April 21, 2020  |  

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

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.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.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.

April 21, 2020  |  

Genome sequence and transcriptomic profiles of a marine bacterium, Pseudoalteromonas agarivorans Hao 2018.

Members of the marine genus Pseudoalteromonas have attracted great interest because of their ability to produce a large number of biologically active substances. Here, we report the complete genome sequence of Pseudoalteromonas agarivorans Hao 2018, a strain isolated from an abalone breeding environment, using second-generation Illumina and third-generation PacBio sequencing technologies. Illumina sequencing offers high quality and short reads, while PacBio technology generates long reads. The scaffolds of the two platforms were assembled to yield a complete genome sequence that included two circular chromosomes and one circular plasmid. Transcriptomic data for Pseudoalteromonas were not available. We therefore collected comprehensive RNA-seq data using Illumina sequencing technology from a fermentation culture of P. agarivorans Hao 2018. Researchers studying the evolution, environmental adaptations and biotechnological applications of Pseudoalteromonas may benefit from our genomic and transcriptomic data to analyze the function and expression of genes of interest.

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