牦牛与普通牛、水牛的X染色体基因编码区比较及密码子偏性分析

doi:10.16431/j.cnki.1671-7236.2022.06.004

Abstract

Abstract: 【Objective】 Analyzing the X chromosome of Bos grunniens and other subfamilies of cattle from the perspective of genome alignment and codon bias was helpful to understand the variety differences and phylogenetic status of Bos grunniens, and provided reference for its adaptation to high altitude low-pressure and hypoxia environment and codon optimization.【Method】 Taking the coding region sequence of Bos grunniens X chromosome reference gene as the reference panel, genome alignment and gene collinearity analysis were carried out with the coding region sequence of X chromosome reference gene of Bos taurus and Bubalus bubalis.At the same time, gene annotation was carried out.The filtered coding region files were analyzed for preference, such as relative synonymous codon usage (RSCU), ENC-plot, PR2-plot and optimal codon determination.【Result】 In the coding region of X chromosome gene of Bos grunniens, genes involved in tracheal contraction, lung respiration and body metabolism were found to be different from Bos taurus and Bubalus bubalis, such as KLHL13, CENPI and PGK1 genes.The collinearity results indicated that the long segment showed an exchange linear region due to strong natural selection and mutation pressure.In codon analysis, the codon usage bias of three species of bovine subfamily was similar, their bias was weak, and their codons were biased towards the end of G/C.Their strong biased codons (RSCU ≥ 1.5) were all CUG, GUG, AGA, AGG and UGA.Among them, 16 optimal codons were selected for Bos grunniens, 13 for Bos taurus and 9 for Bubalus bubalis.These codons all end in A/U.【Conclusion】 By comparing Bos taurus and Bubalus bubalis, Bos grunniens might be under greater natural selection, so its cumulative degree of variation in the process of evolution was also greater.The codon bias of Bos grunniens, Bos taurus and Bubalus bubalis were more affected by natural selection than mutation.These results would provide reference and guidance for Bos grunniens genetic breeding, codon optimization and the development and utilization of genetic resources.

Key words: Bos grunniens; X chromosome; comparative genomes; codon bias

CLC Number:

S823.85

LIU Xinrui, WANG Jiabo, CHAI Zhixin, WU Zhijuan, YIXI Kangzhu, ZHONG Jincheng. Comparison of X Chromosome Gene Coding Regions and Analysis of Codon Bias in Bos grunniens, Bos taurus and Bubalus bubalis[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(6): 2043-2055.

