Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus

Roberto A. Barrero; Gabriel Keeble-Gagnère; Bing Zhang; Paula Moolhuijzen; Kazuho Ikeo; Yoshio Tateno; Takashi Gojobori; Felix D. Guerrero; Ala Lew-Tabor; Matthew Bellgard

doi:10.1186/1471-2164-12-328

Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus

Roberto A. Barrero^*, Gabriel Keeble-Gagnère, Bing Zhang, Paula Moolhuijzen, Kazuho Ikeo, Yoshio Tateno, Takashi Gojobori, Felix D. Guerrero, Ala Lew-Tabor, Matthew Bellgard

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

36 Scopus citations

Abstract

Background: MicroRNAs (miRNAs) are small non-coding RNAs that act as regulators of gene expression in eukaryotes modulating a large diversity of biological processes. The discovery of miRNAs has provided new opportunities to understand the biology of a number of species. The cattle tick, Rhipicephalus (Boophilus) microplus, causes significant economic losses in cattle production worldwide and this drives us to further understand their biology so that effective control measures can be developed. To be able to provide new insights into the biology of cattle ticks and to expand the repertoire of tick miRNAs we utilized Illumina technology to sequence the small RNA transcriptomes derived from various life stages and selected organs of R. microplus.Results: To discover and profile cattle tick miRNAs we employed two complementary approaches, one aiming to find evolutionary conserved miRNAs and another focused on the discovery of novel cattle-tick specific miRNAs. We found 51 evolutionary conserved R. microplus miRNA loci, with 36 of these previously found in the tick Ixodes scapularis. The majority of the R. microplus miRNAs are perfectly conserved throughout evolution with 11, 5 and 15 of these conserved since the Nephrozoan (640 MYA), Protostomian (620MYA) and Arthropoda (540 MYA) ancestor, respectively. We then employed a de novo computational screening for novel tick miRNAs using the draft genome of I. scapularis and genomic contigs of R. microplus as templates. This identified 36 novel R. microplus miRNA loci of which 12 were conserved in I. scapularis. Overall we found 87 R. microplus miRNA loci, of these 15 showed the expression of both miRNA and miRNA* sequences. R. microplus miRNAs showed a variety of expression profiles, with the evolutionary-conserved miRNAs mainly expressed in all life stages at various levels, while the expression of novel tick-specific miRNAs was mostly limited to particular life stages and/or tick organs.Conclusions: Anciently acquired miRNAs in the R. microplus lineage not only tend to accumulate the least amount of nucleotide substitutions as compared to those recently acquired miRNAs, but also show ubiquitous expression profiles through out tick life stages and organs contrasting with the restricted expression profiles of novel tick-specific miRNAs.

Original language	English (US)
Article number	328
Journal	BMC genomics
Volume	12
DOIs	https://doi.org/10.1186/1471-2164-12-328
State	Published - Jun 24 2011
Externally published	Yes

Bibliographical note

Funding Information:
This research was funded in part by the WA State Government and the WA Centre of Excellence in Comparative Genomics. We acknowledge the CRC for Beef Genetic Technologies for partial staff and laboratory support contributing to this study. We thank Dr. Megan Vance and Dr. Louise Jackson of QPI&F Biosecurity at the Animal Research Institute, QLD, Australia for the collection and kind provision (respectively) of NRFS tick stages utilised in this study. We thank Mr Zayed Albertyn for his help with preliminary analysis. We acknowledge the National Collaborative Research Infrastructure (NCRIS) for supporting the implementation of bioinformatics computational pipelines.

ASJC Scopus subject areas

Biotechnology
Genetics

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10.1186/1471-2164-12-328

Cite this

Barrero, R. A., Keeble-Gagnère, G., Zhang, B., Moolhuijzen, P., Ikeo, K., Tateno, Y., Gojobori, T., Guerrero, F. D., Lew-Tabor, A., & Bellgard, M. (2011). Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus. BMC genomics, 12, Article 328. https://doi.org/10.1186/1471-2164-12-328

