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      Whole Genome Sequencing Reveals Genetic Differences Between Symbiodiniaceae Populations Among Reproductively and Geographically Isolated Acropora Colonies in Western Australia

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          ABSTRACT

          Significant genetic differentiation between Symbiodiniaceae populations in coral hosts can be induced by a range of factors including geography, latitude, depth, temperature and light utilisation. The conventional method of measuring Symbiodiniaceae diversity involving the ITS2 region of rDNA has several limitations, stemming from insufficient genetic resolution and the multi‐copy nature of the marker. This could be improved by using higher throughput whole genome sequencing to identify fine‐scale population genetic differences and provide new insight into factors influencing coral‐Symbiodiniaceae associations. The aim of this study was to investigate the genetic diversity of Symbiodiniaceae populations using low‐coverage whole genome sequencing in sympatric populations of Acropora cf. secale and allopatric populations of Acropora millepora that reproduce in different seasons in Western Australia. Genetic diversity of Symbiodiniaceae populations in these two species was examined using principal coordinates analysis and permutational analysis of variance. This analysis revealed that while all colonies were dominated by Cladocopium, there was a significant genetic difference between Symbiodiniaceae populations in both species. In A. millepora , this variation could be due to the latitudinal variation between populations or differences in reproductive seasonality, but in sympatric populations of A. cf. secale, genetic differences between Symbiodiniaceae populations were clearly aligned with the reproductive seasonality of the coral host. The use of whole genome sequencing improved the sensitivity to detect Symbiodiniaceae genetic population structure between coral populations, which increases our ability to identify genetic and potentially functional differences associated with variation in Symbiodiniaceae populations.

          Abstract

          In this study, we used a whole genome sequencing approach to determine whether reproductively and geographically isolated Acropora colonies in Western Australia harbour genetically different Symbiodiniaceae populations. We found that both allopatric and sympatric populations have significantly genetically different symbionts, potentially due to environmental or genetic factors.

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            Cutadapt removes adapter sequences from high-throughput sequencing reads

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              MultiQC: summarize analysis results for multiple tools and samples in a single report

              Motivation: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis. Results: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization. Availability and implementation: MultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.info Contact: phil.ewels@scilifelab.se
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                Author and article information

                Contributors
                seriksson@uow.edu.au
                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                02 January 2025
                January 2025
                : 15
                : 1 ( doiID: 10.1002/ece3.v15.1 )
                : e70771
                Affiliations
                [ 1 ] School of Earth, Atmospheric and Life Sciences University of Wollongong Wollongong New South Wales Australia
                [ 2 ] Climate Change Cluster (C3) University of Technology Sydney Broadway New South Wales Australia
                [ 3 ] Department of Integrative Biology University of Texas at Austin Austin Texas USA
                [ 4 ] Xenbase, Departments of Biological Sciences and Computer Science University of Calgary Calgary Alberta Canada
                [ 5 ] Australian Institute of Marine Science Indian Ocean Marine Research Centre Crawley Western Australia Australia
                Author notes
                [*] [* ] Correspondence:

                Sanna Y. Eriksson ( seriksson@ 123456uow.edu.au )

                Author information
                https://orcid.org/0009-0002-3802-5695
                https://orcid.org/0000-0001-5453-9819
                Article
                ECE370771 ECE-2024-04-00725.R3
                10.1002/ece3.70771
                11695670
                82966f5c-7588-4813-ac17-7279853191a8
                © 2025 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 03 December 2024
                : 15 April 2024
                : 15 December 2024
                Page count
                Figures: 3, Tables: 0, Pages: 8, Words: 6100
                Funding
                Funded by: National Science Foundation , doi 10.13039/100000001;
                Award ID: OCE‐2318775
                Funded by: Minderoo Foundation , doi 10.13039/501100016056;
                Funded by: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada , doi 10.13039/501100002790;
                Categories
                Ecological Genetics
                Genomics
                Research Article
                Research Article
                Custom metadata
                2.0
                January 2025
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.5.1 mode:remove_FC converted:03.01.2025

                Evolutionary Biology
                acropora cf. secale, acropora millepora ,genetic variation,temporal reproductive isolation,whole genome sequencing

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