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

Rootless plants in the genus are some of the fastest growing known plants on Earth. have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for (Benth.) Hartog & Plas, which has the smallest genome size in the gen...

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Published inGenome research Vol. 31; no. 2; pp. 225 - 238
Main Authors 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
Format Journal Article
LanguageEnglish
Published United States Cold Spring Harbor Laboratory Press 01.02.2021
Subjects
Asexual reproduction
BASIC BIOLOGICAL SCIENCES
Budding
Chloroplasts
Flowering
Gene expression
Genomes
Innate immunity
Leucine
Transcriptomes
Wolffia
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Abstract Rootless plants in the genus are some of the fastest growing known plants on Earth. have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for (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 clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. 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 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 and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in , where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.
AbstractList 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.
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.
Rootless plants in the genus are some of the fastest growing known plants on Earth. have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for (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 clones confirmed loss of several hundred genes that are highly conserved among flowering plants, including genes involved in root developmental and light signaling pathways. 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 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 and rice, many of the pathways associated with multicellular and developmental processes are not under TOD control in , where genes that cycle the conditions tested predominantly have carbon processing and chloroplast-related functions. The genome and TOD expression data set thus provide insight into the interplay between a streamlined plant body plan and optimized growth.
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.
Author Sree, K Sowjanya
Mockler, Todd C
Chu, Philomena
Fuchs, Joerg
Ernst, Evan
Hartwick, Nolan
Jupe, Florian
Michael, Todd P
Appenroth, Klaus J
Gilbert, Sarah
Baggs, Erin L
Lam, Eric
Borisjuk, Ljudmylla
Bryant, Douglas
Ortleb, Stefan
Martienssen, Robert A
Krasileva, Ksenia V
Ecker, Joseph R
Sandoval, Justin P
AuthorAffiliation 3 Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
2 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
5 Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
9 Friedrich Schiller University of Jena, Jena 07737, Germany
4 Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
7 Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA
1 Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
6 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben 06466, Germany
10 Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
8 Department of Environmental Science, Central University of Kerala, Periye, Kerala 671316, India
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  organization: Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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Copyright 2021 Michael et al.; Published by Cold Spring Harbor Laboratory Press.
Copyright Cold Spring Harbor Laboratory Press Feb 2021
2021
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Salk Institute for Biological Studies, La Jolla, CA (United States)
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License 2021 Michael et al.; Published by Cold Spring Harbor Laboratory Press.
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USDA
SC0018244; 12116
USDOE Office of Science (SC), Biological and Environmental Research (BER)
These authors contributed equally to this work.
Present addresses: 12Department of Energy and Process Engineering, Norwegian University of Science and Technology, Trondheim NO-7491, Norway; 13NewLeaf Symbiotics, BRDG Park, St. Louis, MO 63132, USA; 14Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA; 15Bayer Crop Science, Chesterfield, MO 63017, USA
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PublicationTitle Genome research
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Snippet Rootless plants in the genus are some of the fastest growing known plants on Earth. have a reduced body plan, primarily multiplying through a budding type of...
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...
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...
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Aggregation Database
Index Database
StartPage 225
SubjectTerms Asexual reproduction
BASIC BIOLOGICAL SCIENCES
Budding
Chloroplasts
Flowering
Gene expression
Genomes
Innate immunity
Leucine
Transcriptomes
Wolffia
Title Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
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