The <i>de novo</i> genome assembly and annotation of a female domestic dromedary of North African origin

Fitak, Robert R.; Mohandesan, Elmira; Corander, Jukka; Burger, Pamela A.

doi:10.1111/1755-0998.12443

Cited by 60 publications

(102 citation statements)

References 70 publications

(149 reference statements)

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“…A weak genetic differentiation has been observed also in the preliminary study by Ciani et al[61], performed using genome-wide SNP markers genotyped by double digest Restriction Associated DNA sequencing (ddRADseq), on African and Asiatic dromedaries. Together with the recent evidence for a low SNP density in dromedary genomes compared to genomes of domestic Bactrian, and even compared to genomes of the very small residual population of wild Camelus ferus animals [62], likely due to successive climate-driven demographic bottlenecks in the wild progenitor of Camelus dromedarius , this lack of genetic structure deserves close attention in view of the ongoing intensification process in the camel farming system [63] and the growing request for application of modern genetic improvement (bio)technologies. Notably, schemes of genomic selection across multiple populations are likely to represent the future choice for this species, in order to allow larger reference populations to be available (thus accounting for possibly lower linkage disequilibrium levels in dromedaries compared to other livestock species), and to take advantage from implementation of cross-border cost-sharing strategies.…”

Section: Discussionmentioning

confidence: 98%

Weak Genetic Structure in Northern African Dromedary Camels Reflects Their Unique Evolutionary History

et al. 2017

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Knowledge on genetic diversity and structure of camel populations is fundamental for sustainable herd management and breeding program implementation in this species. Here we characterized a total of 331 camels from Northern Africa, representative of six populations and thirteen Algerian and Egyptian geographic regions, using 20 STR markers. The nineteen polymorphic loci displayed an average of 9.79 ± 5.31 alleles, ranging from 2 (CVRL8) to 24 (CVRL1D). Average He was 0.647 ± 0.173. Eleven loci deviated significantly from Hardy-Weinberg proportions (P<0.05), due to excess of homozygous genotypes in all cases except one (CMS18). Distribution of genetic diversity along a weak geographic gradient as suggested by network analysis was not supported by either unsupervised and supervised Bayesian clustering. Traditional extensive/nomadic herding practices, together with the historical use as a long-range beast of burden and its peculiar evolutionary history, with domestication likely occurring from a bottlenecked and geographically confined wild progenitor, may explain the observed genetic patterns.

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Section: Discussionmentioning

confidence: 98%

Weak Genetic Structure in Northern African Dromedary Camels Reflects Their Unique Evolutionary History

et al. 2017

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“…This multipurpose animal has outperformed all other domestic mammals, including the donkey, in arid environments and continues to provide basic commodities to millions of people inhabiting marginal agro-ecological zones. In the current context of advancing desertification and global climate change, there is renewed interest in the biology and production traits of the species (2), with the first annotated genome drafts having been recently released (3,4).…”

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confidence: 99%

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Almathen

Charruau

Mohandesan

et al. 2016

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

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Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species' range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the "restocking from the wild" hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.anthropogenic admixture | Camelus dromedarius | demographic history | paleogenetics | wild dromedary T he dromedary (Camelus dromedarius) is one of the largest domestic ungulates and one of the most recent additions to livestock. Known as the "ship of the desert" (1), it enabled the transportation of people and valuable goods (e.g., salt, incense, spices) over long distances connecting Arabia, the Near East, and North Africa. This multipurpose animal has outperformed all other domestic mammals, including the donkey, in arid environments and continues to provide basic commodities to millions of people inhabiting marginal agro-ecological zones. In the current context of advancing desertification and global climate change, there is renewed interest in the biology and production traits of the species (2), with the first annotated genome drafts having been recently released (3, 4). SignificanceThe dromedary is one of the largest domesticates, sustainably used in arid and hostile environments. It provides food and transport to millions of people in marginal agricultural areas. We show how important long-distance and back-and-forth movements in ancient caravan routes shaped the species' genetic diversity. Using a global sample set and ancient mitochondrial DNA analyses, we describe the population structure in modern dromedaries and their wild extinct ancestors. Phylogenetic analyses of ancient and modern dro...

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“…We also included MAKER predicted proteins with an annotation edit distance (AED) <0.75 from the CamDro1 assembly (Fitak et al, ). For the first MAKER run, we trained Augustus using busco v. 3.0.2 (Simão, Waterhouse, Ioannidis, Kriventseva, & Zdobnov, ) searching for Eukaroyota orthodb v. 9.1 genes (Zdobnov et al, ) against CamDro2.…”

Section: Methodsmentioning

confidence: 99%

Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary

Elbers

Rogers

Perelman

et al. 2019

Molecular Ecology Resources

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Researchers have assembled thousands of eukaryotic genomes using Illumina reads, but traditional mate‐pair libraries cannot span all repetitive elements, resulting in highly fragmented assemblies. However, both chromosome conformation capture techniques, such as Hi‐C and Dovetail Genomics Chicago libraries and long‐read sequencing, such as Pacific Biosciences and Oxford Nanopore, help span and resolve repetitive regions and therefore improve genome assemblies. One important livestock species of arid regions that does not have a high‐quality contiguous reference genome is the dromedary ( Camelus dromedarius ). Draft genomes exist but are highly fragmented, and a high‐quality reference genome is needed to understand adaptation to desert environments and artificial selection during domestication. Dromedaries are among the last livestock species to have been domesticated, and together with wild and domestic Bactrian camels, they are the only representatives of the Camelini tribe, which highlights their evolutionary significance. Here we describe our efforts to improve the North African dromedary genome. We used Chicago and Hi‐C sequencing libraries from Dovetail Genomics to resolve the order of previously assembled contigs, producing almost chromosome‐level scaffolds. Remaining gaps were filled with Pacific Biosciences long reads, and then scaffolds were comparatively mapped to chromosomes. Long reads added 99.32 Mbp to the total length of the new assembly. Dovetail Chicago and Hi‐C libraries increased the longest scaffold over 12‐fold, from 9.71 Mbp to 124.99 Mbp and the scaffold N50 over 50‐fold, from 1.48 Mbp to 75.02 Mbp. We demonstrate that Illumina de novo assemblies can be substantially upgraded by combining chromosome conformation capture and long‐read sequencing.

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The de novo genome assembly and annotation of a female domestic dromedary of North African origin

Cited by 60 publications

References 70 publications

Weak Genetic Structure in Northern African Dromedary Camels Reflects Their Unique Evolutionary History

Weak Genetic Structure in Northern African Dromedary Camels Reflects Their Unique Evolutionary History

Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary

Improving Illumina assemblies with Hi‐C and long reads: An example with the North African dromedary

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