Abstract
Diatoms are one of the most successful eukaryotes. There are over 100,000 diatom species contributing nearly half of total algal abundance in the oceans. Diatoms have conquered almost all aquatic environments, with high abundance especially in coastal and polar oceans and inland waters. The first diatom genomes provided important insights into their genetic, metabolic, and morphological diversity, which is unmatched by any other algal class. However, the recent application of long-read sequencing in addition to population genomics and culture-independent approaches enables a step-change in our understanding of diatom genomes. This chapter synthesizes what we have learned about the structure and evolution of diatom nuclear genes and genomes since the genome of Thalassiosira pseudonana became available in 2004. We highlight some of the key findings and discuss mechanisms and drivers of diatom genome evolution and adaptation underpinning the success of the entire class. Considering that most of their genomic diversity is still unknown, large-scale genome projects and culture-independent methods such as metagenome-assembled and single-cell-amplified genomes hold great promise to reveal more of their inter- and intraspecific genomic diversity in an environmental context. Data from these studies will pave the way for novel insights into their genetic versatility, which will enable us to identify the key evolutionary innovations in diatoms, and their adaptive evolution to a wide variety of environments, including to some of the most extreme aquatic environments on Earth such as intertidal zones and polar oceans. These insights are not only critical for advancing diatom-based biotechnology and synthetic biology, but will also improve our knowledge about how the various diatom lineages perform their important roles as key players for capturing CO2 and as the foundation of diverse aquatic food webs, thus providing significant ecosystem services and maintaining the continued habitability on Earth.
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Abbreviations
- BAC :
-
Bacterial Artificial Chromosome
- DAE :
-
Differential Allelic Expression
- EGT :
-
Endosymbiotic Gene Transfer
- GO :
-
Gene Ontology
- HGT :
-
Horizontal Gene Transfer
- ISIPs :
-
Iron Stress-Induced Proteins
- JGI :
-
Joint Genome Institute
- lincRNAs :
-
long intergenic non-coding RNAs
- MAG:
-
Metagenome-assembled genome
- MGT :
-
Metagenomics-based transcriptome
- ncRNAs :
-
non-coding RNAs
- ONT:
-
Oxford Nanopore Technology
- ORF :
-
Open Reading Frame
- PacBio:
-
Pacific Biosciences
- PUFAs :
-
Polyunsaturated Fatty Acids
- SAG:
-
Single-Amplified Genome
- SMRT :
-
Single-Molecule Real-Time
- sRNAs :
-
small non-coding RNAs
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Mock, T. et al. (2022). Structure and Evolution of Diatom Nuclear Genes and Genomes. In: Falciatore, A., Mock, T. (eds) The Molecular Life of Diatoms. Springer, Cham. https://doi.org/10.1007/978-3-030-92499-7_5
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