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      Identification of Philaster apodigitiformis in aquaculture and functional characterization of its β-PKA gene and expression analysis of infected Poecilia reticulata

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          Abstract

          Abstract

          Cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) is a distinctive member of the serine–threonine protein AGC kinase family and an effective kinase for cAMP signal transduction. In recent years, scuticociliate has caused a lot of losses in domestic fishery farming, therefore, we have carried out morphological and molecular biological studies. In this study, diseased guppies ( Poecilia reticulata) were collected from an ornamental fish market, and scuticociliate Philaster apodigitiformis Miao et al., 2009 was isolated. In our prior transcriptome sequencing research, we discovered significant expression of the β-PKA gene in P. apodigitiformis during its infection process, leading us to speculate its involvement in pathogenesis. A complete sequence of the β-PKA gene was cloned, and quantified by quantitative reverse transcription-polymerase chain reaction to analyse or to evaluate the functional characteristics of the β-PKA gene. Morphological identification and phylogenetic analysis based on small subunit rRNA sequence, infection experiments and haematoxylin–eosin staining method were also carried out, in order to study the pathological characteristics and infection mechanism of scuticociliate. The present results showed that: (1) our results revealed that β-PKA is a crucial gene involved in P. apodigitiformis infection in guppies, and the findings provide valuable insights for future studies on scuticociliatosis; (2) we characterized a complete gene, β-PKA, that is generally expressed in parasitic organisms during infection stage and (3) the present study indicates that PKA plays a critical role in scuticociliate when infection occurs by controlling essential steps such as cell growth, development and regulating the activity of the sensory body structures and the irritability system.

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          MrBayes 3: Bayesian phylogenetic inference under mixed models.

          MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types-e.g. morphological, nucleotide, and protein-and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
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            A rapid bootstrap algorithm for the RAxML Web servers.

            Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in the computation of bootstrap support values. Conducting a probably insufficient number of 100 bootstrap (BS) analyses with current ML programs on large datasets-either with respect to the number of taxa or base pairs-can easily require a month of run time. Therefore, we have developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms. These new heuristics can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses. Computational experiments to assess the performance and relative accuracy of these heuristics were conducted on 22 diverse DNA and AA (amino acid), single gene as well as multigene, real-world alignments containing 125 up to 7764 sequences. The standard BS (SBS) and rapid BS (RBS) values drawn on the best-scoring ML tree are highly correlated and show almost identical average support values. The weighted RF (Robinson-Foulds) distance between SBS- and RBS-based consensus trees was smaller than 6% in all cases (average 4%). More importantly, RBS inferences are between 8 and 20 times faster (average 14.73) than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses with competing programs, such as PHYML or GARLI. Moreover, this performance improvement increases with alignment size. Finally, we have set up two freely accessible Web servers for this significantly improved version of RAxML that provide access to the 200-CPU cluster of the Vital-IT unit at the Swiss Institute of Bioinformatics and the 128-CPU cluster of the CIPRES project at the San Diego Supercomputer Center. These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources.
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              BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT.

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                Author and article information

                Journal
                Parasitology
                Parasitology
                PAR
                Parasitology
                Cambridge University Press (Cambridge, UK )
                0031-1820
                1469-8161
                April 2024
                12 February 2024
                : 151
                : 4
                : 370-379
                Affiliations
                [1]Laboratory of Protozoology, Harbin Normal University , Harbin 150025, China
                Author notes
                Corresponding author: Xuming Pan; Email: pppppp206@ 123456126.com
                Author information
                https://orcid.org/0009-0003-8641-3657
                https://orcid.org/0000-0002-6299-339X
                https://orcid.org/0000-0002-7071-1751
                Article
                S0031182024000118
                10.1017/S0031182024000118
                11044068
                38343157
                c65774e8-d936-4582-bd80-bc4bbe7d118b
                © The Author(s) 2024

                This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.

                History
                : 19 May 2023
                : 13 January 2024
                : 22 January 2024
                Page count
                Figures: 8, Tables: 3, References: 43, Pages: 10
                Funding
                Funded by: National Natural Science Foundation of China, doi http://dx.doi.org/10.13039/501100001809;
                Award ID: 31970498
                Categories
                Research Article

                Parasitology
                infection,philaster apodigitiformis,pka,poecilia reticulate
                Parasitology
                infection, philaster apodigitiformis, pka, poecilia reticulate

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