Improved reference genome of the arboviral vector Aedes albopictus

Umberto Palatini; Reem A. Masri; Luciano V. Cosme; Sergey Koren; Françoise Thibaud-Nissen; James K. Biedler; Flavia Krsticevic; J. Spencer Johnston; Rebecca Halbach; Jacob E. Crawford; Igor Antoshechkin; Anna Bella Failloux; Elisa Pischedda; Michele Marconcini; Jay Ghurye; Arang Rhie; Atashi Sharma; Dmitry A. Karagodin; Jeremy Jenrette; Stephanie Gamez; Pascal Miesen; Patrick Masterson; Adalgisa Caccone; Maria V. Sharakhova; Zhijian Tu; Philippos A. Papathanos; Ronald P. Van Rij; Omar S. Akbari; Jeffrey Powell; Adam M. Phillippy; Mariangela Bonizzoni

doi:10.1186/s13059-020-02141-w

Improved reference genome of the arboviral vector Aedes albopictus

Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud-Nissen, James K. Biedler, Flavia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Dmitry A. Karagodin, Jeremy Jenrette, Stephanie GamezPascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos A. Papathanos, Ronald P. Van Rij, Omar S. Akbari, Jeffrey Powell, Adam M. Phillippy, Mariangela Bonizzoni^*

^*Corresponding author for this work

Department of Entomology

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

62 Scopus citations

Abstract

Background: The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results: We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion: The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

Original language	English
Article number	:215
Journal	Genome Biology
Volume	21
Issue number	1
DOIs	https://doi.org/10.1186/s13059-020-02141-w
State	Published - 26 Aug 2020

Bibliographical note

Publisher Copyright:
© 2020 The Author(s).

Keywords

Ae. albopictus
Developmental transcriptome
Genome
Immunity
Population differentiation
Sex locus
Viral integrations
miRNAs
piRNA clusters

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10.1186/s13059-020-02141-w

Cite this

Palatini, U., Masri, R. A., Cosme, L. V., Koren, S., Thibaud-Nissen, F., Biedler, J. K., Krsticevic, F., Johnston, J. S., Halbach, R., Crawford, J. E., Antoshechkin, I., Failloux, A. B., Pischedda, E., Marconcini, M., Ghurye, J., Rhie, A., Sharma, A., Karagodin, D. A., Jenrette, J., ... Bonizzoni, M. (2020). Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology, 21(1), Article :215. https://doi.org/10.1186/s13059-020-02141-w

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title = "Improved reference genome of the arboviral vector Aedes albopictus",

abstract = "Background: The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results: We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion: The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.",

keywords = "Ae. albopictus, Developmental transcriptome, Genome, Immunity, Population differentiation, Sex locus, Viral integrations, miRNAs, piRNA clusters",

author = "Umberto Palatini and Masri, {Reem A.} and Cosme, {Luciano V.} and Sergey Koren and Fran{\c c}oise Thibaud-Nissen and Biedler, {James K.} and Flavia Krsticevic and Johnston, {J. Spencer} and Rebecca Halbach and Crawford, {Jacob E.} and Igor Antoshechkin and Failloux, {Anna Bella} and Elisa Pischedda and Michele Marconcini and Jay Ghurye and Arang Rhie and Atashi Sharma and Karagodin, {Dmitry A.} and Jeremy Jenrette and Stephanie Gamez and Pascal Miesen and Patrick Masterson and Adalgisa Caccone and Sharakhova, {Maria V.} and Zhijian Tu and Papathanos, {Philippos A.} and {Van Rij}, {Ronald P.} and Akbari, {Omar S.} and Jeffrey Powell and Phillippy, {Adam M.} and Mariangela Bonizzoni",

note = "Publisher Copyright: {\textcopyright} 2020 The Author(s).",

year = "2020",

month = aug,

day = "26",

doi = "10.1186/s13059-020-02141-w",

language = "אנגלית",

volume = "21",

journal = "Genome Biology",

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Palatini, U, Masri, RA, Cosme, LV, Koren, S, Thibaud-Nissen, F, Biedler, JK, Krsticevic, F, Johnston, JS, Halbach, R, Crawford, JE, Antoshechkin, I, Failloux, AB, Pischedda, E, Marconcini, M, Ghurye, J, Rhie, A, Sharma, A, Karagodin, DA, Jenrette, J, Gamez, S, Miesen, P, Masterson, P, Caccone, A, Sharakhova, MV, Tu, Z, Papathanos, PA, Van Rij, RP, Akbari, OS, Powell, J, Phillippy, AM & Bonizzoni, M 2020, 'Improved reference genome of the arboviral vector Aedes albopictus', Genome Biology, vol. 21, no. 1, :215. https://doi.org/10.1186/s13059-020-02141-w

TY - JOUR

T1 - Improved reference genome of the arboviral vector Aedes albopictus

AU - Palatini, Umberto

AU - Masri, Reem A.

AU - Cosme, Luciano V.

AU - Koren, Sergey

AU - Thibaud-Nissen, Françoise

AU - Biedler, James K.

AU - Krsticevic, Flavia

AU - Johnston, J. Spencer

AU - Halbach, Rebecca

AU - Crawford, Jacob E.

AU - Antoshechkin, Igor

AU - Failloux, Anna Bella

AU - Pischedda, Elisa

AU - Marconcini, Michele

AU - Ghurye, Jay

AU - Rhie, Arang

AU - Sharma, Atashi

AU - Karagodin, Dmitry A.

AU - Jenrette, Jeremy

AU - Gamez, Stephanie

AU - Miesen, Pascal

AU - Masterson, Patrick

AU - Caccone, Adalgisa

AU - Sharakhova, Maria V.

AU - Tu, Zhijian

AU - Papathanos, Philippos A.

AU - Van Rij, Ronald P.

AU - Akbari, Omar S.

AU - Powell, Jeffrey

AU - Phillippy, Adam M.

AU - Bonizzoni, Mariangela

PY - 2020/8/26

Y1 - 2020/8/26

N2 - Background: The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results: We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion: The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

AB - Background: The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes. Results: We use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes. Conclusion: The AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

KW - Ae. albopictus

KW - Developmental transcriptome

KW - Genome

KW - Immunity

KW - Population differentiation

KW - Sex locus

KW - Viral integrations

KW - miRNAs

KW - piRNA clusters

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DO - 10.1186/s13059-020-02141-w

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AN - SCOPUS:85089994645

SN - 1474-7596

VL - 21

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - :215

ER -

Improved reference genome of the arboviral vector Aedes albopictus

Abstract

Bibliographical note

Keywords

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