Right here https://datingranking.net/cs/fuckbookhookup-recenze/ of the entire genome sequencing from 55 honey bees and also by design a leading quality recombination chart from inside the honey bee, i discovered that crossovers is actually associated with GC blogs, nucleotide diversity, and gene thickness. We and confirmed the previous suggestion one genes shown inside staff member minds features surprisingly higher CO cost. All of our research hold the examine you to definitely variation regarding staff decisions, although not immune means, is actually a drivers of higher crossing-more than speed for the bees. We find zero facts that the crossing-over price try followed by a high NCO speed.
Tips and you may information
Four territories off honeybees (Apis mellifera ligustica Spin) was basically compiled off good bee ranch in Zhenjiang, China. For each and every colony contained you to king, those drones, and you will a huge selection of specialists. Bees from about three territories had been chose getting entire genome sequencing.
This new DNA each and every personal are removed using phenol/chloroform/isoamyl alcoholic drinks approach. To reduce the risk of bacterial toxic contamination, the stomachs out-of bees were got rid of just before DNA removal. On the 3 ?g of DNA out of each test were utilized to have whole genome resequencing as kept DNA try remaining having PCR and you may Sanger sequencing. Build of DNA libraries and you may Illumina sequencing had been performed at BGI-Shenzhen. Inside the short term, paired-avoid sequencing libraries with enter sized five-hundred bp had been created each take to according to the manufacturer’s advice. Next dos ? a hundred bp paired-stop checks out was basically generated into the IlluminaHiSEq 2000. The latest queens was in fact sequenced within whenever 67? publicity normally, drones at the just as much as thirty-five? visibility, and gurus from the whenever 29? visibility (Dining table S1 within the More document 2). Brand new sequences was indeed deposited on the GenBank databases (accession zero. SRP043350).
SNP contacting and you will marker character
Honeybee source genome is installed from NCBI . The new sequencing checks out were earliest mapped onto site genome that have bwa and realigned that have stampy . Upcoming regional realignment doing indels try did by the Genome Study Toolkit (GATK) , and you will variations have been named from the GATK UnifiedGenotyper.
Considering the all the way down precision out-of calling indel versions, only known SNPs are utilized as the indicators. Very first, 920,528 to 960,246 hetSNPs was indeed named in for each king (Desk S2 in A lot more document dos). Upcoming, as much as 22% of these had been got rid of due to the fact that those web sites are also hetSNPs in one or more haploid drone (this could mirror low-allelic series alignments considering CNVs, sequencing error, or lower sequencing quality). Equivalent size of this new hetSNPs in addition to was present in people sperm sequencing . In the long run, 671,690 so you can 740,763 credible hetSNPs within the for every single nest were utilized once the indicators so you can detect recombination incidents (Desk S2 in A lot more document 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.
