A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

Abstract

Background The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera . We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map. Results Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor > 98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features. Conclusions The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics. Electronic supplementary material The online version of this article (10.1186/s12864-019-5642-0) contains supplementary material, which is available to authorized users.

A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome

“…These repeat sequences include long interspersed nuclear elements (LINEs) (0.04%), long terminal repeats (LTRs) (0.20%), DNA elements (0.65%), small RNAs (0.01%), simple repeats (4.03%), low complexity sequences (1.06%), and unclassified repeat sequences (3.16%). Of them, simple repeats with total length of 8,693,708 bp are the richest type (Table 3), which is consistent with the previous reports (Park et al, 2015;Diao et al, 2018) and is the same as in A. mellifera (Wallberg et al, 2019), suggesting that simple repeats are the major type of repeat sequences in honeybees.…”

“…Compared with the second generation sequencing technologies, the TGS technologies also maintain the advantages of high throughput and low cost. Typical TGS technologies are single-molecule real-time (SMRT) sequencing technology developed by Pacific Biosciences company and Nanopore sequencing technology launched by Oxford Nanopore company, which are now widely used in genome sequencing of animals and plants (Jiang et al, 2014;Jiao et al, 2017;Gong et al, 2018;Kronenberg et al, 2018;Ghurye et al, 2019;Low et al, 2019;Wallberg et al, 2019;Zhang et al, 2019).…”

Comprehensive History of CSP Genes: Evolution, Phylogenetic Distribution and Functions

“…Interestingly, we find that in CSP genes such as GB19453, one intron is inserted only a few nucleotides after the start codon encoding the amino acid methionine (Figure 2A). The same observation (intron1 inserted shortly after the start of the signal peptide) was made in AAJJ1196A and BmorCSP19 ( Figure S1) [14,38,[41][42][43]. In the case of these genes, the intron is inserted after the third base and therefore does not cause codon disruption (phase 0 intron).…”

“…In the initial analysis of the honeybee genome, the existence of six CSPs has been reported in A. mellifera: six single-intron structures [37,39,40]. Analyzing a new assembly (sequence update) of the honeybee genome [41], we confirm the existence of only six CSPs in bees (AmelASP3c, AmelGB10389, AmelGB13325, AmelGB17875, AmelGB19242 and AmelGB19453) and localize them on specific chromosomes (Figure 2A, Table S1). However, we find that there is an additional intron inserted in the signal peptide of GB19453.…”

“…Therefore, they might represent successive genome duplications, as described for the red flour beetle T. castaneum genome (beetlebase) [38] (see Figure 2A and Figure S1). Apparently, the duplicated copies of GB19453 and GB17875 were lost following genome duplication [41]; they are found as single genes on LG2 and LG8, respectively (Figure 2A).…”