Abstract
The longhorned tick, Haemaphysalis longicornis, feeds upon a wide range of bird and mammalian hosts. Mammalian hosts include cattle, deer, sheep, goats, humans, and horses. This tick is known to transmit a number of pathogens causing tick-borne diseases, and was the vector of a recent serious outbreak of oriental theileriosis in New Zealand. A New Zealand-USA consortium was established to sequence, assemble, and annotate the genome of this tick, using ticks obtained from New Zealand's North Island. In New Zealand, the tick is considered exclusively parthenogenetic and this trait was deemed useful for genome assembly. Very high molecular weight genomic DNA was sequenced on the Illumina HiSeq4000 and the long-read Pac Bio Sequel platforms. Twenty-eight SMRT cells produced a total of 21.3 million reads which were assembled with Canu on a reserved supercomputer node with access to 12 TB of RAM, running continuously for over 24 days. The final assembly dataset consisted of 34,211 contigs with an average contig length of 215,205 bp. The quality of the annotated genome was assessed by BUSCO analysis, an approach that provides quantitative measures for the quality of an assembled genome. Over 95% of the BUSCO gene set was found in the assembled genome. Only 48 of the 1066 BUSCO genes were missing and only 9 were present in a fragmented condition. The raw sequencing reads and the assembled contigs/scaffolds are archived at the National Center for Biotechnology Information.
Highlights
Data accessibilityBiology Genomics Assembled genome sequences and tables displaying sequencing, assembly, and repeats analysis statistics Long-read sequencing of very high molecular weight genomic DNA using Pacific Biosciences Sequel and Illumina HiSeq4000 Pacific Biosciences raw data in bam format, Illumina HiSeq4000 raw data in fastq format CANU-assembled Pacific Biosciences-only contigs/scaffolds in fasta format The expected large genome size of this tick necessitated the usage of long read sequencing technology and a genomic DNA isolation technique capable of purifying very high molecular weight DNA
The longhorned tick, Haemaphysalis longicornis, feeds upon a wide range of bird and mammalian hosts
Deer, sheep, goats, humans, and horses. This tick is known to transmit a number of pathogens causing tick-borne diseases, and was the vector of a recent serious outbreak of oriental theileriosis in New Zealand
Summary
Biology Genomics Assembled genome sequences and tables displaying sequencing, assembly, and repeats analysis statistics Long-read sequencing of very high molecular weight genomic DNA using Pacific Biosciences Sequel and Illumina HiSeq4000 Pacific Biosciences raw data in bam format, Illumina HiSeq4000 raw data in fastq format CANU-assembled Pacific Biosciences-only contigs/scaffolds in fasta format The expected large genome size of this tick necessitated the usage of long read sequencing technology and a genomic DNA isolation technique capable of purifying very high molecular weight DNA. Eggs from New Zealand-collected H. longicornis females were used to purify very high molecular weight genomic DNA, using a proteinase K/RNAse A/phenol-based extraction protocol. This DNA was sequenced on the Pacific Biosciences Sequel and Illumina HiSeq4000 platforms. Haemaphysalis longicornis is a three-host tick, with a wide distribution in temperate regions of Asia, Australia, and New Zealand [1] This tick is capable of parthenogenetic reproduction, which allows rapid invasion of new areas and explosive population growth in established ranges. Very high molecular weight genomic DNA was purified from eggs collected from parthenogenetic female H. longicornis ticks sourced from New Zealand. Information about the sequence reads, assembled genome, and genome repeats analysis is presented in Tables 1, 2, and 3, respectively
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