️ Episode 159: The Untapped Potential of Short‑Read Sequencing in Biodiversity Research

In this episode of PaperCast Base by Base, we explore how modern short‑read sequencing and genome skimming are reshaping biodiversity science—from rapid species identification and biomass estimation to scalable phylogenomics and holobiont studies—while keeping costs and sample requirements low.

Study Highlights:
This review synthesizes how low‑coverage short‑read data can recover organellar genomes and high‑copy nuclear markers, enabling robust taxonomic identification and phylogenetic inference across diverse taxa. It explains assembly‑free and mapping approaches that extract universal single‑copy orthologs or k‑mer signatures directly from raw reads, expanding analyses even when DNA is degraded or coverage is sparse. The authors show that genome size and repeat content (mobilome) can be estimated accurately from skims, supporting comparative genomics without reference‑quality assemblies. They highlight museum and type specimens as genomic treasure troves for building curated reference databases at scale, crucial for monitoring programs tied to the Global Biodiversity Framework. Finally, the paper surveys emerging short‑read platforms that further reduce per‑gigabase costs, pointing to rapid growth in throughput and accessibility for biodiversity applications.

Conclusion:
Short‑read sequencing remains a powerful, scalable backbone for biodiversity genomics, offering cost‑effective, reference‑complementary insights that accelerate conservation, monitoring, and evolutionary discovery.

Reference:
Bleidorn C, Sandberg F, Martin S, Vogler AP, Podsiadlowski L. The untapped potential of short‑read sequencing in biodiversity research. Trends in Genetics. 2025. https://doi.org/10.1016/j.tig.2025.09.001

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

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