References

[1] FAN Q S, WANAPAT M, YAN T H, et al.Altitude influences microbial diversity and herbage fermentation in the rumen of yaks[J].BMC Microbiology, 2020, 20(1):370.
[2] STUART J A, AIBEUKU O, BAGSHAW O, et al.Hypoxia inducible factors as mediators of reactive Oxygen/Nitrogen species homeostasis in physiological normoxia[J].Medical Hypotheses, 2019, 129:109249.
[3] FRIEDRICH J, WIENER P.Selection signatures for high-altitude adaptation in ruminants[J].Animal Genetics, 2020, 51(2):157-165.
[4] WEN Y L, WANG J Q, LIU X, et al.Regulating glycolysis and heat shock proteins in Gannan yaks (Bos grunniens) in response to hypoxia of the Qinghai-Tibet Plateau[J].Archives Animal Breeding, 2021, 64(2):345-353.
[5] QIU Q, ZHANG G J, MA T, et al.The yak genome and adaptation to life at high altitude[J].Nature Genetics, 2012, 44(8):946-949.
[6] MIZUNO S, ISHIZAKI T, TOGA H, et al.Endogenous asymmetric dimethylarginine pathway in high altitude adapted yaks[J].Biomed Research International, 2015, 2015:196904.
[7] KEINAN A, MULLIKIN J C, PATTERSON N, et al.Accelerated genetic drift on chromosome X during the human dispersal out of Africa[J].Nature Genetics, 2009, 41(1):66-70.
[8] ELLEGREN H.The different levels of genetic diversity in sex chromosomes and autosomes[J].Trends in Genetics, 2009, 25(6):278-284.
[9] SCHULZ E G, HEARD E.Role and control of X chromosome dosage in mammalian development[J].Current Opinion in Genetics & Development, 2013, 23(2):109-115.
[10] SANGRITHI M N, TURNER J M A.Mammalian X chromosome dosage compensation:Perspectives from the germ line[J].Bioessays, 2018, 40(6):e1800024.
[11] KHIL P P, SMIRNOVA N A, ROMANIENKO P J, et al.The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation[J].Nature Genetics, 2004, 36(6):642-646.
[12] PATIL S S, INDRABALAN U B, SURESH K P, et al.Analysis of codon usage bias of Classical swine fever virus[J].Veterinary World, 2021, 14(6):1450.
[13] 宋乔乔.牦牛和普通牛基因组的密码子使用分析[D].成都:西南民族大学, 2015. SONG Q Q.Analysis of codon usage on Bos grunniens and Bos taurus[D].Chengdu:Southwest Minzu University, 2015.(in Chinese)
[14] JI Q M, XIN J W, CHAI Z X, et al.A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak[J].Molecular Ecology Resources, 2021, 21(1):201-211.
[15] MA Z J, XIA X T, CHEN S M, et al.Identification and diversity of Y-chromosome haplotypes in Qinghai yak populations[J].Animal Genetics, 2018, 49(6):618-622.
[16] LIANG C N, WU X Y, DING X Z, et al.Characterization of the complete mitochondrial genome sequence of wild yak (Bos mutus)[J].Mitochondrial DNA Part A, 2016, 27(6):4266-4267.
[17] ZHANG W J, JIE Z, LI Z F, et al.Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L.[J].Journal of Integrative Plant Biology, 2007, 49(2):246-254.
[18] LI N, SUN M H, JIANG Z S, et al.Genome-wide analysis of the synonymous codon usage patterns in apple[J].Journal of Integrative Agriculture, 2016, 15(5):983-991.
[19] ALIKHAN N F, PETTY N K, ZAKOUR N L B, et al.BLAST ring image generator (BRIG):Simple prokaryote genome comparisons[J].BMC Genomics, 2011, 12(1):1-10.
[20] GUY L, KULTIMA J R, ANDERSSON S G.genoPlotR:Comparative gene and genome visualization in R[J].Bioinformatics, 2010, 26(18):2334-2335.
[21] NOVEMBRE J A.Accounting for background nucleotide composition when measuring codon usage bias[J].Molecular Biology and Evolution, 2002, 19(8):1390-1394.
[22] SHARP P M, TUOHY T M, MOSURSKI K R.Codon usage in yeast:Cluster analysis clearly differentiates highly and lowly expressed genes[J].Nucleic Acids Research, 1986, 14(13):5125-5143.
[23] WANG L Y, XING H X, YUAN Y C, et al.Genome-wide analysis of codon usage bias in four sequenced cotton species[J].PLoS One, 2018, 13(3):e0194372.
[24] LIU H B, LU Y Z, LAN B L, et al.Codon usage by chloroplast gene is bias in Hemiptelea davidii[J].Journal of Genetics, 2020, 99(1):1-11.
[25] WRIGHT F.The ‘effective number of codons’ used in a gene[J].Gene, 1990, 87(1):23-29.
[26] WEN W, GUO F B.Strong strand composition bias in the genome of Ehrlichia canis revealed by multiple methods[J].The Open Microbiology Journal, 2010, 4(10):98-102.
[27] YU X L, LIU J X, LI H Z, et al.Comprehensive analysis of synonymous codon usage patterns and influencing factors of Porcine epidemic diarrhea virus[J].Archives of Virology, 2021, 166(1):157-165.
[28] TANG D F, WEI F, CAI Z Q, et al.Analysis of codon usage bias and evolution in the chloroplast genome of Mesona chinensis Benth[J].Development Genes and Evolution, 2021, 231(1-2):1-9.
[29] ZHANG Y J, YU G Z, CHU H Y, et al.Macrophage-associated PGK1 phosphorylation promotes aerobic glycolysis and tumorigenesis[J].Molecular Cell, 2018, 71(2):201-215.
[30] ZHANG K, LENSTRA J A, ZHANG S, et al.Evolution and domestication of the Bovini species[J].Animal Genetics, 2020, 51(5):637-657.
[31] BARBHUIYA R I, UDDIN A, CHAKRABORTY S.Codon usage pattern and its influencing factors for mitochondrial CO genes among different classes of Arthropoda[J].Mitochondrial DNA, 2020, 31(8):313-326.
[32] DEB B, UDDIN A, CHAKRABORTY S.Codon usage pattern and its influencing factors in different genomes of Hepadnaviruses[J].Archives of Virology, 2020, 165(3):557-570.
[33] JENKINS G M, HOLMES E C.The extent of codon usage bias in human RNA viruses and its evolutionary origin[J].Virus Research, 2003, 92(1):1-7.
[34] CHAKRABORTY S, DEB B, BARBHUIYA P A, et al.Analysis of codon usage patterns and influencing factors in Nipah virus[J].Virus Research, 2019, 263:129-138.
[35] CAMIOLO S, TOOME-HELLER M, AIME M C, et al.An analysis of codon bias in six red yeast species[J].Yeast, 2019, 36(1):53-64.
[36] NABIYOUNI M, PRAKASH A, FEDOROV A.Vertebrate codon bias indicates a highly GC-rich ancestral genome[J].Gene, 2013, 519(1):113-119.
[37] MORIYAMA E N, POWELL J R.Codon usage bias and tRNA abundance in Drosophila[J].Journal of Molecular Evolution, 1997, 45(5):514-523.

Comparison of X Chromosome Gene Coding Regions and Analysis of Codon Bias in Bos grunniens, Bos taurus and Bubalus bubalis

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 4

Recommended Articles

Metrics

Comments

[1]	MA Jianqing, YANG Qingfang, SONG Zhanfeng, JIA Dingding, WU Dongwei, MO Xiufang, XU Zengnian, YANG Ke, WU Zhanyong, JI Ying, ZHOU Rongyan. Analysis of Codon Usage Bias of VDR Gene Related to Bone Metabolism in Ovis aries [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 2888-2898.
[2]	TAO Weikun, LIU Bo, HUANG Fei, WANG Jie, GAO Qinghua. Research Progress on Xist lncRNA Mediated X Chromosome Inactivation and Its Application [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(1): 216-223.
[3]	LU Guo-min, ZHANG Can, ZOU Ling, LIU Wen-hua, WEN Jian-xin, REN Hui-ying. Analysis of Codon Bias on Lysozyme Gene of Phage vB_EcoM-Bp7 [J]. , 2015, 42(9): 2233-2239.
[4]	ZHANG Tao, WANG Wen-hao, ZHANG Gen-xi, WANG Jin-yu, FAN Qing-can, HAN Kun-peng, TANG Ying, WANG Yong-juan. Characterization of Codon Usage of GnRHR Gene in Jinghai Yellow Chicken [J]. , 2014, 41(12): 7-15.