Signature selection forces and evolutionary divergence of immune-survival genes compared between two important shrimp species

Tze Chiew Christie Soo; Subha Bhassu

doi:10.1371/journal.pone.0280250

Signature selection forces and evolutionary divergence of immune-survival genes compared between two important shrimp species

PLoS One. 2023 Jan 12;18(1):e0280250. doi: 10.1371/journal.pone.0280250. eCollection 2023.

Authors

Tze Chiew Christie Soo¹, Subha Bhassu^{1

2}

Affiliations

¹ Department of Genetics and Molecular Biology, Animal Genetics and Genome Evolutionary Laboratory (AGAGEL), Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
² Terra Aqua Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), Research Management and Innovation Complex, University of Malaya, Kuala Lumpur, Malaysia.

Abstract

In recent years, shrimp aquaculture industry had grown significantly to become the major source of global shrimp production. Despite that, shrimp aquaculture production was impeded by various shrimp diseases over the past decades. Interestingly, different shrimp species demonstrated variable levels of immune strength and survival (immune-survival) ability towards different diseases, especially the much stronger immune-survival ability shown by the ancient shrimp species, Macrobrachium rosenbergii compared to other shrimp species. In this study, two important shrimp species, M. rosenbergii and Penaeus monodon (disease tolerant strain) (uninfected control and VpAHPND-infected) were compared to uncover the potential underlying genetic factors. The shrimp species were sampled, followed by RNA extraction and cDNA conversion. Five important immune-survival genes (C-type Lectin, HMGB, STAT, ALF3, and ATPase 8/6) were selected for PCR, sequencing, and subsequent genetics analysis. The overall genetic analyses conducted, including Analysis of Molecular Variance (AMOVA) and population differentiation, showed significant genetic differentiation (p<0.05) between different genes of M. rosenbergii and P. monodon. There was greater genetic divergence identified between HMGB subgroups of P. monodon (uninfected control and VpAHPND-infected) compared to other genes. Besides that, based on neutrality tests conducted, purifying selection was determined to be the main evolutionary driving force of M. rosenbergii and P. monodon with stronger purifying selection exhibited in M. rosenbergii genes. Potential balancing selection was identified for VpAHPND-infected HMGB subgroup whereas directional selection was detected for HMGB (both species) and ATPase 8/6 (only P. monodon) genes. The divergence times between M. rosenbergii and P. monodon genes were estimated through Bayesian molecular clock analysis, which were 438.6 mya (C-type Lectin), 1885.4 mya (HMGB), 432.6 mya (STAT), 448.1 mya (ALF3), and 426.4 mya (ATPase 8/6) respectively. In conclusion, important selection forces and evolutionary divergence information of immune-survival genes between M. rosenbergii and P. monodon were successfully identified.

Copyright: © 2023 Soo, Bhassu. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenosine Triphosphatases / genetics
Animals
Bayes Theorem
Biological Evolution*
HMGB Proteins
Lectins, C-Type / genetics
Penaeidae* / genetics

Substances

Lectins, C-Type
Adenosine Triphosphatases
HMGB Proteins

Grants and funding

This work was completed under the funding of ST052-2022 UM International Collaboration Grant awarded to SB under Centre for Research in Biotechnology for Agriculture (CEBAR), IPPP, University of Malaya. URL: https://cebar.um.edu.my/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.