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 (December 2020) Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control. Genome Research, 31 (2). pp. 225-238. ISSN 1088-9051

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Abstract

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.

Item Type:	Paper
Subjects:	organs, tissues, organelles, cell types and functions > cell types and functions > cell functions > cell cycle organs, tissues, organelles, cell types and functions > cell types and functions > cell functions organs, tissues, organelles, cell types and functions > cell types and functions organs, tissues, organelles, cell types and functions organism description > plant
CSHL Authors:	Ernst, Evan Martienssen, Robert A.
Communities:	CSHL labs > Martienssen lab CSHL Cancer Center Program CSHL Cancer Center Program > Gene Regulation and Inheritance Program
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	23 December 2020
Date Deposited:	06 May 2021 16:42
Last Modified:	13 Feb 2024 18:48
PMCID:	PMC7849404
URI:	https://repository.cshl.edu/id/eprint/40014

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