Right here from the whole genome sequencing of 55 honey bees by design a top solution recombination chart from inside the honey bee, we discovered that crossovers try regarding the GC blogs, nucleotide range, and you may gene thickness. I together with confirmed the former idea you to definitely family genes indicated into the worker minds provides unusually highest CO rates. Our study hold the examine you to diversity of staff behavior, however resistant setting, try a motorist of the large crossing-more rates within the bees. We find no facts that the crossing-over rates are accompanied by a high NCO rates.
Tips and you may product
Five territories of honeybees (Apis mellifera ligustica Spin) have been built-up of a beneficial bee farm when you look at the Zhenjiang, China. For every single colony contained you to definitely queen, all those drones, and you may hundreds of pros. Bees away from three territories have been selected to have whole genome sequencing.
The fresh new DNA of every personal is extracted using phenol/chloroform/isoamyl liquor method. To attenuate the possibility of bacterial contamination, brand new abdomens from bees were removed before DNA extraction. Regarding step three ?g away from DNA of for each shot were used to have whole genome resequencing since the left DNA is kept to possess PCR and you may Sanger sequencing. Structure of DNA libraries and you may Illumina sequencing was indeed performed https://datingranking.net/local-hookup/akron/ on BGI-Shenzhen. Into the temporary, paired-avoid sequencing libraries that have enter measurements of five hundred bp was basically built for each and every attempt depending on the maker’s rules. After that dos ? 100 bp matched-end checks out was indeed made for the IlluminaHiSEq 2000. New queens was indeed sequenced in the approximately 67? publicity an average of, drones from the approximately 35? publicity, and you will gurus in the everything 29? visibility (Dining table S1 inside the A lot more file 2). The sequences was indeed deposited throughout the GenBank databases (accession no. SRP043350).
SNP getting in touch with and you will marker identification
Honeybee resource genome was downloaded from NCBI . The sequencing reads was indeed first mapped to source genome having bwa right after which realigned having stampy . Upcoming regional realignment to indels are did by the Genome Study Toolkit (GATK) , and you will versions have been titled because of the GATK UnifiedGenotyper.
As a result of the down accuracy regarding getting in touch with indel versions, only known SNPs can be used while the markers. Very first, 920,528 so you’re able to 960,246 hetSNPs was indeed called when you look at the each queen (Desk S2 for the Most document dos). Up coming, as much as 22% of those were removed because these sites are also hetSNPs inside one haploid drone (this may reflect low-allelic succession alignments because of CNVs, sequencing error, otherwise reduced sequencing top quality). Similar dimensions of the fresh hetSNPs and additionally was found in individual jizz sequencing . Ultimately, 671,690 so you can 740,763 reputable hetSNPs inside each nest were utilized as indicators so you’re able to choose recombination incidents (Table S2 from inside the 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 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.