Around three bee colonies, I, II, and you can III, was tested from countless colonies in identical ranch

Around three bee colonies, I, II, and you can III, was tested from countless colonies in identical ranch

Marker character and you can haplotype phasing

Fifty-five people, including about three queens (you to away from for each and every colony), 18 drones from colony I, 15 drones off nest II, thirteen drones and you can six pros out of colony III, were used to own entire-genome sequencing. Just after sequencing, 43 drones and six gurus was basically resolved as little ones out-of its corresponding queens, while around three drones from nest We was known with a foreign origin. In excess of 150,100000 SNPs was basically mutual because of the such three drones but could not getting sensed within their involved queen (Shape S1 for chatstep log in the Extra document 1). This type of drones have been removed for further studies. The diploid queens were sequenced on everything 67? depth, haploid drones at whenever 35? breadth, and you may specialists at the whenever 29? breadth for every attempt (Table S1 from inside the A lot more document dos).

To ensure the reliability of the titled indicators during the each colony, four methods was indeed functioning (discover Tips for information): (1) just these types of heterozygous unmarried nucleotide polymorphisms (hetSNPs) named into the queens can be used just like the candidate markers, and all of small indels try overlooked; (2) in order to prohibit the possibility of backup amount variations (CNVs) confusing recombination assignment such candidate indicators must be ‘homozygous’ for the drones, all the ‘heterozygous’ indicators identified in the drones being discarded; (3) for every marker webpages, just two nucleotide versions (A/T/G/C) is titled in both the newest king and you may drone genomes, that several nucleotide phase must be consistent involving the queen and drones; (4) brand new candidate indicators must be titled with high sequence quality (?30).