Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song1,
- Edward S. Buckler1,2,3,
- Hai Wang1,4,
- Yaoyao Wu1,5,
- Evan Rees2,
- Elizabeth A. Kellogg6,
- Daniel J. Gates7,
- Merritt Khaipho-Burch2,
- Peter J. Bradbury3,
- Jeffrey Ross-Ibarra7,8,
- Matthew B. Hufford9 and
- M. Cinta Romay1
- 1Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA;
- 2Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA;
- 3Agricultural Research Service, United States Department of Agriculture, Ithaca, New York 14853, USA;
- 4National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing 100193, China;
- 5Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
- 6Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA;
- 7Department of Evolution and Ecology, University of California Davis, Davis, California 95616, USA;
- 8Center for Population Biology and Genome Center, University of California Davis, Davis, California 95616, USA;
- 9Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA
Abstract
Thousands of species will be sequenced in the next few years; however, understanding how their genomes work, without an unlimited budget, requires both molecular and novel evolutionary approaches. We developed a sensitive sequence alignment pipeline to identify conserved noncoding sequences (CNSs) in the Andropogoneae tribe (multiple crop species descended from a common ancestor ∼18 million years ago). The Andropogoneae share similar physiology while being tremendously genomically diverse, harboring a broad range of ploidy levels, structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis-regulatory elements, chromatin loop anchors, noncoding RNA (ncRNA) genes, and several transposable element superfamilies. CNSs were enriched in active regions of DNA replication in the early S phase of the mitotic cell cycle and showed different DNA methylation ratios compared to the genome-wide background. More than half of putative cis-regulatory sequences (identified via other methods) overlapped with CNSs detected in this study. Variants in CNSs were associated with gene expression levels, and CNS absence contributed to loss of gene expression. Furthermore, the evolution of CNSs was associated with the functional diversification of duplicated genes in the context of maize subgenomes. Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.266528.120.
- Received May 27, 2020.
- Accepted May 21, 2021.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
