Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data

Hedayat-Evrigh, Nemat; Khalkhali-Evrigh, Reza; Bakhtiarizadeh, Mohammad Reza

doi:10.1155/2020/2430846

Cited by 11 publications

(8 citation statements)

References 37 publications

(43 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As a result of sequencing, raw data in *.fastq format was obtained, and the total number of reads varied from 717,006,544 to 1,377,460,994 among five camels. This result was consistent with the whole genome sequencing results of Iranian camels, as the average number of reads is fairly similar [23,43]. The average GC content, which typically includes many protein-coding genes, was 41.92%, and Q30 was 92.99%.…”

Section: Whole Genome Sequencing and Data Filteringsupporting

confidence: 87%

A Study of the Genetic Structure of Hybrid Camels in Kazakhstan

Amandykova

Dossybayev

Mussayeva

et al. 2023

Genes

View full text Add to dashboard Cite

Camel farming is gaining scientific interest due to its unique agricultural characteristics. Camels are versatile for milk and meat production, wool, racing, transport, and tourism. To use their full potential, it is essential to improve our understanding of the genetic structure of these animals. One-humped and two-humped camels have received detailed genetic descriptions, while there is no such information for their hybrids, which outperform their parent species in several agricultural characteristics. Thus, in this study, for the first time, the whole genome sequencing data (WGS) of five hybrid camels bred in the Almaty region of Kazakhstan are presented in comparison with the WGS data of one-humped, two-humped, and wild camels. A total of 43,552,164 single-nucleotide polymorphisms were found across the studied groups. Further comparison of these SNPs showed the following number of private SNPs among the populations: hybrid camels (3,271,083), wild camels (2,515,591), Bactrians (1,244,694), and dromedaries (531,224). The genetic structure of the studied animals was described, and a phylogenetic tree was built to assess their genetic distance. It was found that the studied hybrids are genetically closer to dromedaries since they were on the close branch of the phylogenetic tree.

show abstract

Section: Whole Genome Sequencing and Data Filteringsupporting

confidence: 87%

A Study of the Genetic Structure of Hybrid Camels in Kazakhstan

Amandykova

Dossybayev

Mussayeva

et al. 2023

Genes

View full text Add to dashboard Cite

show abstract

“…This result was consistent with the findings based on mitochondrial sequence analysis which revealed that despite the small number of IB camels, they showed higher genetic diversity 19 . Also, based on microsatellite and WGS data, high heterozygosity was calculated for IB camels 5 , 20 , 21 .…”

Section: Discussionmentioning

confidence: 99%

Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data

Khalkhali-Evrigh

Hedayat

Liang

et al. 2022

Sci Rep

Self Cite

View full text Add to dashboard Cite

The Old World camels play an important role as one of the main food sources in large parts of Asia and Africa. Natural selection combined with artificial selection by human has affected parts of the domestic animal genome for adapting them to their habitats and meeting human needs. Here, we used whole genome sequencing data of 34 camels (including 14 dromedaries and 20 Bactrian camels) to identify the genomic signature of selection in the Iranian dromedary (ID) and Bactrian camels (IB). To detect the mentioned regions, we used two methods including population differentiation index (Fst) and cross-population extended haplotype homozygosity (XP-EHH) with 50 kb sliding window and 25 kb step size. Based on gene ontology analysis on the candidate genes identified for IB camels, we found GO terms associated with lung development, nervous system development, immune system and behavior. Also, we identified several genes related to body thermoregulation (ZNF516), meat quality (ANK1 and HSPA13), and high-altitude adaptation (OPA1) for IB camels. In the list of detected candidate genes under selection in ID camels, the genes related to energy metabolism (BDH1), reproduction (DLG1, IMMP2L and FRASI), long-term memory (GRIA1), kidney (SLC12A1), lung development (EMILIN2 and FBN1) and immunity (SOCS2, JAK1, NRROS and SENP1) were found. Our findings, along with further studies in this field, will strengthen our knowledge about the effect of selection on the camelid genome under different geographical, climatic and even cultural conditions.

show abstract

“…They can store energy in the form of fat deposit, and can survive for a long time in the case of water and food shortage. The blood sugar levels of camels are more than twice as high as those of other ruminants, but they do not develop metabolic diseases and show associated pathological features ( 16 , 17 ). It has also been reported that Bactrian camels may have potential immunotherapeutic roles in cancer treatment and prevention because of their unique habits and extreme living conditions ( 18 – 20 ).…”

Section: Introductionmentioning

confidence: 99%

Effects of plasma-derived exosomes from the normal and thin Bactrian camels on hepatocellular carcinoma and their differences at transcriptome and proteomics levels

Yao

Yu²,

Luo³

et al. 2023

Front. Oncol.

View full text Add to dashboard Cite

BackgroundHepatocellular carcinoma (HCC) is a common malignant primary tumor. Bactrian camels have high economic and social values, but their potential medical value has not been studied. This study aimed to investigate the effects of Bactrian camel plasma-derived exosomes on HCC.MethodsPlasma was obtained from thin and normal Bactrian camels, and used to isolate exosomes by ultracentrifugation. The exosomes were then characterized by transmission electron microscopy and Nano particle tracking analyzer. In vivo imaging of nude mice and hematoxylin eosin (HE) staining of liver tissues were used to explore the effects of the exosomes on tumor growth. Finally, the differences of the two exosomes were further analyzed using small RNA sequencing and proteomics.ResultsIn vivo imaging and HE staining showed that no significant differences were found in fluorescence value and liver tissue morphology between the control mice and the mice treated with the exosomes from thin Bactrian camels; while the fluorescence value and the live histology changes were alleviated in the mice with the exosomes from normal Bactrian camels. After sequencing and proteomic analysis, 40 differentially expressed miRNAs (DE-miRNAs, 15 down-regulated and 25 up-regulated) and 172 differentially expressed proteins (DEPs, 77 up-regulated and 95 down-regulated) were identified in the plasma-derived exosomes from normal Bactrian camels. These identified DE-miRNAs and DEPs were significantly enriched in many signaling pathways.ConclusionsNormal Bactrian camel plasma-derived exosomes may inhibit the growth of HCC cells through regulating pathways of Ras, Ras-Association Proximate 1 (Rap1), phosphoinositide 3-kinase-protein kinase B (PI3K-Akt), mitogen-activated protein kinase (MAPK), adenosine monophosphate-activated protein kinase (AMPK), and canonical Wnt signaling pathways.

show abstract

Genome-Wide Identification and Analysis of Variants in Domestic and Wild Bactrian Camels Using Whole-Genome Sequencing Data

Cited by 11 publications

References 37 publications

A Study of the Genetic Structure of Hybrid Camels in Kazakhstan

A Study of the Genetic Structure of Hybrid Camels in Kazakhstan

Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data

Effects of plasma-derived exosomes from the normal and thin Bactrian camels on hepatocellular carcinoma and their differences at transcriptome and proteomics levels

Contact Info

Product

Resources

About