Genotype data and linkage map for Teleopsis dalmanni, described in “Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome

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Wilkinson, Gerald
Reinhardt, Josephine
Baker, Richard
Paczolt, Kimberly
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These files contain genotype matrices used to create a linkage map for the stalk-eyed fly, Teleopsis dalmanni. They were created from individuals derived from a backcross between two populations of flies derived from collections made in peninsular Malaysia and northern Sumatra. These linkage map was used to validate a chromosomal genome assembly, as described in a paper titled, “Transposable element control disrupted by meiotic drive in a stalk-eyed fly genome," which is being submitted for publication.
Multiplex Shotgun Sequencing (MSG) allele determination on scaffolds Linkage groups were created by mating a female hybrid offspring obtained from a cross between a male from the 2A inbred strain and a female from a noninbred population of T. dalmanni collected near Bukit Lawang, Sumatra (3 35’N, 98 6’E) to a male from the Gombak 2A inbred strain. This backcross produced 249 (131 female and 118 male) individuals which were individually genotyped using multiplex shotgun sequencing (Andolfatto et al. 2011) and multiple STR loci (Wilkinson et al. 2014). Genotypes were determined as either heterozygous or homozygous in each individual for each scaffold by combining all loci present on a scaffold into a single “super locus”. Reads were aligned using bwa (Li and Durbin 2009) and genotypes were assessed as either homozygous or heterozygous using samtools v.1.9 (Li et al. 2009) (mpileup -v). Because this was a backcross, for autosomal loci individuals inheriting the backcross allele (pure “Gombak”) should be homozygous at informative markers whereas individuals inheriting the non-backcross allele should be heterozygous, with an expectation of a 1 to 1 ratio of these genotypes. This results in an overall 3 to 1 ratio of the backcross to the non-backcross allele for autosomal markers and an overall 1 to 1 ratio for X linked markers in males. Markers were retained as potentially informative if at least one individual was found to carry the non-backcross Bukit Lawang (Wilkinson et al. 2014) allele, defined as the less common allele across all female individuals. Markers were removed if they violated expected allele ratios using a binomial test against the expectations described above, or if more than 20% of female individuals were found to have only the non-backcross allele. Finally, within each individual all markers from a given scaffold were pooled to give an overall number of reads supporting each genotype, requiring a minimum coverage of 5 reads. Individuals were then assigned in the final matrix as “a” (for 2A/backcross genotypes) or “b” (for Bukit Lawang/foreign genotypes). Scaffold linkage map creation Scaffolds were categorized as being autosomal or X-linked based on relative read coverage between male and female libraries. Separate genotype matrices were then created for the X-linked scaffolds and autosomal scaffolds and rank-ordered by the number of individuals genotyped. We then used JoinMap 4.1 to assign the top 1000 autosomal scaffolds into one of two linkage groups (chromosomes). Only scaffolds with a LOD score > 5 were assigned to a chromosome. We used a similar process for the top 250 X-linked scaffolds but used a LOD score > 10 to assign scaffolds to the chromosome. We then ordered scaffolds by regression mapping using a Haldane mapping function. We used regression mapping, rather than maximum likelihood, because it is less sensitive to missing genotype data as is typical for MSG studies (Van Ooijen 2006). We removed markers from the final map if there was evidence for significant (after Bonferroni correction) lack of fit to their nearest neighbors. The resulting linkage map included 762 scaffolds spanning 147.1 Mbp. Andolfatto P, Davison D, Erezyilmaz D, Hu TT, Mast J, Sunayama-Morita T, Stern DL. 2011. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Research 21: 610–617. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760. (Accessed June 20, 2013). Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078–2079. Van Ooijen JW. 2006. JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen 33: 10–1371. Wilkinson GS, Christianson SJ, Brand CL, Ru G, Shell W. 2014. Haldane’s Rule Is Linked to Extraordinary Sex Ratios and Sperm Length in Stalk-Eyed Flies. Genetics 198: 1167–1181.