Identification and investigation of transposable elements in the Iranian bactrian camel genomes

Document Type : Research Paper


1 Animal science, University of Mohaghegh Ardabili, Ardabil, Iran

2 Assistant professor, Department of Animal Science, Faculty of Agricultural Sciences, University of Mohaghegh Ardabili, Ardabil, Iran.

3 Associated Professor, Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran

4 Animal science, university of Mohaghegh Ardabili, Ardabil, Iran


About half of the human genome is covered by repetitive sequences. These sequences have a large share in the other mammalian genomes, therefore studying this part of the genome can provide researchers valuable information on evolution. The aim of this study was to sequencing and assembly the whole genome of Iranian Bactrian camels to identify transposable elements and their distribution in the genome of this species. In addition, the results of Iranian Bactrian camels were compared with non-Iranian Bactrian camels and dromedary camels.
Materials and methods
In this study, the whole genome of six Iranian Bactrian camels was sequenced to transposable elements identification. Iranian Bactrian camel whole genome sequenced using Illumina HiSeq 2000 system in paired-end. FastQC and Trimmomatic software were used to quality control and quality filtering of raw sequencing reads, respectively. CLC Genomics Workbench (CLC Bio, Aarhus, Denmark) was used to de novo assembly of trimmed reads. Also, we used the RepeatMasker program to search for transposable elements using a homology-based method.
Results of the assembling of sequenced genomes showed that the genome size in these samples ranged from 1.9 to 1.97 Gb. In the present study, the percentage of transposable elements for six Iranian Bactrian camels was 29.89% on average of the whole genome. The percentage of LINE sequences for the Iranian Bactrian camel was 17.58% on average. So, these sequences were considered as the largest group of transposable elements in the Bactrian camel in this study. SINE elements showed a lower number in comparison with LINEs. So that, only 3.45% of the total Bactria camel genome length was dedicated to the SINEs. In accordance with the results of Iranian dromedary camels, no Alu element was identified in the genome of Iranian Bactrian camels.
Shortage of genomic and biological information about camels is one of the inhibiting factors in advancing the breeding goals and programs. Although this study is not enough alone, it can be a step towards starting the production of genomic data for camels. Continuing this kind of study and integrating biological and genomic information will provide the ground for the start of modern breeding in Iranian camels.


