Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Michael, Todd P.; Ernst, Evan; Hartwick, Nolan; Chu, Philomena; Bryant, Douglas; Gilbert, Sarah; Ortleb, Stefan; Baggs, Erin L.; Sree, K. Sowjanya; Appenroth, Klaus J.; Fuchs, Joerg; Jupe, Florian; Sandoval, Justin P.; Krasileva, Ksenia V.; Borisjuk, Ljudmylla; Mockler, Todd C.; Ecker, Joseph R.; Martienssen, Robert A.; Lam, Eric

doi:10.1101/gr.266429.120

Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control

Journal Article · Wed Dec 23 00:00:00 EST 2020 · Genome Research

DOI:https://doi.org/10.1101/gr.266429.120· OSTI ID:1817049

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Salk Institute for Biological Studies, La Jolla, CA (United States); OSTI
Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States)
Salk Institute for Biological Studies, La Jolla, CA (United States)
Rutgers Univ., New Brunswick, NJ (United States); Norwegian Univ. of Science and Technology, Trondheim (Norway)
Donald Danforth Plant Science Center, St. Louis, MO (United States); NewLeaf Symbiotics, St. Louis, MO (United States)
Rutgers Univ., New Brunswick, NJ (United States); Univ. of North Carolina, Chapel Hill, NC (United States)
Leibniz Inst. Plant Genetics and Crop Plant Research (IPK), Berlin (Germany)
Univ. of California, Berkeley, CA (United States)
Central University of Kerala (India)
Friedrich Schiller Univ., Jena (Germany)
Salk Institute for Biological Studies, La Jolla, CA (United States); Bayer Crop Science, Chesterfield, MO (United States)
Donald Danforth Plant Science Center, St. Louis, MO (United States)
Rutgers Univ., New Brunswick, NJ (United States)

Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia australiana (Benth.) Hartog & Plas, which has the smallest genome size in the genus at 357 Mb and has a reduced set of predicted protein-coding genes at about 15,000. Comparison between multiple high-quality draft genome sequences from W. australiana clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. Wolffia has also lost most of the conserved nucleotide-binding leucine-rich repeat (NLR) genes that are known to be involved in innate immunity, as well as those involved in terpene biosynthesis, while having a significant overrepresentation of genes in the sphingolipid pathways that may signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ~40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in W. australiana, where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The Wolffia genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.

View Accepted Manuscript (DOE)

Research Organization:: Rutgers Univ., New Brunswick, NJ (United States); Salk Institute for Biological Studies, La Jolla, CA (United States)

Sponsoring Organization:: USDA; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0018244

OSTI ID:: 1817049

Journal Information:: Genome Research, Journal Name: Genome Research Journal Issue: 2 Vol. 31; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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