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Bergwell M, Smith A, Smith E, Dierlam C, Duran R, Haastrup E, Napier-Jameson R, Seidel R, Potter W, Norris A, Iyer J. A primary microcephaly-associated sas-6 mutation perturbs centrosome duplication, dendrite morphogenesis, and ciliogenesis in Caenorhabditis elegans. Genetics 2023; 224:iyad105. [PMID: 37279547 PMCID: PMC10411591 DOI: 10.1093/genetics/iyad105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023] Open
Abstract
The human SASS6(I62T) missense mutation has been linked with the incidence of primary microcephaly in a Pakistani family, although the mechanisms by which this mutation causes disease remain unclear. The SASS6(I62T) mutation corresponds to SAS-6(L69T) in Caenorhabditis elegans. Given that SAS-6 is highly conserved, we modeled this mutation in C. elegans and examined the sas-6(L69T) effect on centrosome duplication, ciliogenesis, and dendrite morphogenesis. Our studies revealed that all the above processes are perturbed by the sas-6(L69T) mutation. Specifically, C. elegans carrying the sas-6(L69T) mutation exhibit an increased failure of centrosome duplication in a sensitized genetic background. Further, worms carrying this mutation also display shortened phasmid cilia, an abnormal phasmid cilia morphology, shorter phasmid dendrites, and chemotaxis defects. Our data show that the centrosome duplication defects caused by this mutation are only uncovered in a sensitized genetic background, indicating that these defects are mild. However, the ciliogenesis and dendritic defects caused by this mutation are evident in an otherwise wild-type background, indicating that they are stronger defects. Thus, our studies shed light on the novel mechanisms by which the sas-6(L69T) mutation could contribute to the incidence of primary microcephaly in humans.
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Affiliation(s)
- Mary Bergwell
- Oklahoma Medical Research Foundation, Cell Cycle & Cancer Biology Research Program, Oklahoma City, OK 73104, USA
| | - Amy Smith
- Pfizer Inc., Pharmaceutical R&D – Drug Product Design & Development, Chesterfield, MO 63017, USA
| | - Ellie Smith
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - Carter Dierlam
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - Ramon Duran
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - Erin Haastrup
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | | | - Rory Seidel
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - William Potter
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
| | - Adam Norris
- Southern Methodist University, Department of Biological Sciences, Dallas, TX 75275, USA
| | - Jyoti Iyer
- University of Tulsa, Department of Chemistry and Biochemistry, Tulsa, OK 74104, USA
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Andersen EC, Rockman MV. Natural genetic variation as a tool for discovery in Caenorhabditis nematodes. Genetics 2022; 220:iyab156. [PMID: 35134197 PMCID: PMC8733454 DOI: 10.1093/genetics/iyab156] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/11/2021] [Indexed: 11/12/2022] Open
Abstract
Over the last 20 years, studies of Caenorhabditis elegans natural diversity have demonstrated the power of quantitative genetic approaches to reveal the evolutionary, ecological, and genetic factors that shape traits. These studies complement the use of the laboratory-adapted strain N2 and enable additional discoveries not possible using only one genetic background. In this chapter, we describe how to perform quantitative genetic studies in Caenorhabditis, with an emphasis on C. elegans. These approaches use correlations between genotype and phenotype across populations of genetically diverse individuals to discover the genetic causes of phenotypic variation. We present methods that use linkage, near-isogenic lines, association, and bulk-segregant mapping, and we describe the advantages and disadvantages of each approach. The power of C. elegans quantitative genetic mapping is best shown in the ability to connect phenotypic differences to specific genes and variants. We will present methods to narrow genomic regions to candidate genes and then tests to identify the gene or variant involved in a quantitative trait. The same features that make C. elegans a preeminent experimental model animal contribute to its exceptional value as a tool to understand natural phenotypic variation.
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Affiliation(s)
- Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60201, USA
| | - Matthew V Rockman
- Department of Biology and Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
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MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes. Genetics 2017; 207:447-463. [PMID: 28827289 PMCID: PMC5629315 DOI: 10.1534/genetics.117.300179] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/30/2017] [Indexed: 11/18/2022] Open
Abstract
Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2. We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures.
