Potato [Solanum tuberosum L.] is one of the major food plants with complete genome sequences available. Plant genes are subjected to alternative splicing (AS), a process increases both transcriptome and proteome diversities. The work reports a systematic genome-wide study on identification and analysis of AS events by integrating multiple sources of sequencing data in potato plants. A collection of 291,071 expressed sequence tags (ESTs) and mRNA sequences were cleaned and assembled into 150,435 unique transcripts and 87,992 of them were mapped to potato genome. In addition, a total of 5.8 billion out of 7.7 billion RNA-sequencing (RNA-seq) reads, which were collected from 227 samples deposited from 10 published projects, were mapped to potato genome. Combining all mapping data results in identification of a total of 226,769 AS events, which were further classified into basic events (49.0%) and complex events (51.0%), that were generated from 24,650 genes. The basic AS events include intron retention (9.5%), alternative acceptor sites (19.2%), alternative donor site (8.2%), and exon skipping (12.1%). The AS rate of annotated gene models was estimated to be ~45.8% in potato plants. Comparative analysis identified 2,929 alternatively splice genes conserved among potato, tomato, soybean and maize plants. The work provides an important resource for further functional characterization of these genes in potato biology.
| Published in | Journal of Plant Sciences (Volume 11, Issue 3) |
| DOI | 10.11648/j.jps.20231103.19 |
| Page(s) | 98-106 |
| Creative Commons |
This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited. |
| Copyright |
Copyright © The Author(s), 2023. Published by Science Publishing Group |
Alternative Splicing, Expressed Sequence Tags, mRNA, RNA Sequencing, Transcriptome, Potato
| [1] | Wijesinha-Bettoni, R.; Mouillé, B. (2019). The contribution of potatoes to global food security, nutrition and healthy diets. Am. J. Potato Res. 2019, 96, 139-149. |
| [2] | Potato Genome Sequencing Consortium. Genome sequence and analysis of the tuber crop potato. Nature. 2011, 475, 189-195. https://doi:10.1038/nature10158 |
| [3] | Sharma, S. K.; Bolser, D.; de Boer, J.; Sønderkær, M.; Amoros, W.; Carboni, M. F.; D’Ambrosio, J. M.; de la Cruz, G.; Di Genova, A.; Douches, D. S.; Eguiluz, M. Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3 (Bethesda, Md.), 2013, 3 (11): 2031-2047. https://doi.org/10.1534/g3.113.007153 |
| [4] | Staiger, D.; Brown, J. W. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell 2013, 25, 3640-3656. https://doi.org/10.1105/tpc.113.113803 |
| [5] | Reddy, A. S.; Marquez, Y.; Kalyna, M.; Bartab, A. Complexity of the alternative splicing landscape in plants, Plant Cell 2013, 25, 3657-3683. https://doi.org/10.1105/tpc.113.117523 |
| [6] | Chaudhary, S.; Khokhar, W.; Jabre, I.; Reddy, A. S.; Byrne, L. J.; Wilson, C. M.; Syed, N. H. Alternative splicing and protein diversity: plants versus animals. Front. Plant Sci. 2019, 10, 708. https://doi.org/10.3389/fpls.2019.00708 |
| [7] | Clark, S.; Yu F.; Gu, L.; Min, X. Expanding alternative splicing identification by integrating multiple sources of transcription data in tomato. Front. Plant Sci. 2019, 10, 689. https://doi:10.3389/fpls.2019.00689 |
| [8] | Bournay, A.-S.; Hedley, P. E.; Maddison, A.; Waugh, R.; Machray, G. C. Exon skipping induced by cold stress in a potato invertase gene transcript. Nucleic Acids Res. 1996, 24, 2347–2351. https://doi: 10.1093/nar/24.12.2347 |
| [9] | Nicolas, M.; Rodríguez-Buey, M. L.; Franco-Zorrilla, J. M.; Cubas, P. A recently evolved alternative splice site in the BRANCHED1a gene controls potato plant architecture. Curr. Biol. 2015, 25 (14), 1799-809. https://doi.org/10.1016/j.cub.2015.05.053 |
| [10] | Marsh, J. T.; Sullivan, S.; Hartwell, J.; Nimmo, H. G. Structure and expression of phospho enol pyruvate carboxylase kinase genes in Solanaceae. A novel gene exhibits alternative splicing. Plant Physiol. 2003, 133, 2021-2028. https://doi.org/10.1104/pp.103.030775 |
