Try origin, DNA removal, and you can genome sequencing

Right here from the entire genome sequencing of 55 honey bees and by constructing a high solution recombination map in the honey bee, we unearthed that crossovers are on the GC blogs, nucleotide assortment, and gene occurrence. We together with verified the former tip that genetics shown in worker brains enjoys unusually large CO pricing. All of our research secure the evaluate you to definitely diversity out-of personnel decisions, however immune means, is actually a driver of your highest crossing-more than rates for the bees. We find zero evidence the crossing-more price was with a leading NCO rates.

Actions and you will product

Five territories from honeybees (Apis mellifera ligustica Twist) had been collected of a bee farm from inside the Zhenjiang, China. For each and every nest contained you to definitely king, those drones, and you can hundreds of experts. Bees from about three colonies have been chosen getting whole genome sequencing.

The latest DNA each and every personal is actually removed playing with phenol/chloroform/isoamyl liquor strategy. To reduce the possibility of bacterial toxic contamination, the fresh new abdomens out of bees was indeed got rid of just before DNA extraction. Throughout the step three ?g off DNA regarding for every attempt were used to have whole genome resequencing once the remaining DNA are left for PCR and Sanger sequencing. Build of the DNA libraries and you will Illumina sequencing was basically performed at the BGI-Shenzhen. During the short-term, paired-prevent sequencing libraries with insert size of five-hundred bp have been built for each and every test depending on the maker’s guidelines. Upcoming 2 ? one hundred bp matched up-stop checks out were made toward IlluminaHiSEq 2000. Brand new queens were sequenced from the everything 67? coverage an average of, drones at just as much as thirty five? visibility, and you can specialists from the everything 30? visibility (Dining table S1 inside Extra file 2). The brand new sequences was in fact transferred in the GenBank database (accession no. SRP043350).

SNP getting in touch with and you will marker personality

Honeybee source genome was downloaded of NCBI . The sequencing reads was in fact earliest mapped on to site genome with bwa immediately after which realigned that have stampy . Next regional realignment to indels is actually did of the Genome Research Toolkit (GATK) , and you can variations have been entitled because of the GATK UnifiedGenotyper.

As a result of the straight down reliability of getting in touch with indel alternatives, merely known SNPs can be used once the markers. Basic, 920,528 so you’re able to 960,246 hetSNPs was indeed entitled within the for every queen (Dining table S2 into the Even more file 2). After that, just as much as 22% of those was removed due to the fact that these sites are also hetSNPs into the at least one haploid drone (this might mirror low-allelic succession alignments caused by CNVs, sequencing mistake, or reduced sequencing high quality). Comparable size of new hetSNPs in addition to were seen in peoples spunk sequencing . Ultimately, 671,690 in order to 740,763 reliable hetSNPs for the for every single nest were utilized as the indicators so you’re able to select recombination events (Desk S2 inside Even more file 2).

Haploid phasing

For each colony, the identified markers were used for haploid phasing. The linkage of every two adjacent markers was inferred to determine the two chromosome haplotypes of the queen by comparing the SNP linkage information across all drones from the same colony. Detailed methods were described in Lu’s study . In brief, for each pair of adjacent hetSNPs, for example compatible partners dating website A/G and C/T, there could be two types of link in the queen ‘A-C, G-T’ or ‘A-T, G-C’. Assuming recombination events are low probability, if more ‘A-C, G-T’ drones are found than ‘A-T, G-C’ drones, then ‘A-C, G-T’ is assumed to be the correct link in the queen and vice versa. The two haplotypes can be clearly discriminated between >99% of ple). For linkage of the <1% markers, as shown in Additional file 1: Figure S2B, between markers at ‘LG1:20555174' and ‘LG1:20555456' , there are 14 ‘A-A or G-G' type drones against 1 ‘A-G or G-A' type drone, so ‘A-A, G-G' is assumed to be the correct link in queen and a recombination event is identified at this site in sample I-9.