@article{cbee6819f66d4344a065f4d1ab7ed5cf,

title = "Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus",

abstract = "Background: MicroRNAs (miRNAs) are small non-coding RNAs that act as regulators of gene expression in eukaryotes modulating a large diversity of biological processes. The discovery of miRNAs has provided new opportunities to understand the biology of a number of species. The cattle tick, Rhipicephalus (Boophilus) microplus, causes significant economic losses in cattle production worldwide and this drives us to further understand their biology so that effective control measures can be developed. To be able to provide new insights into the biology of cattle ticks and to expand the repertoire of tick miRNAs we utilized Illumina technology to sequence the small RNA transcriptomes derived from various life stages and selected organs of R. microplus.Results: To discover and profile cattle tick miRNAs we employed two complementary approaches, one aiming to find evolutionary conserved miRNAs and another focused on the discovery of novel cattle-tick specific miRNAs. We found 51 evolutionary conserved R. microplus miRNA loci, with 36 of these previously found in the tick Ixodes scapularis. The majority of the R. microplus miRNAs are perfectly conserved throughout evolution with 11, 5 and 15 of these conserved since the Nephrozoan (640 MYA), Protostomian (620MYA) and Arthropoda (540 MYA) ancestor, respectively. We then employed a de novo computational screening for novel tick miRNAs using the draft genome of I. scapularis and genomic contigs of R. microplus as templates. This identified 36 novel R. microplus miRNA loci of which 12 were conserved in I. scapularis. Overall we found 87 R. microplus miRNA loci, of these 15 showed the expression of both miRNA and miRNA* sequences. R. microplus miRNAs showed a variety of expression profiles, with the evolutionary-conserved miRNAs mainly expressed in all life stages at various levels, while the expression of novel tick-specific miRNAs was mostly limited to particular life stages and/or tick organs.Conclusions: Anciently acquired miRNAs in the R. microplus lineage not only tend to accumulate the least amount of nucleotide substitutions as compared to those recently acquired miRNAs, but also show ubiquitous expression profiles through out tick life stages and organs contrasting with the restricted expression profiles of novel tick-specific miRNAs.",

author = "Barrero, {Roberto A.} and Gabriel Keeble-Gagn{\`e}re and Bing Zhang and Paula Moolhuijzen and Kazuho Ikeo and Yoshio Tateno and Takashi Gojobori and Guerrero, {Felix D.} and Ala Lew-Tabor and Matthew Bellgard",

note = "Funding Information: This research was funded in part by the WA State Government and the WA Centre of Excellence in Comparative Genomics. We acknowledge the CRC for Beef Genetic Technologies for partial staff and laboratory support contributing to this study. We thank Dr. Megan Vance and Dr. Louise Jackson of QPI&F Biosecurity at the Animal Research Institute, QLD, Australia for the collection and kind provision (respectively) of NRFS tick stages utilised in this study. We thank Mr Zayed Albertyn for his help with preliminary analysis. We acknowledge the National Collaborative Research Infrastructure (NCRIS) for supporting the implementation of bioinformatics computational pipelines.",

year = "2011",

month = jun,

day = "24",

doi = "10.1186/1471-2164-12-328",

language = "English (US)",

volume = "12",

journal = "BMC genomics",

issn = "1471-2164",

publisher = "Springer Verlag",

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TY - JOUR

T1 - Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus

AU - Barrero, Roberto A.

AU - Keeble-Gagnère, Gabriel

AU - Zhang, Bing

AU - Moolhuijzen, Paula

AU - Ikeo, Kazuho

AU - Tateno, Yoshio

AU - Gojobori, Takashi

AU - Guerrero, Felix D.

AU - Lew-Tabor, Ala

AU - Bellgard, Matthew

N1 - Funding Information: This research was funded in part by the WA State Government and the WA Centre of Excellence in Comparative Genomics. We acknowledge the CRC for Beef Genetic Technologies for partial staff and laboratory support contributing to this study. We thank Dr. Megan Vance and Dr. Louise Jackson of QPI&F Biosecurity at the Animal Research Institute, QLD, Australia for the collection and kind provision (respectively) of NRFS tick stages utilised in this study. We thank Mr Zayed Albertyn for his help with preliminary analysis. We acknowledge the National Collaborative Research Infrastructure (NCRIS) for supporting the implementation of bioinformatics computational pipelines.

