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MICROALGAL GENOME SEQUENCING REVEALS A VIRAL LEGACY
The ability of algae species to inhabit specific environments is facilitated by genes acquired from viruses by their ancient ancestors, according to a study led by New York University Abu Dhabi.
Algae form a diverse category of organisms that, like plants, produce oxygen through photosynthesis. However, unlike multicellular plants, they can be single-celled organisms, multi-celled organisms, or even colonies of organisms. Algae are primarily located in water but can also be found on land and in microhabitats. For example, they live in the fur on the backs of sloths and within the translucent bodies of marine slugs in unique symbiotic relationships. Algae can be large (like the giant sea kelp that grows up to 45 meters) or small (like the microscopic phytoplankton).
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While algae may be considered uninteresting to the average person, their role in the global ecosystem is critical – they produce half of the planet’s annual oxygen supply and are a foundational food source in the marine world. Some species also fix nitrogen from an inert gas to deposit it in the soil, thereby providing necessary nutrients to plant life. Despite the integral role that algae play in our environment, they are relatively understudied, particularly the smaller category known as microalgae.
“Microalgae produce most of the Earth’s oxygen, sequester carbon dioxide, and even promote raincloud formation, but relatively few microalgal genomes were studied before this project. Although microalgae are fundamental to global ecosystems and have the potential for sustainable biotechnological development, they have received far less research attention than other microbes. For example, more than 30,000 bacteria have been sequenced, while only 62 microalgae had been sequenced before our project,” explained Dr. David Nelson, Senior Research Scientist at New York University Abu Dhabi (NYUAD).
Dr. Nelson recently collaborated with researchers from NYUAD, King Abdullah University of Science and Technology, The University of Texas at Austin, and the National Center for Marine Algae and Microbiota in Maine to sequence 107 microalgae species representing 11 phyla, which is a zoological category below kingdom and above class. Collaborators from NYUAD included Associate Professor of Biology Dr. Kourosh Salehi-Ashtiani, Postdoctoral Associate Dr. Alexandra Mystikou, Research Scientist Dr. Weiqi Fu, Postdoctoral Associate Dr. Sarah Daakour, Researcher Bushra Dohai, and Research Assistant Amnah Alzahmi.
Their investigation into the microalgae species’ genomes – which Dr. Nelson referred to as “the core, indivisible coding apparatus for all organisms” – was intended to clarify the expanse of their protein-coding and viral elements. Identifying the protein-coding region of a genome enables comparative analysis of physical characteristics as genes encode proteins, and proteins dictate cell function.
Evidence has been mounting that algae genomes have been permanently changed by past viral infections – some estimated to have occurred millions of years ago.
“The viral contribution to algal genomes has not been studied on a large scale, but evidence suggests that viruses have contributed to their hosts’ adaptation of different environments. Gene shuffling between algae and viruses has led to the emergence of giant viruses that incorporate entire biosynthetic pathways, sourced from their algal hosts, into their enormous genomes. When host specificity expands, viral genes can be transferred to distantly related organisms and confer specific evolutionary adaptations, such as the introduction of new metabolic pathways. These facilitate the assimilation of fresh nutrients or abiotic stress resistance genes that promote survival in niche habitats,” stated the research team in a paper that was recently published in leading journal Cell Host & Microbe.
IDENTIFYING THE GENES THAT CONFER HALOTOLERANCE – OR THE ABILITY TO THRIVE IN HIGH-SALT ENVIRONMENTS – MAY HELP SCIENTISTS ENHANCE THE ABILITY OF CROP SPECIES TO GROW IN SALINE ENVIRONMENTS, THEREBY INCREASING AVAILABLE FARMLAND AND CROP YIELDS
To address the knowledge gap in algal genomics and investigate their heritage, the team set out to sequence a large sample of algae representing diverse phyla, geographies, and climates. It gathered 107 algae samples from the collections of The University of Texas at Austin, the National Center for Marine Algae and Microbiota, and NYUAD. The microalgae samples were cultured and then sequenced before the new sequencing was compared to those available from the National Center for Biotechnology Information (NCBI) in Maryland and Phytozome (the Plant Comparative Genomics portal of the US Department of Energy).
This was done to further investigate the differences between microalgae from saltwater and freshwater habitats and natural groups (called clades). The results of the genetic sequencing and analysis revealed fundamental differences between the genomes of freshwater and saltwater algae and identified genes of viral heritage. Researchers found that each of the sequenced microalgal phyla had its own unique set of viral-origin sequences, with over 90,000 found in 184 algal genomes. This ubiquity implies that viruses donated functional genes to these algae very early in their evolution, perhaps billions of years ago.
Marine species contained significantly more viral-origin genes in their genomes than freshwater algae. In the latter, the viral sequences were likely to have enhanced metal assimilation as well as their ability to metabolize sugars and amino acids. The viral-origin genes from saltwater algae tended to provide photosynthetic machinery and enabled their ability to maintain membrane integrity in a saline environment.
“We discovered that all microalgal genomes had a core set of viralorigin genes, but throughout the multibillion-year course of microalgal evolution, various lineages acquired different sets of ‘donations,’ thus defining their potential to operate within a given environmental niche,” Dr. Nelson explained. Among the more notable findings from the study was the identification of the specific genes responsible for maintaining marine algae’s membrane integrity in saline environments. Identifying the genes that confer halotolerance – or the ability to thrive in high-salt environments – may help scientists enhance the ability of crop species to grow in saline environments, thereby increasing available farmland and crop yields.
- Dr. David Nelson, Senior Research Scientist New York University Abu Dhabi
“Any crop species whose development would benefit from using more saline water, such as in cases where freshwater is limited, could benefit from the insertion of a halotolerance genetic cassette. I would specifically recommend looking at cell membrane reinforcement bioengineering as a way to enhance the turgor response in crop species subjected to hypersaline watering regimes,” Dr. Nelson shared.
The results of the project are hosted at several international data repositories, including the NCBI and open-access repository of research data Dryad. Dr. Nelson and his collaborators hope this massive increase in sequenced algae will serve as a resource to the international science community and accelerate efforts to identify and leverage algae strains unique to the UAE.