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Davies T, Sundaramoorthy S, Jordan S, Shirasu-Hiza M, Dumont J, Canman J. Using fast-acting temperature-sensitive mutants to study cell division in Caenorhabditis elegans. Methods Cell Biol 2017; 137:283-306. [DOI: 10.1016/bs.mcb.2016.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Doitsidou M, Jarriault S, Poole RJ. Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification in Caenorhabditis elegans. Genetics 2016; 204:451-474. [PMID: 27729495 PMCID: PMC5068839 DOI: 10.1534/genetics.115.186197] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023] Open
Abstract
The use of next-generation sequencing (NGS) has revolutionized the way phenotypic traits are assigned to genes. In this review, we describe NGS-based methods for mapping a mutation and identifying its molecular identity, with an emphasis on applications in Caenorhabditis elegans In addition to an overview of the general principles and concepts, we discuss the main methods, provide practical and conceptual pointers, and guide the reader in the types of bioinformatics analyses that are required. Owing to the speed and the plummeting costs of NGS-based methods, mapping and cloning a mutation of interest has become straightforward, quick, and relatively easy. Removing this bottleneck previously associated with forward genetic screens has significantly advanced the use of genetics to probe fundamental biological processes in an unbiased manner.
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Affiliation(s)
- Maria Doitsidou
- Centre for Integrative Physiology, University of Edinburgh, EH8 9XD, Scotland
| | - Sophie Jarriault
- L'Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR 7104/Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, 67404, France
| | - Richard J Poole
- Department of Cell and Developmental Biology, University College London, WC1E 6BT, United Kingdom
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Lowry J, Yochem J, Chuang CH, Sugioka K, Connolly AA, Bowerman B. High-Throughput Cloning of Temperature-Sensitive Caenorhabditis elegans Mutants with Adult Syncytial Germline Membrane Architecture Defects. G3 (BETHESDA, MD.) 2015; 5:2241-55. [PMID: 26311651 PMCID: PMC4632044 DOI: 10.1534/g3.115.021451] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/21/2015] [Indexed: 12/30/2022]
Abstract
The adult Caenorhabditis elegans hermaphrodite gonad consists of two mirror-symmetric U-shaped arms, with germline nuclei located peripherally in the distal regions of each arm. The nuclei are housed within membrane cubicles that are open to the center, forming a syncytium with a shared cytoplasmic core called the rachis. As the distal germline nuclei progress through meiotic prophase, they move proximally and eventually cellularize as their compartments grow in size. The development and maintenance of this complex and dynamic germline membrane architecture are relatively unexplored, and we have used a forward genetic screen to identify 20 temperature-sensitive mutations in 19 essential genes that cause defects in the germline membrane architecture. Using a combined genome-wide SNP mapping and whole genome sequencing strategy, we have identified the causal mutations in 10 of these mutants. Four of the genes we have identified are conserved, with orthologs known to be involved in membrane biology, and are required for proper development or maintenance of the adult germline membrane architecture. This work provides a starting point for further investigation of the mechanisms that control the dynamics of syncytial membrane architecture during adult oogenesis.
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Affiliation(s)
- Josh Lowry
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - John Yochem
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Chien-Hui Chuang
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Kenji Sugioka
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Amy A Connolly
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Bruce Bowerman
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
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Candela H, Casanova-Sáez R, Micol JL. Getting started in mapping-by-sequencing. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:606-12. [PMID: 25359627 DOI: 10.1111/jipb.12305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/28/2014] [Indexed: 05/06/2023]
Abstract
Next-generation sequencing (NGS) technologies allow the cost-effective sequencing of whole genomes and have expanded the scope of genomics to novel applications, such as the genome-wide characterization of intraspecific polymorphisms and the rapid mapping and identification of point mutations. Next-generation sequencing platforms, such as the Illumina HiSeq2000 platform, are now commercially available at affordable prices and routinely produce an enormous amount of sequence data, but their wide use is often hindered by a lack of knowledge on how to manipulate and process the information produced. In this review, we focus on the strategies that are available to geneticists who wish to incorporate these novel approaches into their research but who are not familiar with the necessary bioinformatic concepts and computational tools. In particular, we comprehensively summarize case studies where the use of NGS technologies has led to the identification of point mutations, a strategy that has been dubbed "mapping-by-sequencing", and review examples from plants and other model species such as Caenorhabditis elegans, Saccharomyces cerevisiae, and Drosophila melanogaster. As these technologies are becoming cheaper and more powerful, their use is also expanding to allow mutation identification in species with larger genomes, such as many crop plants.
