGRAS31 | TCM_030733 | 5.56 | 60,140.03 | 540 | 58.44 | 79.35 | nucleus | 1623 |
TcGRAS32 | TCM_031132 | 6.13 | 66,239.71 | 596 | 52.40 | 80.54 | nucleus | 1791 |
TcGRAS33 | TCM_033446 | 4.94 | 58,582.29 | 521 | 39.07 | 86.91 | nucleus | 1566 |
TcGRAS34 | TCM_035069 | 5.28 | 53,980.68 | 487 | 40.15 | 85.15 | nucleus | 1464 |
TcGRAS35 | TCM_035362 | 5.06 | 63,856.24 | 570 | 49.25 | 82.14 | nucleus | 1713 |
TcGRAS36 | TCM_036707 | 6.31 | 52,208.63 | 457 | 43.57 | 86.81 | nucleus | 1374 |
TcGRAS37 | TCM_037975 | 5.62 | 60,414.53 | 548 | 49.30 | 87.08 | nucleus | 1647 |
TcGRAS38 | TCM_040833 | 5.61 | 52,722.63 | 470 | 50.42 | 98.81 | nucleus | 1413 |
TcGRAS39 | TCM_041810 | 6.33 | 79,445.42 | 705 | 46.24 | 71.65 | nucleus | 2118 |
TcGRAS40 | TCM_041812 | 6.17 | 78,589.84 | 690 | 51.06 | 80.39 | nucleus | 2073 |
TcGRAS41 | TCM_041813 | 5.40 | 75,260.51 | 666 | 53.55 | 81.14 | nucleus | 2001 |
TcGRAS42 | TCM_041814 | 5.16 | 89,125.20 | 790 | 45.83 | 71.96 | nucleus | 2373 |
TcGRAS43 | TCM_041815 | 6.30 | 92,905.70 | 829 | 46.81 | 70.95 | nucleus | 2490 |
TcGRAS44 | TCM_042194 | 4.63 | 60,211.98 | 537 | 45.66 | 85.74 | nucleus | 1614 |
TcGRAS45 | TCM_042392 | 5.80 | 54,285.57 | 483 | 62.33 | 96.15 | nucleus | 1452 |
TcGRAS46 | TCM_042705 | 5.62 | 83,092.65 | 737 | 52.65 | 76.73 | nucleus | 2214 |
Tandem Duplication | Chromosome Name | Ka | Ks | Ka/Ks |
---|---|---|---|---|
TcGRAS24 and TcGRAS25 | Chr04 | 5.21 | 2.66 | 1.96 |
TcGRAS42 and TcGRAS43 | Chr09 | 5.62 | 1.41 | 3.99 |
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Hou, S.; Zhang, Q.; Chen, J.; Meng, J.; Wang, C.; Du, J.; Guo, Y. Genome-Wide Identification and Analysis of the GRAS Transcription Factor Gene Family in Theobroma cacao. Genes 2023, 14, 57. https://doi.org/10.3390/genes14010057
Hou S, Zhang Q, Chen J, Meng J, Wang C, Du J, Guo Y. Genome-Wide Identification and Analysis of the GRAS Transcription Factor Gene Family in Theobroma cacao. Genes. 2023; 14(1):57. https://doi.org/10.3390/genes14010057
Chicago/Turabian StyleHou, Sijia, Qianqian Zhang, Jing Chen, Jianqiao Meng, Cong Wang, Junhong Du, and Yunqian Guo. 2023. "Genome-Wide Identification and Analysis of the GRAS Transcription Factor Gene Family in Theobroma cacao" Genes 14, no. 1: 57. https://doi.org/10.3390/genes14010057
APA StyleHou, S., Zhang, Q., Chen, J., Meng, J., Wang, C., Du, J., & Guo, Y. (2023). Genome-Wide Identification and Analysis of the GRAS Transcription Factor Gene Family in Theobroma cacao. Genes, 14(1), 57. https://doi.org/10.3390/genes14010057