Transcriptome analysis of Haemaphysalis flava female using Illumina HiSeq 4000 sequencing: de novo assembly, functional annotation and discovery of SSR markers

Min Kyu Sang; Hongray Howrelia Patnaik; Jie Eun Park; Dae Kwon Song; Jun Yang Jeong; Chan Eui Hong; Yong Tae Kim; Hyeon Jun Shin; Liu Ziwei; Hee Ju Hwang; So Young Park; Se Won Kang; Seung-Hwan Park; Sung-Jae Cha; Jung Ho Ko; E Hyun Shin; Hong Seog Park; Yong Hun Jo; Yeon Soo Han; Bharat Bhusan Patnaik; Yong Seok Lee

doi:10.1186/s13071-023-05923-w

Transcriptome analysis of Haemaphysalis flava female using Illumina HiSeq 4000 sequencing: de novo assembly, functional annotation and discovery of SSR markers

Parasit Vectors. 2023 Oct 17;16(1):367. doi: 10.1186/s13071-023-05923-w.

Authors

Min Kyu Sang^#^{1

2}, Hongray Howrelia Patnaik^#¹, Jie Eun Park^{1

2}, Dae Kwon Song^{1

2}, Jun Yang Jeong^{1

3}, Chan Eui Hong^{1

3}, Yong Tae Kim^{1

3}, Hyeon Jun Shin^{1

3}, Liu Ziwei^{1

3}, Hee Ju Hwang³, So Young Park⁴, Se Won Kang⁵, Seung-Hwan Park⁵, Sung-Jae Cha⁶, Jung Ho Ko⁷, E Hyun Shin⁸, Hong Seog Park⁹, Yong Hun Jo^{1

3}, Yeon Soo Han¹⁰, Bharat Bhusan Patnaik^{1

3

11}, Yong Seok Lee^{12

13

14}

Affiliations

¹ Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea.
² Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea.
³ Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, South Korea.
⁴ Biodiversity Research Team, Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Gyeongbuk, South Korea.
⁵ Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, Jeonbuk, South Korea.
⁶ Johns Hopkins Malaria Research Institute, Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
⁷ Police Science Institute, Korean National Police University, Asan, Chungnam, 31539, South Korea.
⁸ Research Institute, Korea Pest Control Association, Seoul, 08501, South Korea.
⁹ Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 34069, South Korea.
¹⁰ College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, South Korea.
¹¹ PG Department of Biosciences and Biotechnology, Fakir Mohan University, Nuapadhi, Balasore , Odisha, 756089, India.
¹² Korea Native Animal Resources Utilization Convergence Research Institute (KNAR), Soonchunhyang University, Asan, Chungnam, South Korea. yslee@sch.ac.kr.
¹³ Research Support Center for Bio-Bigdata Analysis and Utilization of Biological Resources, Soonchunhyang University, Asan, Chungnam, South Korea. yslee@sch.ac.kr.
¹⁴ Department of Biology, College of Natural Sciences, Soonchunhyang University, Asan, 31538, Chungnam, South Korea. yslee@sch.ac.kr.

^# Contributed equally.

Abstract

Background: Ticks are ectoparasites capable of directly damaging their hosts and transmitting vector-borne diseases. The ixodid tick Haemaphysalis flava has a broad distribution that extends from East to South Asia. This tick is a reservoir of severe fever with thrombocytopenia syndrome virus (SFTSV) that causes severe hemorrhagic disease, with cases reported from China, Japan and South Korea. Recently, the distribution of H. flava in South Korea was found to overlap with the occurrence of SFTSV.

Methods: This study was undertaken to discover the molecular resources of H. flava female ticks using the Illumina HiSeq 4000 system, the Trinity de novo sequence assembler and annotation against public databases. The locally curated Protostome database (PANM-DB) was used to screen the putative adaptation-related transcripts classified to gene families, such as angiotensin-converting enzyme, aquaporin, adenylate cyclase, AMP-activated protein kinase, glutamate receptors, heat shock proteins, molecular chaperones, insulin receptor, mitogen-activated protein kinase and solute carrier family proteins. Also, the repeats and simple sequence repeats (SSRs) were screened from the unigenes using RepeatMasker (v4.0.6) and MISA (v1.0) software tools, followed by the designing of SSRs flanking primers using BatchPrimer 3 (v1.0) software.

Results: The transcriptome produced a total of 69,822 unigenes, of which 46,175 annotated to the homologous proteins in the PANM-DB. The unigenes were also mapped to the EuKaryotic Orthologous Groups (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) specializations. Promiscuous presence of protein kinase, zinc finger (C2H2-type), reverse transcriptase, and RNA recognition motif domains was observed in the unigenes. A total of 3480 SSRs were screened, of which 1907 and 1274 were found as tri- and dinucleotide repeats, respectively. A list of primer sequences flanking the SSR motifs was detailed for validation of polymorphism in H. flava and the related tick species.

Conclusions: The reference transcriptome information on H. flava female ticks will be useful for an enriched understanding of tick biology, its competency to act as a vector and the study of species diversity related to disease transmission.

Keywords: Haemaphysalis flava; SSR markers; Tick; Transcriptome; Vector.

MeSH terms

Animals
Female
Gene Expression Profiling*
Genome
Ixodidae* / genetics
Microsatellite Repeats
Molecular Sequence Annotation
Transcriptome

Abstract

MeSH terms

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