The state of algal genome quality and diversity

Hanschen, Erik Richard; Starkenburg, Shawn Robert

doi:10.1016/j.algal.2020.101968

The state of algal genome quality and diversity

Journal Article · Sat Jun 20 00:00:00 EDT 2020 · Algal Research

DOI:https://doi.org/10.1016/j.algal.2020.101968· OSTI ID:3009680

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Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

The genomic era of biology has created unprecedented opportunity to study how life works, including understanding evolutionary principles, bioprospecting for novel antibiotics, and genetic manipulation of bioeconomically-relevant species. While genome sequencing and genomic analysis was previously restricted to large-scale projects and consortia, sequencing has become democratized. However, as genomics has become commonplace, the cataloging of sequenced organisms has become challenging, and standardized practices for sequencing, assembly, and annotation have not been adopted. This is equally true in research fields such as algal biology, despite the growing importance of algae in a bio-based economy. Here, in this study, we provide a comprehensive review of the state of eukaryotic algal genomics, explore the quality of algal genome assemblies, and identify the biases and gaps in the current species distribution to inform the development of future genome projects. Overall, we find a trend of declining quality of genomic resources, including a reduction in assembly quality, gene annotation quality, and genome completeness. Potential solutions to improve genome quality include widespread utilization of long read and scaffolding technologies, implementation of standards for assembly quality, evidence-based gene annotation and requisite publication, and support of continued development of gene prediction and genome assessment software.

View Accepted Manuscript (DOE)

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE; USDOE Laboratory Directed Research and Development (LDRD) Program; USDOE National Nuclear Security Administration (NNSA); USDOE Office of Energy Efficiency and Renewable Energy (EERE), Office of Sustainable Transportation. Bioenergy Technologies Office (BETO)

Grant/Contract Number:: 89233218CNA000001

OSTI ID:: 3009680

Alternate ID(s):: OSTI ID: 1780159

Report Number(s):: LA-UR--20-21021; 10.1016/j.algal.2020.101968

Journal Information:: Algal Research, Journal Name: Algal Research Vol. 50; ISSN 2211-9264

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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