Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (Citrullus lanatus)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sequence Retrieval and Bioinformatic Analysis
2.2. Plant Materials and RNA Extraction
2.3. Expression Analysis
3. Results
3.1. Genome-Wide Identification and Phylogenetic Analysis of PINs in Cucurbitaceae Species
3.2. Cis-Element and Gene Structure Analysis of Watermelon PINs
3.3. In Silico Expression of PINs in Watermelon Tissues
3.4. Expression Profiles of Watermelon PINs during Shoot Regeneration
4. Discussion
4.1. Identification of PINs in Cucurbitaceae Species
4.2. Putative Regulators in ClaPINs
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 ID. | CuGenDB Accession | Chromosome Location | Coding Sequence (bp) | Predicted Protein (aa) | Molecular Weight | Theoretical pI | CELLO Localization | |
---|---|---|---|---|---|---|---|---|
97103_v2 | 97103_v1 | |||||||
ClaPIN1-1 | Cla97C04G072260.1 | Cla012098 | Chr04: 19082426–19084800(−) | 1878 | 625 | 67109.39 | 8.22 | PlasmaMembrane (4.260) |
ClaPIN1-2 | Cla97C04G077450.1 | Cla018455 | Chr04: 25019277–25022350(+) | 1860 | 619 | 67585.84 | 9.13 | PlasmaMembrane (4.643) |
ClaPIN1-3 | Cla97C06G123780.1 | Cla018924 | Chr06: 26050523–26053439(+) | 1824 | 607 | 66418.71 | 9.19 | PlasmaMembrane (4.680) |
ClaPIN2 | Cla97C06G123240.1 | Cla018871 | Chr06: 25556363–25559538(+) | 1938 | 645 | 70749.52 | 9.28 | PlasmaMembrane (4.073) |
ClaPIN3-1 | Cla97C01G006350.1 | Cla003909 | Chr01: 6303561–6306905(−) | 1926 | 641 | 69902.79 | 7.12 | PlasmaMembrane (4.561) |
ClaPIN3-2 | Cla97C07G134150.1 | Cla011708-Cla011709 | Chr07: 9679960–9684183(−) | 1872 | 623 | 68190.85 | 8.67 | PlasmaMembrane (4.735) |
ClaPIN5 | Cla97C11G217020.1 | Cla010530 | Chr11: 20331421–20339597(−) | 1113 | 370 | 40169.63 | 7.61 | PlasmaMembrane (4.639) |
ClaPIN6 | Na | Cla015026 | Chr09: 9050290–9056689(+) | 1449 | 482 | 53345.31 | 9.25 | PlasmaMembrane (4.712) |
ClaPIN8 | Cla97C10G197710.1 | Cla017028 | Chr10: 27449992–27452031(−) | 1071 | 356 | 38907.61 | 9.53 | PlasmaMembrane (4.913) |
CsaPIN1-1 | CsaV3_1G004350.1 | Chr01: 2730713–2733712(−) | 1827 | 608 | 66630.87 | 9.09 | PlasmaMembrane (4.798) | |
CsaPIN1-2 | CsaV3_1G007160.1 | Chr01: 4542181–4545627(−) | 1857 | 618 | 67443.68 | 9.13 | PlasmaMembrane (4.630) | |
CsaPIN1-3 | CsaV3_4G029470.1 | Chr04: 19013177–19015651(+) | 1791 | 596 | 63704.54 | 8.77 | PlasmaMembrane (4.476) | |
CsaPIN2 | CsaV3_1G032010.1 | Chr01: 19030317–19033521(+) | 1938 | 645 | 70831.58 | 9.29 | PlasmaMembrane (4.272) | |
CsaPIN3-1 | CsaV3_5G013380.1 | Chr05: 9982996–9987048(−) | 1890 | 629 | 68479.02 | 8.5 | PlasmaMembrane (4.767) | |
CsaPIN3-2 | CsaV3_5G028620.1 | Chr05: 23739663–23744022(−) | 1911 | 636 | 69462.29 | 7.12 | PlasmaMembrane (4.600) | |
CsaPIN5-1 | CsaV3_2G009610.1 | Chr02: 6112179–6116586(+) | 1116 | 371 | 40371.92 | 7.04 | PlasmaMembrane (4.592) | |
