Data from: The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901
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.
Funded by USDA-ARS Knipling-Bushland US Livestock Insects Research Laboratory CRIS project 3094-32000-036-00
Resources in this dataset:
Resource Title: The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901.
File Name: Web Page, url: https://doi.org/10.1016/j.dib.2019.104602
NCBI data referenced in the article can be found in the related content links of this record
Funding
USDA-ARS: 3094-32000-036-00
History
Data contact name
Bendele, KylieData contact email
Kylie.Bendele@usda.govPublisher
National Center for Biotechnology InformationIntended use
This assembled genome is the highest quality tick genome publicly available. Researchers studying arachnid and tick genomics, arachnid evolution, and comparative genomics will find the assembled genome valuable. The dataset can be used to study parthenogenesis-related genes, as this tick exclusively utilizes parthenogenetic reproduction in New Zealand. The developers of novel tick control technologies for this and other species of ticks will find this genome very useful.Temporal Extent Start Date
2018-02-04Theme
- Not specified
Geographic Coverage
{"type":"FeatureCollection","features":[{"geometry":{"type":"Point","coordinates":[175.616241,-40.382671]},"type":"Feature","properties":{}}]}Geographic location - description
Massey University, School of Veterinary Sciences, Palmerston North, New ZealandISO Topic Category
- biota
Ag Data Commons Group
- Veterinary Pest Genomics Center
National Agricultural Library Thesaurus terms
genome; parthenogenesis; ticks; Haemaphysalis longicornis; birds; hosts; cattle; deer; sheep; goats; humans; horses; pathogens; theileriosis; New Zealand; genome assembly; molecular weight; DNA; computers; data collection; genes; National Center for Biotechnology Information; arthropod pests; tick infestations; tick-borne diseasesOMB Bureau Code
- 005:18 - Agricultural Research Service
OMB Program Code
- 005:040 - National Research
ARS National Program Number
- 104
Primary article PubAg Handle
Pending citation
- No
Public Access Level
- Public
