A Genomic Reference Panel for Drosophila serrata

G3 : Genes - Genomes - Genetics
Adam J ReddiexS F Chenoweth

Abstract

Here we describe a collection of re-sequenced inbred lines of Drosophila serrata, sampled from a natural population situated deep within the species endemic distribution in Brisbane, Australia. D. serrata is a member of the speciose montium group whose members inhabit much of south east Asia and has been well studied for aspects of climatic adaptation, sexual selection, sexual dimorphism, and mate recognition. We sequenced 110 lines that were inbred via 17-20 generations of full-sib mating at an average coverage of 23.5x with paired-end Illumina reads. 15,228,692 biallelic SNPs passed quality control after being called using the Joint Genotyper for Inbred Lines (JGIL). Inbreeding was highly effective and the average levels of residual heterozygosity (0.86%) were well below theoretical expectations. As expected, linkage disequilibrium decayed rapidly, with r2 dropping below 0.1 within 100 base pairs. With the exception of four closely related pairs of lines which may have been due to technical errors, there was no statistical support for population substructure. Consistent with other endemic populations of other Drosophila species, preliminary population genetic analyses revealed high nucleotide diversity and, on average, negati...Continue Reading

Associated Datasets

Feb 23, 2018·Stephen F. ChenowethScott L. Allen

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Citations

May 8, 2018·Proceedings of the National Academy of Sciences of the United States of America·Thomas P GosdenStephen F Chenoweth
Jul 31, 2021·Proceedings of the National Academy of Sciences of the United States of America·Robert J DugandKatrina McGuigan
May 6, 2021·Genome Biology and Evolution·Zachery Tiedeman, Sarah Signor

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Datasets Mentioned

BETA
PRJNA419238

Methods Mentioned

BETA
dissection
genotyping

Software Mentioned

AsReml
vcftools
Revolution Analytics
GCTA
Joint Genotyper for ( JGIL )
GATK IndelRealigner
R
Joint Genotyper
PLINK
FaST

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