Automated genotyping of microsatellite loci from feces with high throughput sequences

Autor: Jennifer A. Leonard, Isabel Salado, Carles Vilà, Alberto Fernández-Gil
Přispěvatelé: Ministerio de Ciencia, Innovación y Universidades (España)
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Heredity
Artificial Gene Amplification and Extension
Polymerase Chain Reaction
Homozygosity
law.invention
Feces
Sequencing techniques
law
Genotype
Multiplex
DNA sequencing
Throughput (business)
Polymerase chain reaction
education.field_of_study
Multidisciplinary
Heterozygosity
Software Engineering
High-Throughput Nucleotide Sequencing
Genomics
Genetic Mapping
Microsatellite
Engineering and Technology
Medicine
Transcriptome Analysis
Research Article
Next-Generation Sequencing
Genotyping
Computer and Information Sciences
Science
Population
Variant Genotypes
Computational biology
Biology
Research and Analysis Methods
Computer Software
Genetics
Animals
education
Molecular Biology Techniques
Molecular Biology
Wolves
Software Tools
Biology and Life Sciences
Computational Biology
Genome Analysis
Genetic Loci
Microsatellite Repeats
Zdroj: PLoS ONE, Vol 16, Iss 10, p e0258906 (2021)
PLoS ONE
PLoS ONE, Vol 16, Iss 10 (2021)
Digital.CSIC. Repositorio Institucional del CSIC
instname
Popis: Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat was the software that provided genotypes with fewer errors. Coverage over 100X provided little additional information, but a relatively high number of PCR replicates were necessary to obtain a high quality genotype from highly unoptimized, multiplexed reactions (10 replicates for 18 of the 19 loci analyzed here). This could be reduced through optimization. The use of new bioinformatic tools and next-generation sequencing data to genotype these highly informative markers may increase throughput at a reasonable cost and with a smaller amount of laboratory work. Thus, high throughput sequencing approaches could facilitate the use of microsatellites with fecal DNA to address ecological and conservation questions
Databáze: OpenAIRE