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

Document Type : Research Paper

Authors

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

Abstract

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 
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.
 
Conclusion
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.

Keywords


 
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. 
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