Whole-Genome Sequence Analysis of Italian Honeybees (Apis mellifera)

Abstract

At the end of the last glaciation, Apis mellifera was established in northern Europe. In Italy, Apis melliferaligustica adapted to the mild climate and to the rich floristic biodiversity. Today, with the spread of Varroa destructor and with the increasing use of pesticides in agriculture, the Ligustica subspecies is increasingly dependent on human action for its survival. In addition, the effects of globalization of bee keeping favored the spread in Italy of other honeybee stocks of A. mellifera, in particular the Buckfast bee. The purpose of this study was to characterize the Italian honeybee’s population by sequencing the whole genome of 124 honeybees. Whole genome sequencing was performed by Illumina technology, obtaining a total coverage of 3720.89X, with a mean sample coverage of 29.77X. A total of 4,380,004 SNP variants, mapping on Amel_HAv3.1 chromosomes, were detected. Results of the analysis of the patterns of genetic variation allowed us to identify and subgroup bees according to their type. The investigation revealed the genetic originality of the Sicula, and in A.m. ligustica limited genetic introgression from the other breeds. Morphometric analysis of 5800 worker bees was in agreement with genomic data.

Genetic Drift and Purifying Selection Shaped Mitochondrial Genome Variation in the High Royal Jelly-Producing Honeybee Strain (Apis mellifera ligustica)

“…These findings could be used to trace the maternal origin of the divergent individuals. The presence of the two divergent ITB individuals could be due to genetic introgression from other breeds into A. m. ligustica populations in Italy (Minozzi et al, 2021). We propose that RJB14 maternally originated in recent years from the S lineage reared in China, while the three RJBs (RJB13, RJB57, and RJB59) were derived from the undescribed lineage containing ITB16 in Italy.…”

“…m . ligustica populations in Italy ( Minozzi et al, 2021 ). We propose that RJB14 maternally originated in recent years from the S lineage reared in China, while the three RJBs (RJB13, RJB57, and RJB59) were derived from the undescribed lineage containing ITB16 in Italy.…”

Analysis of Complementary Sex-Determiner (csd) Allele Diversity in Different Honeybee Subspecies from Italy Based on NGS Data

“…One hundred twenty-five worker colonies were sampled between summer 2017 and summer 2018 [ 24 ] in twelve different Italian regions: Abruzzo, Emilia Romagna, Liguria, Lombardy, Marche, Piedmont, Sicily, Trentino, Tuscany, Umbria and Veneto. Newly hatched worker bees were collected from each hive and used to perform a whole genome DNA sequencing analysis.…”

“…Bees were individually placed in 1.5 mL Eppendorf tubes containing 95% ethanol and kept at −4 °C. The 125 colonies belonged to seven different subspecies [ 24 ], two autochthonous A. m. ligustica ( n = 61) and A. m. sicula ( n = 6); three allochthonous A. m. mellifera ( n = 4), A. m. carnica ( n = 8) and A. m. cecropia ( n = 1); and two hybrids: A. m. carnica by A. m. ligustica hybrids ( n = 2), and Buckfast bees ( n = 43).…”

“…To further investigate the applicability of bioinformatic approaches for csd allele assessment and variability investigation from NGS data, we propose an alternative method based on local de novo assembly of Illumina reads matching the HVR, integrated by manual inspection and curation. The aim of this work was to exploit the existing Illumina genomic resequencing data collection described in Minozzi et al [ 24 ] and retrieve csd HVR allele-specific sequences from diploid worker bees, thus describing the inter- and intra- genetic variability of seven Apis mellifera subspecies on 125 diploid worker bees sampled in different Italian regions.…”