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Foster TL, Kloiber-Maitz M, Gilles L, Frei UK, Pfeffer S, Chen YR, Dutta S, Seetharam AS, Hufford MB, Lübberstedt T. Fine mapping of major QTL qshgd1 for spontaneous haploid genome doubling in maize (Zea mays L.). Theor Appl Genet 2024; 137:117. [PMID: 38700534 DOI: 10.1007/s00122-024-04615-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/04/2024] [Indexed: 05/09/2024]
Abstract
KEY MESSAGE A large-effect QTL was fine mapped, which revealed 79 gene models, with 10 promising candidate genes, along with a novel inversion. In commercial maize breeding, doubled haploid (DH) technology is arguably the most efficient resource for rapidly developing novel, completely homozygous lines. However, the DH strategy, using in vivo haploid induction, currently requires the use of mutagenic agents which can be not only hazardous, but laborious. This study focuses on an alternative approach to develop DH lines-spontaneous haploid genome duplication (SHGD) via naturally restored haploid male fertility (HMF). Inbred lines A427 and Wf9, the former with high HMF and the latter with low HMF, were selected to fine-map a large-effect QTL associated with SHGD-qshgd1. SHGD alleles were derived from A427, with novel haploid recombinant groups having varying levels of the A427 chromosomal region recovered. The chromosomal region of interest is composed of 45 megabases (Mb) of genetic information on chromosome 5. Significant differences between haploid recombinant groups for HMF were identified, signaling the possibility of mapping the QTL more closely. Due to suppression of recombination from the proximity of the centromere, and a newly discovered inversion region, the associated QTL was only confined to a 25 Mb region, within which only a single recombinant was observed among ca. 9,000 BC1 individuals. Nevertheless, 79 gene models were identified within this 25 Mb region. Additionally, 10 promising candidate genes, based on RNA-seq data, are described for future evaluation, while the narrowed down genome region is accessible for straightforward introgression into elite germplasm by BC methods.
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Affiliation(s)
- Tyler L Foster
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
| | | | - Laurine Gilles
- Limagrain Europe SAS, Research Centre, 63720, Chappes, France
| | - Ursula K Frei
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Sarah Pfeffer
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Yu-Ru Chen
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Somak Dutta
- Department of Statistics, Iowa State University, Ames, IA, 50011, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
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2
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Kinkade JA, Seetharam AS, Sachdev S, Bivens NJ, Phinney BS, Grigorean G, Roberts RM, Tuteja G, Rosenfeld CS. Extracellular vesicles from mouse trophoblast cells: Effects on neural progenitor cells and potential participants in the placenta-brain axis†. Biol Reprod 2024; 110:310-328. [PMID: 37883444 PMCID: PMC10873279 DOI: 10.1093/biolre/ioad146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/12/2023] [Accepted: 10/21/2023] [Indexed: 10/28/2023] Open
Abstract
The fetal brain of the mouse is thought to be dependent upon the placenta as a source of serotonin (5-hydroxytryptamine; 5-HT) and other factors. How factors reach the developing brain remains uncertain but are postulated here to be part of the cargo carried by placental extracellular vesicles (EV). We have analyzed the protein, catecholamine, and small RNA content of EV from mouse trophoblast stem cells (TSC) and TSC differentiated into parietal trophoblast giant cells (pTGC), potential primary purveyors of 5-HT. Current studies examined how exposure of mouse neural progenitor cells (NPC) to EV from either TSC or pTGC affect their transcriptome profiles. The EV from trophoblast cells contained relatively high amounts of 5-HT, as well as dopamine and norepinephrine, but there were no significant differences between EV derived from pTGC and from TSC. Content of miRNA and small nucleolar (sno)RNA, however, did differ according to EV source, and snoRNA were upregulated in EV from pTGC. The primary inferred targets of the microRNA (miRNA) from both pTGC and TSC were mRNA enriched in the fetal brain. NPC readily internalized EV, leading to changes in their transcriptome profiles. Transcripts regulated were mainly ones enriched in neural tissues. The transcripts in EV-treated NPC that demonstrated a likely complementarity with miRNA in EV were mainly up- rather than downregulated, with functions linked to neuronal processes. Our results are consistent with placenta-derived EV providing direct support for fetal brain development and being an integral part of the placenta-brain axis.
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Affiliation(s)
- Jessica A Kinkade
- Biomedical Sciences, University of Missouri, Columbia, MO, USA
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Shrikesh Sachdev
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Nathan J Bivens
- Genomics Technology Core Facility, University of Missouri, Columbia, MO, USA
| | - Brett S Phinney
- Proteomics Core UC Davis Genome Center, University of California, Davis, CA, USA
| | - Gabriela Grigorean
- Proteomics Core UC Davis Genome Center, University of California, Davis, CA, USA
| | - R Michael Roberts
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Geetu Tuteja
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Cheryl S Rosenfeld
- Biomedical Sciences, University of Missouri, Columbia, MO, USA
- MU Institute of Data Science and Informatics, University of Missouri, Columbia, MO, USA
- Genetics Area Program, University of Missouri, Columbia, MO, USA
- Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, USA
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3
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Hartwig T, Banf M, Prietsch GP, Zhu JY, Mora-Ramírez I, Schippers JHM, Snodgrass SJ, Seetharam AS, Huettel B, Kolkman JM, Yang J, Engelhorn J, Wang ZY. Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize. Genome Biol 2023; 24:108. [PMID: 37158941 PMCID: PMC10165856 DOI: 10.1186/s13059-023-02909-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/23/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Genetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroid-responsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches. RESULTS Here, we use a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. HASCh-seq in the B73xMo17 F1s identifies thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits. CONCLUSION Our study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.
