Data from: Expected genotype quality and diploidized marker data from genotyping-by-sequencing of Urochloa spp. tetraploids

Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification, conditioned on the true genotype, which we call Expected Genotype Quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) compared with 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in Variant Call Format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa (syn. Brachiaria). When reads were aligned to a mock reference genome created from GBS data of the U. brizantha cultivar ‘Marandu’, 25,678 bi-allelic SNPs were discovered, compared to approximately 3000 SNPs when aligning to the closest true reference genomes, Setaria viridis and S. italica. Cross-validation revealed that missing genotypes were imputed by the Random Forest method with a median accuracy of 0.85, regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on GQ creates genotype bias; a depth threshold based on EGQ is also needed, regardless of whether genotypes are called using a diploidized or allele dosage model

Fungal L-asparaginase : strategies for production and food applications

L-asparaginase (L-asparagine amidohydrolase EC 3.5.1.1) is of great importance in pharmaceutical and food applications. This review aims to describe the production and use of fungal L-asparaginase focusing on its potential as an effective reducer of acrylamide in different food applications. Fungal asparaginases have been used as food additives and have gained importance due to some technical advantages, for example, fungi can grow using low-cost culture mediums, and the enzyme is extracellular, which facilitates purification steps. Research aimed at the discovery of new L-asparaginases, mainly those produced by fungi, have great potential to obtain cheaper enzymes with desirable properties for application in food aiming at the reduction of acrylamide126COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPES23038.000795/2018-61; 00

Expected genotype quality and diploidized marker data from genotyping-by-sequencing of Urochloa spp. Tetraploids

Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with similar to 3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Cross-validation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model.12319CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESSem informaçãoSem informaçã

Genome assembly of a highly aldehyde-resistant saccharomyces cerevisiae SA1-derived industrial strain

Here, we report the genome assembly of a Saccharomyces cerevisiae SA1-derived haploid (FMY097) indigenous strain isolated from a Brazilian ethanol distillery. FMY097 was recently reported to be a highly aldehyde-resistant strain capable of producing bioethanol in the presence of up to 40 mM furfural and 80 mM 5-hydroxymethylfurfural813COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPnão tem2013/08293-7; 2014/26905-2; 2015/06263-9; 2015/06677-8; 2016/02506-