CsaPIN5-2 | CsaV3_2G009700.1 | Chr02: 6189126–6193716(+) | 1191 | 396 | 43043.53 | 7.57 | PlasmaMembrane (4.916) | |
CsaPIN8 | CsaV3_3G041710.1 | Chr03: 34023847–34026847(+) | 1071 | 356 | 38980.69 | 9.59 | PlasmaMembrane (4.895) | |
CmePIN1-1 | MELO3C017357.2.1 | Chr02: 24004740–24008031(+) | 1776 | 591 | 64524.14 | 8.5 | PlasmaMembrane (4.654) | |
CmePIN1-2 | MELO3C019102.2.1 | Chr08: 13382844–13385789(+) | 1836 | 611 | 65374.38 | 8.75 | PlasmaMembrane (4.526) | |
CmePIN1-3 | MELO3C002132.2.1 | Chr12: 26099882–26104026(+) | 1929 | 642 | 70303.64 | 9.01 | PlasmaMembrane (4.183) | |
CmePIN2 | MELO3C017414.2.1 | Chr02: 23469145–23472527(+) | 1872 | 623 | 68443.69 | 9.22 | PlasmaMembrane (3.928) | |
CmePIN3-1 | MELO3C005326.2.1 | Chr09: 20480725–20484941(−) | 1911 | 636 | 69499.35 | 7.15 | PlasmaMembrane (4.624) | |
CmePIN3-2 | MELO3C018353.2.1 | Chr10: 18871332–18876126(+) | 1887 | 628 | 68548.23 | 8.69 | PlasmaMembrane (4.729) | |
CmePIN5 | MELO3C008726.2.1 | Chr05: 18006724–18012271(−) | 1209 | 402 | 43622.16 | 6.23 | PlasmaMembrane (4.858) | |
CmePIN8 | MELO3C009892.2.1 | Chr04: 28346209–28350422(−) | 1038 | 345 | 37657.14 | 9.54 | PlasmaMembrane (4.939) |
Gene ID. | Forward Primers | Reverse Primers | References |
---|---|---|---|
ClaPIN1-1 | CTCTGTTTCTGACCTCTACC | TACGGCGAGGGCGGCAAGGA | [32] |
ClaPIN1-2 | TCTTGCTGTTCTTGCCGTTT | GCTCAGAAATCAGCATTCTG | |
ClaPIN1-3 | TACATTATCAGACTTTTACC | GTCCAGATACCGAGCACCAC | |
ClaPIN2 | ACATATACGATGTATTCTCAG | GTGGAAGGAGAGTAATGG | |
ClaPIN3-1 | ATCATGGAAGGATCTTTACA | AAATCCCAAGAAAGAACAAC | |
ClaPIN3-2 | ACTGTCTTGACGGCGGTCAT | AATTGTAAGAGCAACAAGCA | |
ClaPIN5 | CCATGGCCCCATTGTACTTC | AAGACGAGAACGATAACGAT | |
ClaPIN6 | AAGGTGATGTGTGCGATGGT | TTGCCGGAGAAGAAAACAGC | |
ClaPIN8 | TTCGTTGTCTGATGTCTATC | TATCAGTTGCAGGGTCATTT | |
GAPDH | TGGAAGAATCGGTAGGTTGG | CTGTCACTGTTTTTGGCGTC | [27] |
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Shang, H.; Zhang, N.; Xie, Z.; Deng, S.; Yi, L.; Huang, X. Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (Citrullus lanatus). Agriculture 2021, 11, 447. https://doi.org/10.3390/agriculture11050447
Shang H, Zhang N, Xie Z, Deng S, Yi L, Huang X. Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (Citrullus lanatus). Agriculture. 2021; 11(5):447. https://doi.org/10.3390/agriculture11050447
Chicago/Turabian StyleShang, Huaiguo, Na Zhang, Zhouli Xie, Siyu Deng, Licong Yi, and Xing Huang. 2021. "Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (Citrullus lanatus)" Agriculture 11, no. 5: 447. https://doi.org/10.3390/agriculture11050447
APA StyleShang, H., Zhang, N., Xie, Z., Deng, S., Yi, L., & Huang, X. (2021). Genome-Wide Identification and Expression of the PIN Auxin Efflux Carrier Gene Family in Watermelon (Citrullus lanatus). Agriculture, 11(5), 447. https://doi.org/10.3390/agriculture11050447