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The state of algal genome quality and diversity
Algal Research ( IF 5.1 ) Pub Date : 2020-06-20 , DOI: 10.1016/j.algal.2020.101968
Erik R. Hanschen , Shawn R. Starkenburg

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 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.



中文翻译:

藻类基因组质量和多样性的状态

生物学的基因组时代为研究生命的工作方式提供了前所未有的机会,包括了解进化原理,新型抗生素的生物勘探以及对与生物经济相关物种的基因操作。尽管基因组测序和基因组分析以前仅限于大型项目和财团,但测序已变得民主化。但是,由于基因组学已变得司空见惯,因此对测序生物的分类已变得充满挑战,并且尚未采用用于测序,组装和注释的标准化方法。尽管藻类在基于生物的经济中日益重要,但在藻类生物学等研究领域中也是如此。在这里,我们提供了对真核藻基因组学状态的全面综述,探讨了藻类基因组装配的质量,并找出当前物种分布中的偏差和差距,以为将来的基因组计划的发展提供信息。总的来说,我们发现基因组资源质量下降的趋势,包括装配质量,基因注释质量和基因组完整性的下降。改善基因组质量的潜在解决方案包括广泛使用长读和脚手架技术,实施装配质量标准,基于证据的基因注释和必要的出版物,以及支持继续开发基因预测和基因组评估软件。和基因组完整性。改善基因组质量的潜在解决方案包括广泛使用长读和脚手架技术,实施装配质量标准,基于证据的基因注释和必要的出版物,以及支持继续开发基因预测和基因组评估软件。和基因组完整性。改善基因组质量的潜在解决方案包括广泛使用长读和脚手架技术,实施装配质量标准,基于证据的基因注释和必要的出版物,以及支持继续开发基因预测和基因组评估软件。

更新日期:2020-06-20
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