ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2018
Design and evaluation of a sequence capture system for genome-wide SNP genotyping in highly heterozygous plant genomes: a case study with a keystone Neotropical hardwood tree genome.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 10 citations in OpenAlex.
- Article
- Comparative population genomics in Tabebuia alliance shows evidence of adaptation in Neotropical tree species.Heredity · 2022Article
- Article
- Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm.Frontiers in genetics · 2020Article
- A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree.Heredity · 2019Article
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Authors and funding
4 authors at 3 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Targeted sequence capture coupled to high-throughput sequencing has become a powerful method for the study of genome-wide sequence variation. Following our recent development of a genome assembly for the Pink Ipê tree (Handroanthus impetiginosus), a widely distributed Neotropical timber species, we now report the development of a set of 24,751 capture probes for single-nucleotide polymorphisms (SNPs) characterization and genotyping across 18,216 distinct loci, sampling more than 10 Mbp of the species genome. This system identifies nearly 200,000 SNPs located inside or in close proximity to almost 14,000 annotated protein-coding genes, generating quality genotypic data in populations spanning wide geographic distances across the species native range. To provide recommendations for future developments of similar systems for highly heterozygous plant genomes we investigated issues such as probe design, sequencing coverage and bioinformatics, including the evaluation of the capture efficiency and a reassessment of the technical reproducibility of the assay for SNPs recall and genotyping precision. Our results highlight the value of a detailed probe screening on a preliminary genome assembly to produce reliable data for downstream genetic studies. This work should inspire and assist the development of similar genomic resources for other orphan crops and forest trees with highly heterozygous genomes.
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