International Journal of Marine Science, 2024, Vol.14, No.3, 172-181 http://www.aquapublisher.com/index.php/ijms 178 6.3 Molecular and genetic tools Molecular and genetic tools have revolutionized the study of ciliate communities by detecting genetic diversity that is not apparent in morphological examinations. Techniques such as Sanger sequencing, pyrosequencing, and Illumina sequencing are used to assess ciliate diversity and community structure (Santoferrara et al., 2014; Rossi et al., 2016; Kulaš et al., 2021). DNA barcoding (metabarcoding) effectively enhances the accuracy and efficiency of biodiversity surveys of ciliates (Figure 3). This method improves understanding of ciliate community assembly and their ecological functions (Zhao et al., 2022). Mitochondrial cox1 gene, nuclear ITS1 and ITS2, and the highly variable D2 region of LSU rDNA are promising candidate genes for species delimitation, providing high-resolution analysis below the species level (Zhao et al., 2016). Combining molecular techniques with morphological analysis offers a robust framework for resolving conflicts in species identification and understanding the ecological functions of ciliate communities (Zhao et al., 2016). Figure 3 The flow chart of the metabarcoding processing steps (water sampling collection, sample pretreatment, DNA extraction, and PCR amplification, NGS-Illumina sequencing for example, reference database selection, and taxonomic assignment) of ciliate biodiversity (Adopted from Zhao et al., 2022)
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