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

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Zare Nahideh; Hedayat Evrigh Nemat; SEYED SHARIFI REZA; Khalkhali Evrigh Reza

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Journal: JOURNAL OF AGRICULTURAL BIOTECHNOLOGY Year:2021 | Volume:12 | Issue:4 Page(s): 43-60

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Information Journal Paper

Title

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

Author(s)

Zare Nahideh | Hedayat Evrigh Nemat | SEYED SHARIFI REZA | Khalkhali Evrigh Reza | Issue Writer Certificate

Keywords

Iranian Bactrian Camel

Repetitive Sequences

Transposable Elements

Whole Genome Sequencing

Abstract

Objective 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.

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APA: Copy

Zare, Nahideh, Hedayat Evrigh, Nemat, SEYED SHARIFI, REZA, & Khalkhali Evrigh, Reza. (2021). Identification and investigation of transposable elements in the Iranian bactrian camel genomes. JOURNAL OF AGRICULTURAL BIOTECHNOLOGY, 12(4 ), 43-60. SID. https://sid.ir/paper/965024/en

Vancouver: Copy

Zare Nahideh, Hedayat Evrigh Nemat, SEYED SHARIFI REZA, Khalkhali Evrigh Reza. Identification and investigation of transposable elements in the Iranian bactrian camel genomes. JOURNAL OF AGRICULTURAL BIOTECHNOLOGY[Internet]. 2021;12(4 ):43-60. Available from: https://sid.ir/paper/965024/en

IEEE: Copy

Nahideh Zare, Nemat Hedayat Evrigh, REZA SEYED SHARIFI, and Reza Khalkhali Evrigh, “Identification and investigation of transposable elements in the Iranian bactrian camel genomes,” JOURNAL OF AGRICULTURAL BIOTECHNOLOGY, vol. 12, no. 4 , pp. 43–60, 2021, [Online]. Available: https://sid.ir/paper/965024/en

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