| [11] | Dubey, N.; Trivedi, M.; Varsani, S.; Vyas, V.; Farsodia, M.; Singh, S. K. Genome-wide characterization, molecular evolution and expression profiling of the metacaspases in potato (Solanum tuberosum L.). Heliyon. 2019, 5, e01162. https://doi.org/10.1016/j.heliyon.2019.e01162 |
| [12] | Wang, Z.; Gerstein, M.; Snyder, M. RNA-seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57-63. https://doi.org/10.1038/nrg2484 |
| [13] | Chu, Y.; Corey, D. R. RNA sequencing: platform selection, experimental design, and data interpretation. Nucleic Acid Ther. 2012, 22, 271-274. https://doi.org/10.1089/nat.2012.0367 |
| [14] | Gao, L.; Tu, Z. J.; Millett, B. P.; Bradeen, J. M. Insights into organ-specific pathogen defense responses in plants: RNA-seq analysis of potato tuber-Phytophthora infestans interactions. BMC Genomics. 2013, 14, 340. https://doi.org/10.1186/1471-2164-14-340 |
| [15] | Gao, L.; Bradeen, J. M. Contrasting potato foliage and tuber defense mechanisms against the late blight pathogen Phytophthora infestans. PLoS One. 2016, 11, e0159969. https://doi.org/10.1371/journal.pone.0159969 |
| [16] | Zhang, W.; Zuo, C.; Chen, Z.; Kang, Y.; Qin, S. RNA sequencing reveals that both abiotic and biotic stress-responsive genes are induced during expression of steroidal glycoalkaloid in potato tuber subjected to light exposure. Genes. 2019, 10, 920. http://dx.doi.org/10.3390/genes10110920 |
| [17] | Kwenda, S.; Motlolometsi, T. V.; Birch, P. R.; Moleleki, L. N. RNA-seq profiling reveals defense responses in a tolerant potato cultivar to stem infection by Pectobacterium carotovorum ssp. brasiliense. Front. Plant Sci. 2016, 7, 1905. https://doi.org/10.3389/fpls.2016.01905 |
| [18] | Goyer, A.; Hamlin, L.; Crosslin, J. M.; Buchanan, A.; Chang, J. H. RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection. BMC Genomics. 2015, 16, 1-3. https://doi.org/10.1186/s12864-015-1666-2 |
| [19] | Sprenger, H.; Kurowsky, C.; Horn, R.; Erban, A.; Seddig, S.; Rudack, K.; Fischer, A.; Walther, D.; Zuther, E.; Köhl, K.; Hincha, D. K.; J. Kopka. The drought response of potato reference cultivars with contrasting tolerance. Plant Cell Environ. 2016, 39, 2370-2389. https://doi.org/10.1111/pce.12780 |
| [20] | Moon, K. B.; Ahn, D. J.; Park, J. S.; Jung, W. Y.; Cho, H. S.; Kim, H. R.; Jeon, J. H.; Park, Y. I.; Kim, H. S. Transcriptome profiling and characterization of drought-tolerant potato plant (Solanum tuberosum L.). Mol. Cells. 2018, 41, 979. http://dx.doi.org/10.14348/molcells.2018.0312 |
| [21] | Tiwari J. K.; Buckseth, T.; Devi, S.; Varshney, S.; Sahu, S.; Patil, V. U.; Zinta, R.; Ali, N.; Moudgil, V.; Singh, R. K.; Rawat, S. Physiological and genome-wide RNA-sequencing analyses identify candidate genes in a nitrogen-use efficient potato cv. Kufri Gaurav. Plant Physiol. Biochem. 2020, 154, 171-183. https://doi.org/10.1016/j.plaphy.2020.05.041 |
| [22] | Tiwari, J. K.; Buckseth, T.; Zinta, R.; Saraswati, A.; Singh, R. K.; Rawat, S.; Dua, V. K.; Chakrabarti, S. K. Transcriptome analysis of potato shoots, roots and stolons under nitrogen stress. Sci. Rep. 2020, 10, 1-8. https://doi.org/10.1038/s41598-020-58167-4 |
| [23] | Herath, V.; Verchot, J. Transcriptional regulatory networks associate with early stages of potato virus X infection of Solanum tuberosum. Int. J. Mol. Sci. 2021, 22, 2837. https://doi.org/10.3390/ijms22062837 |
| [24] | Wai, C. M.; Powell, B.; Ming, R.; Min, X. J. Analysis of alternative splicing landscape in pineapple (Ananas comosus). Tropical Plant Biol. 2016, 9, 150-160. https://doi.org/10.1007/s12042-016-9168-1 |
| [25] | Min, X.; Kasamias, T.; Wagner, M.; Ogungbayi, A.; Yu, F. Identification and analysis of alternative splicing in soybean plants. Proceedings of 14th Int. Conf. on Bioinformatics and Computational Biol. 2022, 83, 1-9. https://doi.org/10.29007/2qv6 |
| [26] | Min, X. J. ASFinder: a tool for genome-wide identification of alternatively spliced transcripts from EST-derived sequences. Int. J. Bioinform. Res. Appl. 2013, 9, 221-226. https://doi.org/10.1504/IJBRA.2013.053603 |
