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Comparative analysis of shrimp (Penaeus vannamei) miRNAs expression profiles during WSSV infection under experimental conditions and in pond culture

Comparative analysis of shrimp (Penaeus vannamei) miRNAs expression profiles during WSSV infection under experimental conditions and in pond culture
Comparative analysis of shrimp (Penaeus vannamei) miRNAs expression profiles during WSSV infection under experimental conditions and in pond culture

In recent years, the importance of viral and host microRNAs (miRNAs) in mediating viral replication and control of host cellular machinery, has been realised and increasing efforts have been taken in order to understand the interactions of miRNAs from host and pathogen during infection. However, all existing studies has thus far been conducted in controlled experimental conditions and the veracity of these data for field conditions are yet to be established. In this framework, small RNA sequencing was performed to identify the miRNAs involved in shrimp (Penaeus vannamei) immune responses under two different WSSV infection conditions of natural infection and experimentally challenged conditions. The expression profiles of miRNAs of shrimp infected with WSSV under two contrasting conditions were compared and as a result, 23365 known miRNAs and 481 novel miRNAs were identified. Amongst the most abundantly expressed miRNAs, the hypoxia related miR-210 and immune pathway related miR-29b were expressed only in infected shrimps of both conditions. miR-8-5p, having a functional role in modulation of chitin biosynthesis was exclusively represented in higher numbers in the WSSV -infected shrimps under natural conditions whilst four of the miRNAs (mja-miR-6493–5p, mja-miR-6492, mmu-miR-3968, tcf-miR-9b-5p) identified from shrimps collected from pond culture targeted chitinase, an important enzyme involved in growth and moulting in shrimps, indicating an interaction between WSSV infection and moult cycle under culture conditions. Some of the miRNAs (tca-miR-87b-3p, cte-miR-277a) and miRNAs belonging to class miR-9, miR-981 that were identified only in WSSV infected shrimps under experimental conditions, are known to respond against WSSV infection in shrimps. Moreover, the miRNA target prediction revealed several immune-related gene targets such as cathepsin, c-type lectin, haemocyanin and ubiquitin protein ligase were commonly identified under both the conditions. However, the miRNAs identified from challenge experiment had wide number of gene targets as compared to the miRNAs of natural infection. The shrimp miRNA mja-miR-6489–3p, was also found to target early virus gene wsv001 of WSSV. Our study, therefore, provides the comparative analysis of miRNA expression from shrimp during WSSV infection in two different conditions.

miRNA, P.vannamei, WSSV
1050-4648
288-295
Shekhar, M. S.
7cc1c236-cf3e-42d5-a131-792ddd0af0c1
Karthic, K.
32f22523-7047-4fcd-bfbc-9bc703ad92ab
Kumar, K. Vinaya
8d5bbe22-16ba-46dd-8e5e-907e806bb510
Kumar, J. Ashok
7a840727-8026-42a2-82e5-b3cf740b5bd5
Swathi, A.
487276ba-dcbc-4bce-8850-b375c864e492
Hauton, C.
7706f6ba-4497-42b2-8c6d-00df81676331
Peruzza, L.
c01f028c-1fb4-44a4-83b9-f24698a9c9e5
Vijayan, K.K.
0b05a8b9-f6c8-4c37-8b34-6012fc746830
Shekhar, M. S.
7cc1c236-cf3e-42d5-a131-792ddd0af0c1
Karthic, K.
32f22523-7047-4fcd-bfbc-9bc703ad92ab
Kumar, K. Vinaya
8d5bbe22-16ba-46dd-8e5e-907e806bb510
Kumar, J. Ashok
7a840727-8026-42a2-82e5-b3cf740b5bd5
Swathi, A.
487276ba-dcbc-4bce-8850-b375c864e492
Hauton, C.
7706f6ba-4497-42b2-8c6d-00df81676331
Peruzza, L.
c01f028c-1fb4-44a4-83b9-f24698a9c9e5
Vijayan, K.K.
0b05a8b9-f6c8-4c37-8b34-6012fc746830

Shekhar, M. S., Karthic, K., Kumar, K. Vinaya, Kumar, J. Ashok, Swathi, A., Hauton, C., Peruzza, L. and Vijayan, K.K. (2019) Comparative analysis of shrimp (Penaeus vannamei) miRNAs expression profiles during WSSV infection under experimental conditions and in pond culture. Fish and Shellfish Immunology, 93, 288-295. (doi:10.1016/j.fsi.2019.07.057).

Record type: Article

Abstract

In recent years, the importance of viral and host microRNAs (miRNAs) in mediating viral replication and control of host cellular machinery, has been realised and increasing efforts have been taken in order to understand the interactions of miRNAs from host and pathogen during infection. However, all existing studies has thus far been conducted in controlled experimental conditions and the veracity of these data for field conditions are yet to be established. In this framework, small RNA sequencing was performed to identify the miRNAs involved in shrimp (Penaeus vannamei) immune responses under two different WSSV infection conditions of natural infection and experimentally challenged conditions. The expression profiles of miRNAs of shrimp infected with WSSV under two contrasting conditions were compared and as a result, 23365 known miRNAs and 481 novel miRNAs were identified. Amongst the most abundantly expressed miRNAs, the hypoxia related miR-210 and immune pathway related miR-29b were expressed only in infected shrimps of both conditions. miR-8-5p, having a functional role in modulation of chitin biosynthesis was exclusively represented in higher numbers in the WSSV -infected shrimps under natural conditions whilst four of the miRNAs (mja-miR-6493–5p, mja-miR-6492, mmu-miR-3968, tcf-miR-9b-5p) identified from shrimps collected from pond culture targeted chitinase, an important enzyme involved in growth and moulting in shrimps, indicating an interaction between WSSV infection and moult cycle under culture conditions. Some of the miRNAs (tca-miR-87b-3p, cte-miR-277a) and miRNAs belonging to class miR-9, miR-981 that were identified only in WSSV infected shrimps under experimental conditions, are known to respond against WSSV infection in shrimps. Moreover, the miRNA target prediction revealed several immune-related gene targets such as cathepsin, c-type lectin, haemocyanin and ubiquitin protein ligase were commonly identified under both the conditions. However, the miRNAs identified from challenge experiment had wide number of gene targets as compared to the miRNAs of natural infection. The shrimp miRNA mja-miR-6489–3p, was also found to target early virus gene wsv001 of WSSV. Our study, therefore, provides the comparative analysis of miRNA expression from shrimp during WSSV infection in two different conditions.

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More information

Accepted/In Press date: 19 July 2019
e-pub ahead of print date: 19 July 2019
Published date: 1 October 2019
Keywords: miRNA, P.vannamei, WSSV

Identifiers

Local EPrints ID: 436848
URI: http://eprints.soton.ac.uk/id/eprint/436848
ISSN: 1050-4648
PURE UUID: c3383010-1cb0-42f6-807d-207266b09cfa
ORCID for C. Hauton: ORCID iD orcid.org/0000-0002-2313-4226

Catalogue record

Date deposited: 10 Jan 2020 17:35
Last modified: 26 Nov 2021 02:38

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Contributors

Author: M. S. Shekhar
Author: K. Karthic
Author: K. Vinaya Kumar
Author: J. Ashok Kumar
Author: A. Swathi
Author: C. Hauton ORCID iD
Author: L. Peruzza
Author: K.K. Vijayan

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