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Affiliation(s)
- Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Rubén Casanova-Sáez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
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Zhang N, Zhang L, Tao Y, Guo L, Sun J, Li X, Zhao N, Peng J, Li X, Zeng L, Chen J, Yang G. Construction of a high density SNP linkage map of kelp (Saccharina japonica) by sequencing Taq I site associated DNA and mapping of a sex determining locus. BMC Genomics 2015; 16:189. [PMID: 25887315 PMCID: PMC4369078 DOI: 10.1186/s12864-015-1371-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Kelp (Saccharina japonica) has been intensively cultured in China for almost a century. Its genetic improvement is comparable with that of rice. However, the development of its molecular tools is extremely limited, thus its genes, genetics and genomics. Kelp performs an alternative life cycle during which sporophyte generation alternates with gametophyte generation. The gametophytes of kelp can be cloned and crossed. Due to these characteristics, kelp may serve as a reference for the biological and genetic studies of Volvox, mosses and ferns. RESULTS We constructed a high density single nucleotide polymorphism (SNP) linkage map for kelp by restriction site associated DNA (RAD) sequencing. In total, 4,994 SNP-containing physical (tag-defined) RAD loci were mapped on 31 linkage groups. The map expanded a total genetic distance of 1,782.75 cM, covering 98.66% of the expected (1,806.94 cM). The length of RAD tags (85 bp) was extended to 400-500 bp with Miseq method, offering us an easiness of developing SNP chips and shifting SNP genotyping to a high throughput track. The number of linkage groups was in accordance with the documented with cytological methods. In addition, we identified a set of microsatellites (99 in total) from the extended RAD tags. A gametophyte sex determining locus was mapped on linkage group 2 in a window about 9.0 cM in width, which was 2.66 cM up to marker_40567 and 6.42 cM down to marker_23595. CONCLUSIONS A high density SNP linkage map was constructed for kelp, an intensively cultured brown alga in China. The RAD tags were also extended so that a SNP chip could be developed. In addition, a set of microsatellites were identified among mapped loci, and a gametophyte sex determining locus was mapped. This map will facilitate the genetic studies of kelp including for example the evaluation of germplasm and the decipherment of the genetic bases of economic traits.
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Affiliation(s)
- Ning Zhang
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Linan Zhang
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Ye Tao
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Li Guo
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
| | - Juan Sun
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Xia Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Nan Zhao
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Jie Peng
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China; Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-tech Co., Ltd, Yantai, Shandong, 264003, China.
| | - Liang Zeng
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Jinsa Chen
- Majorbio Pharm Technology Co., Ltd, Shanghai, 201203, China.
| | - Guanpin Yang
- Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 2014; 15:662-76. [PMID: 25139187 DOI: 10.1038/nrg3745] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The long-lasting success of forward genetic screens relies on the simple molecular basis of the characterized phenotypes, which are typically caused by mutations in single genes. Mapping the location of causal mutations using genetic crosses has traditionally been a complex, multistep procedure, but next-generation sequencing now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds. Recent advances of this mapping-by-sequencing approach include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information, which make forward genetics amenable for species that have not been considered for forward genetic screens so far.
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Affiliation(s)
- Korbinian Schneeberger
- Genome Plasticity and Computational Genetics, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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Zuryn S, Jarriault S. Deep sequencing strategies for mapping and identifying mutations from genetic screens. WORM 2013; 2:e25081. [PMID: 24778934 PMCID: PMC3875646 DOI: 10.4161/worm.25081] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 11/23/2022]
Abstract
The development of next-generation sequencing technologies has enabled rapid and cost effective whole genome sequencing. This technology has allowed researchers to shortcut time-consuming and laborious methods used to identify nucleotide mutations in forward genetic screens in model organisms. However, causal mutations must still be mapped to a region of the genome so as to aid in their identification. This can be achieved simultaneously with deep sequencing through various methods. Here we discuss alternative deep sequencing strategies for simultaneously mapping and identifying causal mutations in Caenorhabditis elegans from mutagenesis screens. Focusing on practical considerations, such as the particular mutant phenotype obtained, this review aims to aid the reader in choosing which strategy to adopt to successfully clone their mutant.
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Affiliation(s)
- Steven Zuryn
- Institut de GA(c)nA(c)tique et de Biologie MolA(c)culaire et Cellulaire (IGBMC); Institut National de la SantA(c) et de la Recherche MA(c)dicale (INSERM) U964/Centre National de la Recherche Scientifique (CNRS) UMR 1704/UniversitA(c) de Strasbourg; Strasbourg, France
| | - Sophie Jarriault
- Institut de GA(c)nA(c)tique et de Biologie MolA(c)culaire et Cellulaire (IGBMC); Institut National de la SantA(c) et de la Recherche MA(c)dicale (INSERM) U964/Centre National de la Recherche Scientifique (CNRS) UMR 1704/UniversitA(c) de Strasbourg; Strasbourg, France
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Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted Bornean elephant. PLoS One 2012. [PMID: 23185354 PMCID: PMC3504023 DOI: 10.1371/journal.pone.0049533] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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 (Ho = 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.
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