پژوهشهای علوم دامی ایران (Oct 2022)
Molecular Diversity and Phylogenetic Analysis of Turkmen Camel and Different Species of Camels based on CYTB Gene Sequence
Abstract
Introduction: Camels play a major role in the life of people in parts of Africa and Asia, especially in the desert areas. Today, camels are important for sustainable livestock production species in many arid regions of the world. Camels are economically important in terms of meat, milk and wool production in the desert. Due to climate change, camel as a desirable animal for arid areas, requires more extensive scientific view. According to FAO statistics, about 95% of 35 million humped camels worldwide are single-humped camels. The cytochrome b sequence is part of the mitochondrial DNA, passing from mother to offspring’s, can be used to elucidate genetic diversity and evolutionary history within and between different species. The aim of this study was to compare the genetic diversity using cytochrome b sequence in Turkmen camel and its genetic relationship with one and two-humped camels. In addition, the genetic relationship of within and between different species of camels has been objected.Materials and Methods: After preparing a blood sample from the abdominal vein of Turkmen camel, DNA extraction was performed using salting out method. Turkmen camel sequencing was performed using Illumina HighSeq 2000. Sequencing creates 150 bp reads of the genome sequence. The reads were assembled by Denovo method using CLC software and the contig of containing the cytochrome b gene was isolated based on the reference gene, NC_009849. Relevant data were obtained to compare the CYTB reference gene in new (Lamini) and old (Camelini) world species of camels. To study the genetic diversity of the camel species, a total of 42 one-humped camels, 31 wild tow-humped camels, 121 domestic tow-humped camels, and wild lamas including 31 guanicoe (Lama guanico) And 6 vicogna-vicogna (vicogna vicogna) and domestic llamas including 6 lama glama and 5 alpaca (Lama pacos) were compared. The alignment of CYTB gene sequence samples of different species was performed using CLC Genomics Workbench 12 software. Then the number of gaps, the number of differences and identities were obtained. A phylogenetic tree was drawn to investigate the genetic relationships between and within species. Sequences of Turkmen camels and other Iranian and Arabian one-humped camels along with other species were analyzed for alignment using CLC software. Phylogenetic tree of DNA and proteins sequences of the gene was performed using Neighbor Joining method with Jukes-Cantor protein distance size with 1000 bootstrap replications.Results and Discussion: DNA extraction based on spectrophotometry was 304 ng/μl and was suitable for sequencing. After sequencing, 589,326,158 readings of 150 base-pairs containing more than 88 billion bases were obtained. Assembling of the obtained reads produced 235978 contigs from which the contig of containing cytochrome b gene was selected based on the reference gene. The sequence of other camel species was extracted from the database and used based on the fact that the data contained the entire cytochrome b gene, which corresponds to 1140 bp of the reference gene. There is the biggest difference between new world of wild and domestic camels. There was a minimal difference between Arabian and Turkmen camels with 100% similarity, followed by Lama Glama and Lama Guanico, as well as between wild and domestic two-humped camels. The Turkmen camel was completely similar to the Arabian camel and had the greatest difference with wild two-humped camels. In the study of Di Rocco et al. (2010) it was shown that the difference of cytochrome b sequence between wild camels (VV and L Cuanicoe) was 6.4%, which in this study was 6.3% which could be due to the larger number of samples in this study. The phylogenetic tree of cytochrome b protein sequence showed that the llamas and one and two-humped camels are located in different branches of the tree. According to the results of DNA phylogenetic tree, llamas were on one side and two-humped camels were on the other side of the tree and one-humped camels were located between them. There was a great diversity within the population of llamas. Some domestic one and two-humped camels are associated with wild two-humped camels. The results indicate that wild two-humped female camels were mated with domestic one and two-humped males that resulted one and two-humped domestic camels phenotype. The same is true of llamas, with domesticated Lama Glama and Lama Pacos locating among the wild species of Lama Guanicoe and Vicogna vicogna phylogenetic branch. Ming et al. (2016) demonstrated that domestic and wild two-humped camel species are genetically distinct from each other. In this study, it was shown that the domestic and wild two-humped camels is phylogenetically close to each other and distanced from one-humped camels. Based on the cytochrome b sequence, Cui et al. (2007) were concluded that one and two-humped camels separated before migrating to Eurasia. Similarly, in this study, it has been shown that one-humped camels are separated from two-humped camels, then wild and domestic two-humped camels are separated from each other. As a result, there is a greater phylogenetic distance between llamas and humped camels.Conclusion: Iranian one-humped camels can be classified into four genetic groups, two of which are originated from wild and domestic two-humped camels and the other two groups are among the one-humped camels. Iranian domestic two-humped camels were also phylogenetically divided into four genetic groups.
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