Comparative Analysis of Differential Exon Usage between the Breeds of Sheep and Goats Using RNA-Seq Data

Document Type : Original Research

Authors
F. Nikookalam Azim 1
A. A. Masoudi 1
A. Ehsani 2
R. Vaez Torshizi 1
P. Shariati Gazgazareh 1
1 Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Islamic Republic of Iran.
2 Department of Animal Science, Faculty of Agriculture, Tarbiat Modares UniversityTehran, Iran
10.22034/jast.25.3.581
Abstract
Alternative splicing, alternative transcript start site, and alternative transcript polyadenylation site are the main factors resulting in diversity of the transcripts of a gene. The main objectives of this study were to analyze the alternation process in breeds of sheep and goat, and to identify its role in differentiation of breeds of a species. RNA-seq data were prepared from ovarian tissue of two breeds of Shal and Sangsari sheep and two breeds of Tibetan and Jintang black goats. Reads were aligned to the reference genome and significant genes with respect to differential exon usage were identified. The statistical comparison revealed that 8,104 genes were significantly different in exon usage between the sheep breeds and 173 genes differed between the goat breeds. Out of the 121,861 studied exons, only 22.7% were preserved during future generations between the breeds, of which 99.3% did not display any alternatives. The high protection was probably due to the lack of involvement of the exons in alternative process. The genes with differential exon usage in goat had a higher percentage of alternatives than those in sheep. The interracial analysis showed that alternative splicing was the most influential type of alternatives in the breeds of sheep and goats. It seems that the conservation process of the exons is related to the contribution of these exons in alterative process in both sheep and goat breeds. The significant PI3K-Akt and alternative splicing pathways play a role in cell growth, development of ovaries, and mRNAs splicing.

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1. Pertea M, Salzberg SL, Between a chicken and a grape: estimating the number of human genes, Genome biology 11(5) :1-7, 2010.
2. Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, Sabatini DM, Identification and characterization of essential genes in the human genome, Science 350(6264) :1096-1101, 2015.
3. Piovesan A, Antonaros F, Vitale L, Strippoli P, Pelleri MC, Caracausi M, Human protein-coding genes and gene feature statistics in 2019, BMC Research Notes 12 :1-5, 2019.
4. Brown TA. Genomes 4, Published by Garland Science 544 Pages.
5. Vogel F, A preliminary estimate of the number of human genes, Nature 201(4921) :847-847, 1964.
6. Mills JD, Janitz M, Alternative splicing of mRNA in the molecular pathology of neurode generative diseases, Neurobiology of aging 33(5) :1012. e11-1012. e24, 2012.
7. Tang JY, Lee JC, Hou MF, Wang CL, Chen CC, Huang HW, Chang HW, Alternative splicing for diseases, cancers, drugs, and databases, The Scientific World Journal, 2013.
8. Yap K , Makeyev EV, Regulation of gene expression in mammalian nervous system through alternative pre-mRNA splicing coupled with RNA quality control mechanisms, Molecular and Cellular Neuroscience 56: 420-428, 2013.
9. Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, Huber W, Drift and conservation of differential exon usage across tissues in primate species, Proceedings of the National Academy of Sciences 110 :15377-15382, 2013.
10. Anders S, Reyes A Huber W, Detecting differential usage of exons from RNA-seq data, Nature Precedings, 1-1, 2012.
11. Stark R, Grzelak M, Hadfield J, RNA sequencing: the teenage years, Nature Reviews Genetics 20(11): 631-656, 2019.
12. Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Graveley BR, Conservation of an RNA regulatory map between Drosophila and mammals, Genome Research 21(2): 193-202, 2011.
13. Katz Y, Wang ET, Airoldi EM, Burge CB, Analysis and design of RNA sequencing experiments for identifying isoform regulation, Nature Methods 7, 1009-1015.
14. Reyes A, Huber W, Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues, Nucleic acids research,46(2): 582-592, 2013.
15. Rischkowsky B,Pilling D, The State of the World's Animal Genetic Resources for Food and Agriculturein Brief, Food & Agriculture Org , 2007.
16. Gottfredson R, Hormonal control of ewe reproduction, Departament of Animal University of Wisconsin-Madison, 2001.
17. Zi XD, Lu JY, Zhou H, Ma L, Xia W, Xiong XR, Wu XH, Comparative analysis of ovarian transcriptomes between prolific and non‐prolific goat breeds via high‐throughput sequencing, Reproduction in Domestic Animals 53(2) :344-351.
18. Acland A, Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Church DM, Database resources of the national center for biotechnology information, Nucleic Acids Research 42(D1): D7-D17, 2014.
19. Belabdi I, Ouhrouch A, Lafri M, Gaouar SBS, Ciani E, Benali AR, Blanquet V, Genetic homogenization of indigenous sheep breeds in Northwest Africa, Scientific Reports 9(1) :1-13, 2019.
20. Evfratov SA, Osterman IA, Komarova ES, Pogorelskaya AM, Rubtsova MP, Zatsepin TS, Burnaev E, Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli, Nucleic Acids Research 45(6) :3487-3502, 2017.
21. Grishkevich V, Yanai I, Gene length and expression level shape genomic novelties, Genome Research 24(9) :1497-1503, 2014.
22. EI-Shehawi A, Elseehy M , Genome size and chromosome number relationship contradicts the principle of Darwinian evolution from common ancestor, Journal of Phylogenetics and Evolutionary Biology 5 :179, 2017.
23. Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, Huber W, Drift and conservation of differential exon usage across tissues in primate species, Proceedings of the National Academy of Sciences 110(38), 15377-15382, 2013.
Journal of Agricultural Science and Technology
Volume 25, Issue 3
May and June 2023
Pages 581-594