Development of transcriptomics-based growth rate indices in two model eukaryotes and relevance to metatranscriptomics...

Area of Science:

• Molecular Biology
• Ecology
• Bioinformatics

Background:

• Accurate growth rate estimation is crucial for understanding ecosystem dynamics, particularly for microscopic organisms.
• Current methods for growth rate determination in microorganisms present significant challenges.

Purpose of the Study:

• To develop and validate novel indices for estimating growth rates using mRNA abundance ratios.
• To investigate the utility of nuclear and mitochondrial gene mRNA ratios for growth rate estimation.

Main Methods:

• Proposed four mRNA ratio indices: total nuclear and mitochondrial mRNA ratio (Nuc:Mito-TmRNA), nuclear and mitochondrial ribosomal protein mRNA ratio (Nuc:Mito-RPmRNA), gene ontology (GO) terms and total mitochondrial mRNA ratios, and nuclear and mitochondrial specific gene mRNA ratio.
• Analyzed RNA-Seq datasets from Daphnia magna and Saccharomyces cerevisiae obtained from the NCBI Short Read Archive.

Main Results:

• Both Nuc:Mito-TmRNA and Nuc:Mito-RPmRNA ratio indices demonstrated significant correlations with growth rates in both species.
• Numerous GO terms mRNA ratios correlated significantly with the growth rate of S. cerevisiae.
• Identified specific nuclear and mitochondrial gene pairs whose mRNA ratios significantly correlated with growth rate.

Conclusions:

• The proposed mRNA ratio indices, particularly Nuc:Mito-TmRNA and Nuc:Mito-RPmRNA, are effective for estimating growth rates in different species.
• These mRNA ratios hold promise for future applications in metatranscriptome analyses to assess community and species growth rates.