| [27] | Florea, L.; Hartzell, G.; Zhang, Z.; Rubin, G. M.; Miller, W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 1998, 8, 967-974. https://doi.org/10.1101/gr.8.9.967 |
| [28] | Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S. L. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013, 14, R36. https://doi.org/10.1186/gb-2013-14-4-r36 |
| [29] | Trapnell, C.; Williams, B. A.; Pertea, G.; Mortazavi, A.; Kwan, G.; Van Baren, M. J.; Salzberg, S. L.; Wold, B. J.; Pachter, L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28, 511-515. https://doi.org/10.1038/nbt.1621 |
| [30] | Foissac, S.; Sammeth, M. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res. 2007, 35, W297–299. https://doi.org/10.1093/nar/gkm311 |
| [31] | Min, X. J.; Powell B.; Braessler J.; Meinken, J.; Yu, F.; Sablok, G. Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops. BMC Genomics. 2015, 16, 721. https://doi.org/10.1186/s12864-015-1914-5 |
| [32] | Walters, B., Lum, G., Sablok, G., Min, X. J. Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res. 2013, 20, 163-171. https://doi.org/10.1093/dnares/dss041 |
| [33] | VanBuren, R.; Walters, B.; Ming, R.; Min, X. J. Analysis of expressed sequence tags and alternative splicing genes in sacred lotus (Nelumbo nucifera Gaertn.). Plant Omics J. 2013, 6, 311-317. |
| [34] | Sablok, G.; Powell, B.; Braessler, J.; Yu, F.; Min, X. J. Comparative landscape of alternative splicing in fruit plants. Current Plant Biol. 2017, 9, 29-36. https://doi.org/10.1016/j.cpb.2017.06.001. |
| [35] | Min, X. J. A survey of alternative splicing in allotetraploid cotton (Gossypium hirsutum L.). Comp. Mol. Biol. 2018, 8, 1-13. https://doi.org/10.5376/cmb.2018.08.0001 |
| [36] | Min, X. J. Comprehensive cataloging and analysis of alternative splicing in maize. Comp. Mol. Biol. 2017, 7, 1-11. https://doi.org/10.5376/cmb.2017.07.0001 |
| [37] | Mei, W.; Boatwright, L.; Feng, G.; Schnable, J. C.; Barbazuk, W. B. Evolutionarily conserved alternative splicing across monocots. Genetics. 2017, 207, 465-480. https://doi.org/10.1534/genetics.117.300189 |
| [38] | Marquez, Y.; Brown, J. W.; Simpson, C.; Barta, A.; Kalyna, M. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res. 2012, 22, 1184-1195. https://doi.org/10.1101/gr.134106.111 |
| [39] | Wolfe, K. H.; Gouy, M.; Yang, Y. W.; Sharp, P. M.; Li, W. H. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. U. S. A. 1989, 86, 6201-6205. |
| [40] | Lee, J.; Min, X. (2023). Comparative analysis of alternative splicing events in foliar transcriptomes of potato plants inoculated with Phytophthora infestans. Comput. Mol. Biol. 2023, 13, 1-8. https://doi.org/10.5376/cmb.2023.13.0001 |
| [41] | Ogungbayi, A. Analysis of alternative splicing events in the transcriptome of potato plants. Youngstown State University, Master's thesis. 2023, OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ysu1651817160842415. |
| [42] | Yan, C.; Zhang, N.; Wang, Q;, Fu, Y.; Zhao, H.; Wang, J.; Wu, G.; Wang, F.; Li, X; Liao, H. Full-length transcriptome sequencing reveals the molecular mechanism of potato seedlings responding to low-temperature. BMC Plant Biology. 2022, 22, 1-20. https://doi.org/10.1186/s12870-022-03461-8 |
| [43] | Petek, M.; Zagorščak, M.; Ramšak, Ž.; Sanders, S.; Tomaž, Š.; Tseng, E.; Zouine, M.; Coll, A.; Gruden, K. Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato. Scientific Data. 2020, 7, 249. https://doi.org/10.1038/s41597-020-00581-4 |
APA Style
Atinuke Ogungbayi, Jessica Lee, Vishwa Vaghela, Feng Yu, Xiangjia Min. (2023). Systematic Collection and Analysis of Alternative Splicing Events in Potato Plants. Journal of Plant Sciences, 11(3), 98-106. https://doi.org/10.11648/j.jps.20231103.19
ACS Style
Atinuke Ogungbayi; Jessica Lee; Vishwa Vaghela; Feng Yu; Xiangjia Min. Systematic Collection and Analysis of Alternative Splicing Events in Potato Plants. J. Plant Sci. 2023, 11(3), 98-106. doi: 10.11648/j.jps.20231103.19
AMA Style
Atinuke Ogungbayi, Jessica Lee, Vishwa Vaghela, Feng Yu, Xiangjia Min. Systematic Collection and Analysis of Alternative Splicing Events in Potato Plants. J Plant Sci. 2023;11(3):98-106. doi: 10.11648/j.jps.20231103.19