PY - 2011/6/24

Y1 - 2011/6/24

N2 - Background: MicroRNAs (miRNAs) are small non-coding RNAs that act as regulators of gene expression in eukaryotes modulating a large diversity of biological processes. The discovery of miRNAs has provided new opportunities to understand the biology of a number of species. The cattle tick, Rhipicephalus (Boophilus) microplus, causes significant economic losses in cattle production worldwide and this drives us to further understand their biology so that effective control measures can be developed. To be able to provide new insights into the biology of cattle ticks and to expand the repertoire of tick miRNAs we utilized Illumina technology to sequence the small RNA transcriptomes derived from various life stages and selected organs of R. microplus.Results: To discover and profile cattle tick miRNAs we employed two complementary approaches, one aiming to find evolutionary conserved miRNAs and another focused on the discovery of novel cattle-tick specific miRNAs. We found 51 evolutionary conserved R. microplus miRNA loci, with 36 of these previously found in the tick Ixodes scapularis. The majority of the R. microplus miRNAs are perfectly conserved throughout evolution with 11, 5 and 15 of these conserved since the Nephrozoan (640 MYA), Protostomian (620MYA) and Arthropoda (540 MYA) ancestor, respectively. We then employed a de novo computational screening for novel tick miRNAs using the draft genome of I. scapularis and genomic contigs of R. microplus as templates. This identified 36 novel R. microplus miRNA loci of which 12 were conserved in I. scapularis. Overall we found 87 R. microplus miRNA loci, of these 15 showed the expression of both miRNA and miRNA* sequences. R. microplus miRNAs showed a variety of expression profiles, with the evolutionary-conserved miRNAs mainly expressed in all life stages at various levels, while the expression of novel tick-specific miRNAs was mostly limited to particular life stages and/or tick organs.Conclusions: Anciently acquired miRNAs in the R. microplus lineage not only tend to accumulate the least amount of nucleotide substitutions as compared to those recently acquired miRNAs, but also show ubiquitous expression profiles through out tick life stages and organs contrasting with the restricted expression profiles of novel tick-specific miRNAs.

AB - Background: MicroRNAs (miRNAs) are small non-coding RNAs that act as regulators of gene expression in eukaryotes modulating a large diversity of biological processes. The discovery of miRNAs has provided new opportunities to understand the biology of a number of species. The cattle tick, Rhipicephalus (Boophilus) microplus, causes significant economic losses in cattle production worldwide and this drives us to further understand their biology so that effective control measures can be developed. To be able to provide new insights into the biology of cattle ticks and to expand the repertoire of tick miRNAs we utilized Illumina technology to sequence the small RNA transcriptomes derived from various life stages and selected organs of R. microplus.Results: To discover and profile cattle tick miRNAs we employed two complementary approaches, one aiming to find evolutionary conserved miRNAs and another focused on the discovery of novel cattle-tick specific miRNAs. We found 51 evolutionary conserved R. microplus miRNA loci, with 36 of these previously found in the tick Ixodes scapularis. The majority of the R. microplus miRNAs are perfectly conserved throughout evolution with 11, 5 and 15 of these conserved since the Nephrozoan (640 MYA), Protostomian (620MYA) and Arthropoda (540 MYA) ancestor, respectively. We then employed a de novo computational screening for novel tick miRNAs using the draft genome of I. scapularis and genomic contigs of R. microplus as templates. This identified 36 novel R. microplus miRNA loci of which 12 were conserved in I. scapularis. Overall we found 87 R. microplus miRNA loci, of these 15 showed the expression of both miRNA and miRNA* sequences. R. microplus miRNAs showed a variety of expression profiles, with the evolutionary-conserved miRNAs mainly expressed in all life stages at various levels, while the expression of novel tick-specific miRNAs was mostly limited to particular life stages and/or tick organs.Conclusions: Anciently acquired miRNAs in the R. microplus lineage not only tend to accumulate the least amount of nucleotide substitutions as compared to those recently acquired miRNAs, but also show ubiquitous expression profiles through out tick life stages and organs contrasting with the restricted expression profiles of novel tick-specific miRNAs.

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Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus

Abstract

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ASJC Scopus subject areas

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