Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Expression partitioning of duplicate genes at single cell resolution in Arabidopsis roots

View ORCID ProfileJeremy E. Coate, View ORCID ProfileAndrew D. Farmer, View ORCID ProfileJohn Schiefelbein, Jeff J. Doyle
doi: https://doi.org/10.1101/2020.08.20.260117
Jeremy E. Coate
1Department of Biology, Reed College, Portland, OR USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jeremy E. Coate
Andrew D. Farmer
2National Center for Genome Resources, Santa Fe, NM USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Andrew D. Farmer
John Schiefelbein
3Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for John Schiefelbein
Jeff J. Doyle
4School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: jjd5@cornell.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

Gene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralogue pairs rapidly return to single copy status whereas, in other pairs, paralogues are retained and may (or may not) diverge in expression pattern or function. The effect of a gene—its site of expression and thus the initial locus of its function—occurs at the level of a cell comprising a single cell type at a given state of the cell’s development. Thus, it is critical to understand the expression of duplicated gene pairs at a cellular level of resolution. Using Arabidopsis thaliana root single cell transcriptomic data we identify 36 cell clusters, each representing a cell type at a particular developmental state, and analyze expression patterns of over 11,000 duplicate gene pairs produced by three cycles of polyploidy as well as by various types of single gene duplication mechanisms. We categorize paralogue pairs by their patterns of expression, identifying pairs showing strongly biased paralogue/homoeologue expression in different cell clusters. Notably, the precision of cell-level expression data permits the identification of pairs showing alternate bias, with each paralogue comprising 90% or greater of the pair’s expression in different cell clusters, consistent with subfunctionalization at the cell type or cell state level, and, in some cases, at the level of individual cells. We identify a set of over 7,000 genes whose expression in all 36 cell clusters suggests that the single copy ancestor of each was also expressed in all root cells. With this cell-level expression information we hypothesize that there have been major shifts in expression for the majority of duplicated genes, to different degrees depending, as expected, on gene function and duplication type, but also on the particular cell type and state.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted August 22, 2020.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Expression partitioning of duplicate genes at single cell resolution in Arabidopsis roots
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Expression partitioning of duplicate genes at single cell resolution in Arabidopsis roots
Jeremy E. Coate, Andrew D. Farmer, John Schiefelbein, Jeff J. Doyle
bioRxiv 2020.08.20.260117; doi: https://doi.org/10.1101/2020.08.20.260117
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Expression partitioning of duplicate genes at single cell resolution in Arabidopsis roots
Jeremy E. Coate, Andrew D. Farmer, John Schiefelbein, Jeff J. Doyle
bioRxiv 2020.08.20.260117; doi: https://doi.org/10.1101/2020.08.20.260117

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Plant Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3688)
  • Biochemistry (7783)
  • Bioengineering (5673)
  • Bioinformatics (21267)
  • Biophysics (10574)
  • Cancer Biology (8170)
  • Cell Biology (11929)
  • Clinical Trials (138)
  • Developmental Biology (6757)
  • Ecology (10394)
  • Epidemiology (2065)
  • Evolutionary Biology (13853)
  • Genetics (9702)
  • Genomics (13063)
  • Immunology (8136)
  • Microbiology (19976)
  • Molecular Biology (7841)
  • Neuroscience (43032)
  • Paleontology (318)
  • Pathology (1278)
  • Pharmacology and Toxicology (2258)
  • Physiology (3350)
  • Plant Biology (7221)
  • Scientific Communication and Education (1311)
  • Synthetic Biology (2000)
  • Systems Biology (5533)
  • Zoology (1127)