Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius

Al-Swailem, Abdulaziz M.; Shehata, Maher M.; Abuduhier, Faisel M.; Alyamani, Essam J.; Al-Busadah, Khalid A.; Alarawi, Mohammed; Al-Khider, Ali Y.; Almuhaimeed, Abdullah; Alqahtani, Fahad; Manee, Manee M.; Al-Shomrani, Badr M.; Al-Qhtani, Saad M.; Alharthi, Amer S.; Akdemir, Kadir C.; Inan, Mehmet Sait; Otu, Hasan H.

doi:10.1371/journal.pone.0010720

Cited by 39 publications

(31 citation statements)

References 44 publications

(44 reference statements)

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“…According to the InterProScan22 annotation (Supplementary Fig. S5), the most common protein domains found in the camel genome are immunoglobulin-like domains, consistent with a previous report18. The largest protein family identified from the camel genome is the rhodopsin-like G protein-coupled receptor family, which, with 1,011 members, is well-known for controlling the signalling pathways of many biological and physiological processes such as feeding, reproduction and behaviour.…”

Section: Resultssupporting

confidence: 86%

“…We also utilized the homology-based method, comparing it with several other mammalian genomes, including human, chimpanzee, mouse, rat, dog, horse and cattle, as well as the published expressed sequence tag data18 of dromedary camels. Combining these two methods, we predicted 20,821 bactrian camel genes, averaging eight exons and 1,322 bps coding region (CDS) per gene.…”

Section: Resultsmentioning

confidence: 99%

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Genome sequences of wild and domestic bactrian camels

Jirimutu¹,

Wang²,

Ding³

et al. 2012

Nat Commun

153

105

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Bactrian camels serve as an important means of transportation in the cold desert regions of China and Mongolia. Here we present a 2.01 Gb draft genome sequence from both a wild and a domestic bactrian camel. We estimate the camel genome to be 2.38 Gb, containing 20,821 protein-coding genes. Our phylogenomics analysis reveals that camels shared common ancestors with other even-toed ungulates about 55–60 million years ago. Rapidly evolving genes in the camel lineage are significantly enriched in metabolic pathways, and these changes may underlie the insulin resistance typically observed in these animals. We estimate the genome-wide heterozygosity rates in both wild and domestic camels to be 1.0 × 10−3. However, genomic regions with significantly lower heterozygosity are found in the domestic camel, and olfactory receptors are enriched in these regions. Our comparative genomics analyses may also shed light on the genetic basis of the camel's remarkable salt tolerance and unusual immune system.

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Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 99%

Genome sequences of wild and domestic bactrian camels

Jirimutu¹,

Wang²,

Ding³

et al. 2012

Nat Commun

153

105

View full text Add to dashboard Cite

show abstract

“…The domestication of a related camelid-the dromedary-also indicates both intentional and chance breeding of domestic and wild camels. Dromedaries are adapted to hot deserts and were domesticated in Arabia (35). Their wild ancestor (Camelus sp.)…”

Section: Management and Gene Flowmentioning

confidence: 99%

“…Culling takes place at low levels and principally affects males, therefore directed selection is low. In contrast, high environmental selection on domestic camel herds is indicated by camelid genetics (30,35). As shown by Bactrian-dromedary crosses, strength and hardiness were important to ancient herders and admixture is thought to have played a role in wild camelid extinctions.…”

Section: Management and Gene Flowmentioning

confidence: 99%

Evaluating the roles of directed breeding and gene flow in animal domestication

Marshall

Dobney

Denham

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

111

117

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For the last 150 y scholars have focused upon the roles of intentional breeding and genetic isolation as fundamental to understanding the process of animal domestication. This analysis of ethnoarchaeological, archaeological, and genetic data suggests that long-term gene flow between wild and domestic stocks was much more common than previously assumed, and that selective breeding of females was largely absent during the early phases of animal domestication. These findings challenge assumptions about severe genetic bottlenecks during domestication, expectations regarding monophyletic origins, and interpretations of multiple domestications. The findings also raise new questions regarding ways in which behavioral and phenotypic domestication traits were developed and maintained.reproductive isolation | selected breeding | zooarchaeology | donkey | pig Domestication resulted in diverse phenotypic and behavioral changes to wild animals, including decreased flight responses, increased sociality, earlier reproduction, and modification of endocrine and metabolic systems (1-4). Darwin's (5) seminal research, heavily influenced by European animal breeding practices during the 19th century, led subsequent scholars studying animal domestication to prioritize the central roles of human intentionality, directed or controlled breeding of individuals, and genetic isolation of captive herds from wild relatives (6). This anthropocentric legacy is evident in various widely used definitions of domestication that emphasize isolation of captive animals from wild species and total human control over breeding and animal care (6-8). However, a growing body of archaeological, genetic, and ethnohistorical evidence discussed here shows that neither reproductive isolation nor intentional breeding of individuals was as significant as traditionally thought. Our findings indicate long-term gene flow between managed and wild animal populations, and little control of breeding of domestic females. These findings challenge assumptions about severe genetic bottlenecks during domestication and interpretations of genetic variability in terms of multiple instances of domestication. The findings also raise questions about ways in which behavioral and phenotypic domestication traits were maintained.Research into dog and pig domestication over the last several decades has drawn attention to the roles of nonhuman drivers in the domestication process (9, 10)

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“…There are transcripts homologous to hspA1A and hspA1B in the transcriptome [18]. However, the genome of C. dromedarius has not yet been sequenced, and the general organization of the cluster and the promoter structure of hsp70 family genes of this exceptionally thermoresistant organism are unknown.…”

Section: Introductionmentioning

confidence: 99%

Functional Organization of hsp70 Cluster in Camel (Camelus dromedarius) and Other Mammals

et al. 2011

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Heat shock protein 70 (Hsp70) is a molecular chaperone providing tolerance to heat and other challenges at the cellular and organismal levels. We sequenced a genomic cluster containing three hsp70 family genes linked with major histocompatibility complex (MHC) class III region from an extremely heat tolerant animal, camel (Camelus dromedarius). Two hsp70 family genes comprising the cluster contain heat shock elements (HSEs), while the third gene lacks HSEs and should not be induced by heat shock. Comparison of the camel hsp70 cluster with the corresponding regions from several mammalian species revealed similar organization of genes forming the cluster. Specifically, the two heat inducible hsp70 genes are arranged in tandem, while the third constitutively expressed hsp70 family member is present in inverted orientation. Comparison of regulatory regions of hsp70 genes from camel and other mammals demonstrates that transcription factor matches with highest significance are located in the highly conserved 250-bp upstream region and correspond to HSEs followed by NF-Y and Sp1 binding sites. The high degree of sequence conservation leaves little room for putative camel-specific regulatory elements. Surprisingly, RT-PCR and 5′/3′-RACE analysis demonstrated that all three hsp70 genes are expressed in camel's muscle and blood cells not only after heat shock, but under normal physiological conditions as well, and may account for tolerance of camel cells to extreme environmental conditions. A high degree of evolutionary conservation observed for the hsp70 cluster always linked with MHC locus in mammals suggests an important role of such organization for coordinated functioning of these vital genes.

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Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius

Cited by 39 publications

References 44 publications

Genome sequences of wild and domestic bactrian camels

Genome sequences of wild and domestic bactrian camels

Evaluating the roles of directed breeding and gene flow in animal domestication

Functional Organization of hsp70 Cluster in Camel (Camelus dromedarius) and Other Mammals

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