dc.contributor.author	Sharma, Reeta
dc.contributor.author	Goossens, Benoit
dc.contributor.author	Kun-Rodrigues, Célia
dc.contributor.author	Teixeira, Tatiana
dc.contributor.author	Othman, Nurzhafarina
dc.contributor.author	Boone, Jason Q.
dc.contributor.author	Jue, Nathaniel K.
dc.contributor.author	Obergfell, Craig
dc.contributor.author	O'Neill, Rachel J.
dc.contributor.author	Chikhi, Lounès
dc.date.accessioned	2017-04-06T11:05:15Z
dc.date.available	2017-04-06T11:05:15Z
dc.date.issued	2012-11-21
dc.description.abstract	High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering genomic data in natural populations, laying the empirical foundation for future research in the field of conservation and population genomics. Here we present the case study of the Bornean elephant, which is the most endangered subspecies of Asian elephant and exhibits very low genetic diversity. We used two different sequencing platforms, the Roche 454 FLX (shotgun) and Illumina, GAIIx (Restriction site associated DNA, RAD) to evaluate the feasibility of the two methodologies for the discovery of de novo markers (single nucleotide polymorphism, SNPs and microsatellites) using low coverage data. Approximately, 6,683 (shotgun) and 14,724 (RAD) SNPs were detected within our elephant sequence dataset. Genotyping of a representative sample of 194 SNPs resulted in a SNP validation rate of ~83 to 94% and 17% of the loci were polymorphic with a low diversity (H(o)=0.057). Different numbers of microsatellites were identified through shotgun (27,226) and RAD (868) techniques. Out of all di-, tri-, and tetra-microsatellite loci, 1,706 loci had sufficient flanking regions (shotgun) while only 7 were found with RAD. All microsatellites were monomorphic in the Bornean but polymorphic in another elephant subspecies. Despite using different sample sizes, and the well known differences in the two platforms used regarding sequence length and throughput, the two approaches showed high validation rate. The approaches used here for marker development in a threatened species demonstrate the utility of high throughput sequencing technologies as a starting point for the development of genomic tools in a non-model species and in particular for a species with low genetic diversity.	pt_PT
dc.description.sponsorship	‘‘Laboratoire d’Excellence (LABEX)’’ entitled TULIP grant: (ANR-10-LABX-41); Darwin Initiative for the Survival of Species grant: (09/016, DEFRA, UK).	pt_PT
dc.description.version	info:eu-repo/semantics/publishedVersion	pt_PT
dc.identifier.citation	Sharma R, Goossens B, Kun-Rodrigues C, Teixeira T, Othman N, et al. (2012) Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant. PLoS ONE 7(11): e49533. doi:10.1371/journal.pone.0049533	pt_PT
dc.identifier.doi	10.1371/journal.pone.0049533	pt_PT
dc.identifier.uri	http://hdl.handle.net/10400.7/745
dc.language.iso	eng	pt_PT
dc.peerreviewed	yes	pt_PT
dc.publisher	Public Library of Science	pt_PT
dc.relation	DEMOGRAPHIC AND GENETICS RESPONSE TO HABITAT FRAGMENTATION AND HABITAT LOSS IN LARGE FOREST MAMMALS OF BORNEO
dc.relation.publisherversion	http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049533	pt_PT
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	pt_PT
dc.subject	Animals	pt_PT
dc.subject	Chromosome Mapping	pt_PT
dc.subject	Contig Mapping	pt_PT
dc.subject	Elephants	pt_PT
dc.subject	Genetic Markers	pt_PT
dc.subject	Genetic Variation	pt_PT
dc.subject	Genetics, Population	pt_PT
dc.subject	Genome	pt_PT
dc.subject	Genotype	pt_PT
dc.subject	High-Throughput Nucleotide Sequencing	pt_PT
dc.subject	Microsatellite Repeats	pt_PT
dc.subject	Models, Genetic	pt_PT
dc.subject	Polymorphism, Single Nucleotide	pt_PT
dc.subject	Sequence Analysis, DNA	pt_PT
dc.subject	Genomics	pt_PT
dc.title	Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant	pt_PT
dc.type	journal article
dspace.entity.type	Publication
oaire.awardTitle	DEMOGRAPHIC AND GENETICS RESPONSE TO HABITAT FRAGMENTATION AND HABITAT LOSS IN LARGE FOREST MAMMALS OF BORNEO
oaire.awardURI	info:eu-repo/grantAgreement/FCT//SFRH%2FBPD%2F64837%2F2009/PT
oaire.awardURI	info:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBIA-BDE%2F71299%2F2006/PT
oaire.citation.endPage	11	pt_PT
oaire.citation.issue	11	pt_PT
oaire.citation.startPage	1	pt_PT
oaire.citation.title	PLoS ONE	pt_PT
oaire.citation.volume	7	pt_PT
oaire.fundingStream	3599-PPCDT
project.funder.identifier	http://doi.org/10.13039/501100001871
project.funder.identifier	http://doi.org/10.13039/501100001871
project.funder.name	Fundação para a Ciência e a Tecnologia
project.funder.name	Fundação para a Ciência e a Tecnologia
rcaap.rights	openAccess	pt_PT
rcaap.type	article	pt_PT
relation.isProjectOfPublication	478d0d4e-6e0b-493c-93cd-2d13a1ddc3ac
relation.isProjectOfPublication	052afccd-1dd7-4ed6-ac05-2791a8f2730d
relation.isProjectOfPublication.latestForDiscovery	478d0d4e-6e0b-493c-93cd-2d13a1ddc3ac

Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant

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