ترابی آزاده، رودباری زهرا، طهمورث پور مجتبی (1399) تجزیه و تحلیل ژنتیکی ناحیه S rRNA 12 شترهای تک‌کوهانه و دوکوهانه ایران. مجله بیوتکنولوژی کشاورزی 12، 209-223.
قاسمی میمندی مهرداد، محمدآبادی محمدرضا، اسمعیلی زاده کشکوئیه علی، منتظری مهدیه (1395a) بررسی انتساب افراد به جمعیت‌هایی از شترهای شمال استان کرمان با استفاده از نشانگرهای ریزماهواره‎. فصلنامه علمی ژنتیک نوین 11، 329-335‎.
قاسمی مهرداد، محمدآبادی محمدرضا، اسمعیلی زاده‎ علی (1394) تنوع ژنتیکی شترهای شمال استان کرمان با استفاده از نشانگرهای ریز ماهواره‎. مجله تحقیقات تولیدات دامی 4 ، 35-45.
قاسمی میمندی مهرداد، محمدآبادی محمدرضا، منتظری مهدیه‎ (1395b) ارزیابی ساختار ژنتیکی شتر با استفاده از روش های PCA و خوشه بندی سلسله مراتبی‎. مجله بیوتکنولوژی کشاورزی 8 ، 96-83.
محمدآبادی محمدرضا، قاسمی میمندی مهرداد، منتظری مهدیه‎ (1397) بررسی تنوع ژنتیکی شترهای بومی شمال استان کرمان با استفاده از آمارهF. نشریه اصلاح و بهنژادی دام 1، 1-13. 
Adelson DL, Raison JM, Edgar RC (2009) Characterization and distribution of retrotransposons and simple sequence repeats in the bovine genome. Proc Nat Acad Sci 106, 12855-12860.
Adelson DL, Raison JM, Garber M, Edgar RC (2010) Interspersed repeats in the horse (Equus caballus) spatial correlations highlight conserved chromosomal domains. Anim gene 41, 91-99.
Akopov SB, Nikolaev LG, Khil PP et al. (1998) Long terminal repeats of human endogenous retrovirus K family (HERV-K) specifically bind host cell nuclear proteins. FEBS Lett 421, 229–233.
Andrews S (2010) FastQC, A quality control tool for high throughput sequence data. Last accessed 11 November 2020.
Arensburger P, Hice RH, Zhou L et al. (2011) Phylogenetic and functional characterization of the hAT transposon superfamily. Genetics 188, 45-57.
Bao W, Kojima KK, Kohany O (2015) Repbase Update, a database of repetitive elements in eukaryotic genomes. Mobile DNA 6, 11-16.
Barazandeh A, Mohammadabadi MR, Ghaderi M, Nezamabadipour H (2016) Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features. Czech J Anim Sci 61, 487-495.
Barazandeh A, Mohammadabadi MR, Ghaderi-Zefrehei M et al. (2019) Whole genome comparative analysis of CpG islands in camelid and other mammalian genomes. Mamm Biol 98, 73-79. 
Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Gene Dev 15, 621–627.
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. J Bioinform 30, 2114-2120.
Compagnoni B, Tosi M (1978) In Approaches to Faunal Analysis in the Middle East (eds Richard H. Meadow & Melinda A. Zeder). Peabody Mus Press 119–128 
De Koning AP, Gu W, Castoe TA et al. (2011) Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet 7, e1002384.
Elbarbary RA, Lucas BA, Maquat LE (2016) Retrotransposons as regulators of gene expression. Science, 351, 679-687.
Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9, 397–405.
Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5, 103–107.
Fitak RR, Mohandesan E, Corander J, Burger PA (2016) The de novo genome assembly and annotation of a female domestic dromedary of North African origin. Mol Ecol Res 16, 314–324.
Fowler ME (1998) Medicine and surgery of south american camelids. 2nd ed. USA: Iowa State Press Blackwell.
Ghasemi Meymandi M, Mohammadabadi MR, Esmailizadeh A (2015) Genetic variation of camels in the North of Kerman province using microsatellite markers. Anim Prod Sci 4, 35-45 (In Persian).
Ghasemi Meymandi M, Mohammadabadi MR, Montazeri M (2016a) Analysing Genetic Structure of Camelus dromedarius Using PCA and Hierarchical clustering methods. Agric Biotechnol J 3, 83-96 (In Persian).
Ghasemi Meymandi M, Mohammadabadi MR, Esmailizadeh Kashkoieh A, Montazeri M (2016b) Investigation of individuals' attribution to populations of camels in the north of Kerman province using microsatellite markers. 3, 329-335 (In Persian).
Grabundzija I, Messing SA, Thomas J et al. (2016) A Helitron transposon reconstructed from bats reveals a novel mechanism of genome shuffling in eukaryotes. Nat Commun 7, 1-12.
Hedayat-Evrigh N, Khalkhali-Evrigh R, Bakhtiarizadeh MR (2020). Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data. Int J Genomics 2430846.
Hubley R, Finn RD, Clements J et al. (2015) The Dfam database of repetitive DNA families. Nucleic Acids Res 44, 81-89.
Ji R, Cui P, Ding F et al. (2009) Monophyletic origin of domestic bactrian camel (Camelus bactrianus) and its evolutionary relationship with the extant wild camel (Camelus bactrianus ferus). Anim Genet 40, 377–82.
Jirimutu, Wang Z, Ding G et al. (2012) Genome sequences of wild and domestic Bactrian camels. Nat Commun 3, 1202.
Jjingo D, Huda A, Gundapuneni M et al. (2011) Effect of the transposable element environment of human genes on gene length and expression. Genome Biol. Evol 3, 259–271. 
Jjingo D, Conley AB, Wang J et al. (2014) Mammalian-wide interspersed repeat (MIR)-derived enhancers and the regulation of human gene expression. Mobile DNA 5, 14-25. 
Jurka J, Zietkiewicz E, Labuda D (1995) Ubiquitous mammalian-wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era. Nucleic Acids Res 23, 170–175.
Katoh I, Kurata SI (2013) Association of endogenous retroviruses and long terminal repeats with human disorders. Front Oncol 3, 1-8.
Khalkhali-Evrigh R, Hafezian SH, Hedayat-Evrigh N et al. (2018) Genetic variants analysis of three dromedary camels using whole genome sequencing data. PLoS One 13, p. e0204028.
Khalkhali-Evrigh R, Hafezian SH, Hedayat-Evrigh N et al. (2019) Genome-Wide Identification of Microsatellites and Transposable Elements in the Dromedary Camel Genome Using Whole-Genome Sequencing Data. Front Genet 692.
Lander ES, Linton LM, Birren B et al. (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921.
Luvsan B (1986) Breeding strategies of Mongolian Bactrian camel. Ulaanbaatar p, 92.
McClintock B (1950) The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA 36, 344–355.
McNab BK (2002) The physiological ecology of vertebrates. Coms, Cor Uni Ithaca, New York, USA.
Mohammadabadi MR, Ghasemi Meymandi M, Montazeri M (2018). The Study of Genetic Diversity of Camels in North of Kerman Province Using F Statistics. Breed Improv Livest 1, 1-13.
Nellaker C, Keane TM, Yalcin B et al. (2012) The genomic landscape shaped by selectio on transposable elements across 18 mouse strains. Genome Biol 13, R45.
Oliver KR, Greene WK (2009) Transposable elements: powerful facilitators of evolution. Bio Essays 31, 703–714.
Ramet JP (2001) The technology of making cheese in Butana and Northern Sudan. Nomadic from camel milk (Camelus dromedaries). FAO. People 31, 64-84. 
Ray DA, Feschotte C, Pagan HJ et al. (2008) Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus. Genome Res 18, 717–728.
Rowold DJ, Herrara RJ (2000) Alu elements and the human genome. Genetica 108, 57–72. 
Silva JC, Shabalina SA, Harris DG et al. (2003) Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIRand L2-derived sequences within the mouse and human genomes. Genetical Res 82, 1–18.
Smit AFA, Riggs AD (1995) MIRs are classic, transfer-RNA-derived SINEs that amplified before the mammalian radiation. Nucleic Acids Res 23, 98–102.
Torabi A, Roudbari Z, Tahmoorespour M (2020) Genetic and phylogenetic analysis of 12S rRNA region in camelus dromedaries and camelus bactrianus of Iran. J Agri Biotechnol 12, 209-223 (In Persian)
Walsh AM, Kortschak RD, Gardner MG et al. (2013) Widespread horizontal transfer of retrotransposons. PNAS 110, 1012– 1016. 
Wicker T, Sabot F, Hua-Van A et al. (2007) A unified classification system for eukaryotic transposable elements. Nature Rev Genetics 8, 973–982.
Wu H, Guang X, Al-Fageeh MB et al. (2014) Camelid genomes reveal evolution and adaptation to desert environments. Nat commun 5, 5188.
Yam BAZ, Khomeiri M (2015) Introduction to camel origin, history, raising, characteristics, and wool, hair and skin: a review. Int J Res Innov Earth Sci 2, 177–187.