Comparative Genomics of Stress-Associated Gene Family Copy Number Variation in Chlorophyte Microalgae

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Abiotic stresses severely limit agricultural productivity and have stimulated growing interest in microalgae as sources of stress-resilient traits and biostimulants. However, comparative genomic assessments integrating multiple stress-associated gene families across chlorophyte genome assemblies are limited. Here, we analyzed 19 chlorophyte genome assemblies to investigate the distribution and copy-number variation of 11 gene families associated with antioxidant defense, osmoprotection, and carotenoid biosynthesis. Candidate genes were identified using standardized InterPro annotations and manually curated to ensure consistent gene copy-number estimation. Hierarchical clustering, principal component analysis (PCA), descriptive statistics, and Pearson’s correlation analysis were performed to characterize gene-family copy-number patterns and multivariate similarities among genome assemblies. Multiple tests in the correlation analysis were controlled using the Benjamini–Hochberg false discovery rate procedure. The total functional family assignments ranged from 28 to 51 across the analyzed genome assemblies. Thioredoxin (TRX) exhibited the highest mean copy number (17.26 copies per genome) and the lowest coefficient of variation (15.43%), whereas catalase (CAT) showed the greatest variability (CV = 59.28%). The first two principal components explained 50.18% of the total variation, with PC1 accounting for 30.86% and PC2 for 19.32%, and differentiated genome assemblies according to their stress-associated gene copy-number profiles. Several moderate-to-strong pairwise correlations were observed, but none were significant after FDR correction. Overall, this study provides a curated comparative genomic framework for identifying stress-associated gene-family copy-number patterns across chlorophyte genome assemblies and generating testable hypotheses for subsequent functional studies.

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