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Download@article{10.11648/j.jps.20231103.19,
author = {Atinuke Ogungbayi and Jessica Lee and Vishwa Vaghela and Feng Yu and Xiangjia Min},
title = {Systematic Collection and Analysis of Alternative Splicing Events in Potato Plants},
journal = {Journal of Plant Sciences},
volume = {11},
number = {3},
pages = {98-106},
doi = {10.11648/j.jps.20231103.19},
url = {https://doi.org/10.11648/j.jps.20231103.19},
eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.jps.20231103.19},
abstract = {Potato [Solanum tuberosum L.] is one of the major food plants with complete genome sequences available. Plant genes are subjected to alternative splicing (AS), a process increases both transcriptome and proteome diversities. The work reports a systematic genome-wide study on identification and analysis of AS events by integrating multiple sources of sequencing data in potato plants. A collection of 291,071 expressed sequence tags (ESTs) and mRNA sequences were cleaned and assembled into 150,435 unique transcripts and 87,992 of them were mapped to potato genome. In addition, a total of 5.8 billion out of 7.7 billion RNA-sequencing (RNA-seq) reads, which were collected from 227 samples deposited from 10 published projects, were mapped to potato genome. Combining all mapping data results in identification of a total of 226,769 AS events, which were further classified into basic events (49.0%) and complex events (51.0%), that were generated from 24,650 genes. The basic AS events include intron retention (9.5%), alternative acceptor sites (19.2%), alternative donor site (8.2%), and exon skipping (12.1%). The AS rate of annotated gene models was estimated to be ~45.8% in potato plants. Comparative analysis identified 2,929 alternatively splice genes conserved among potato, tomato, soybean and maize plants. The work provides an important resource for further functional characterization of these genes in potato biology.},
year = {2023}
}
TY - JOUR T1 - Systematic Collection and Analysis of Alternative Splicing Events in Potato Plants AU - Atinuke Ogungbayi AU - Jessica Lee AU - Vishwa Vaghela AU - Feng Yu AU - Xiangjia Min Y1 - 2023/06/27 PY - 2023 N1 - https://doi.org/10.11648/j.jps.20231103.19 DO - 10.11648/j.jps.20231103.19 T2 - Journal of Plant Sciences JF - Journal of Plant Sciences JO - Journal of Plant Sciences SP - 98 EP - 106 PB - Science Publishing Group SN - 2331-0731 UR - https://doi.org/10.11648/j.jps.20231103.19 AB - Potato [Solanum tuberosum L.] is one of the major food plants with complete genome sequences available. Plant genes are subjected to alternative splicing (AS), a process increases both transcriptome and proteome diversities. The work reports a systematic genome-wide study on identification and analysis of AS events by integrating multiple sources of sequencing data in potato plants. A collection of 291,071 expressed sequence tags (ESTs) and mRNA sequences were cleaned and assembled into 150,435 unique transcripts and 87,992 of them were mapped to potato genome. In addition, a total of 5.8 billion out of 7.7 billion RNA-sequencing (RNA-seq) reads, which were collected from 227 samples deposited from 10 published projects, were mapped to potato genome. Combining all mapping data results in identification of a total of 226,769 AS events, which were further classified into basic events (49.0%) and complex events (51.0%), that were generated from 24,650 genes. The basic AS events include intron retention (9.5%), alternative acceptor sites (19.2%), alternative donor site (8.2%), and exon skipping (12.1%). The AS rate of annotated gene models was estimated to be ~45.8% in potato plants. Comparative analysis identified 2,929 alternatively splice genes conserved among potato, tomato, soybean and maize plants. The work provides an important resource for further functional characterization of these genes in potato biology. VL - 11 IS - 3 ER -
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