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Affiliation(s)
- Thomas Hartwig
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA.
- Heinrich-Heine University, Universitätsstraße 1, Düsseldorf, NRW, 40225, Germany.
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, NRW, 50829, Germany.
| | - Michael Banf
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
| | - Gisele Passaia Prietsch
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
| | - Jia-Ying Zhu
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, Seeland, SA, 06466, Germany
| | - Isabel Mora-Ramírez
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, Seeland, SA, 06466, Germany
| | - Jos H M Schippers
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, Seeland, SA, 06466, Germany
| | - Samantha J Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 339A Bessey Hall, Ames, IA, 50011, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 339A Bessey Hall, Ames, IA, 50011, USA
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, NRW, 50829, Germany
| | - Judith M Kolkman
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, 413 Bradfield Hall, Ithaca, NY, 14853, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 363 Keim Hall, Lincoln, NE, 68583, USA
| | - Julia Engelhorn
- Heinrich-Heine University, Universitätsstraße 1, Düsseldorf, NRW, 40225, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, NRW, 50829, Germany
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA.
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Phillips AR, Seetharam AS, Albert PS, AuBuchon-Elder T, Birchler JA, Buckler ES, Gillespie LJ, Hufford MB, Llaca V, Romay MC, Soreng RJ, Kellogg EA, Ross-Ibarra J. A happy accident: a novel turfgrass reference genome. G3 Genes|Genomes|Genetics 2023:7099442. [DOI: 10.1093/g3journal/jkad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/03/2022] [Accepted: 03/30/2023] [Indexed: 04/04/2023]
Abstract
Abstract
Poa pratensis, commonly known as Kentucky bluegrass, is a popular cool-season grass species used as turf in lawns and recreation areas globally. Despite its substantial economic value, a reference genome had not previously been assembled due to the genome’s relatively large size and biological complexity that includes apomixis, polyploidy, and interspecific hybridization. We report here a fortuitous de novo assembly and annotation of a P. pratensis genome. Instead of sequencing the genome of a C4 grass, we accidentally sampled and sequenced tissue from a weedy P. pratensis whose stolon was intertwined with that of the C4 grass. The draft assembly consists of 6.09 Gbp with an N50 scaffold length of 65.1 Mbp, and a total of 118 scaffolds, generated using PacBio long reads and Bionano optical map technology. We annotated 256 K gene models and found 58% of the genome to be composed of transposable elements. To demonstrate the applicability of the reference genome, we evaluated population structure and estimated genetic diversity in P. pratensis collected from three North American prairies, two in Manitoba, Canada and one in Colorado, USA. Our results support previous studies that found high genetic diversity and population structure within the species. The reference genome and annotation will be an important resource for turfgrass breeding and study of bluegrasses.
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Affiliation(s)
- Alyssa R Phillips
- Department of Evolution and Ecology and Center for Population Biology, University of California , Davis, Davis, CA 95616 , USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University , Ames, IA 50011 , USA
| | - Patrice S Albert
- Division of Biological Sciences, University of Missouri , Columbia, MO 65201 , USA
| | | | - James A Birchler
- Division of Biological Sciences, University of Missouri , Columbia, MO 65201 , USA
| | - Edward S Buckler
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University , Ithaca, NY 14850 , USA
- Institute for Genomic Diversity, Cornell University , Ithaca, NY 14850 , USA
- Agricultural Research Service, United States Department of Agriculture , Ithaca, NY 14850 , USA
| | - Lynn J Gillespie
- Botany Section, Research and Collections, Canadian Museum of Nature , Ottawa, ON K2P 2R1 , Canada
| | - Matthew B Hufford
- Division of Biological Sciences, University of Missouri , Columbia, MO 65201 , USA
| | | | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University , Ithaca, NY 14850 , USA
| | - Robert J Soreng
- Deptartment of Botany, Smithsonian Institution , Washington, DC 20560 , USA
| | | | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology and Center for Population Biology, University of California , Davis, Davis, CA 95616 , USA
- Genome Center, University of California , Davis, Davis, CA 95616 , USA
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5
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Seetharam AS, Vu HTH, Choi S, Khan T, Sheridan MA, Ezashi T, Roberts RM, Tuteja G. The product of BMP-directed differentiation protocols for human primed pluripotent stem cells is placental trophoblast and not amnion. Stem Cell Reports 2022; 17:1289-1302. [PMID: 35594861 PMCID: PMC9214062 DOI: 10.1016/j.stemcr.2022.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The observation that trophoblast (TB) can be generated from primed pluripotent stem cells (PSCs) by exposure to bone morphogenetic protein-4 (BMP4) when FGF2 and ACTIVIN signaling is minimized has recently been challenged with the suggestion that the procedure instead produces amnion. Here, by analyzing transcriptome data from multiple sources, including bulk and single-cell data, we show that the BMP4 procedure generates bona fide TB with similarities to both placental villous TB and TB generated from TB stem cells. The analyses also suggest that the transcriptomic signatures between embryonic amnion and different forms of TB have commonalities. Our data provide justification for the continued use of TB derived from PSCs as a model for investigating placental development. Cells differentiated by using BAP protocols resemble TB more than embryonic amnion Deviation from the standard BAP protocol results in less differentiated TB Single-cell/nucleus RNA-seq analysis identifies two syncytiotrophoblast populations
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Affiliation(s)
- Arun S Seetharam
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA; Genetics Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Ha T H Vu
- Genetics Development and Cell Biology, Iowa State University, Ames, IA, USA; Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA
| | - Sehee Choi
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Obstetrics and Gynecology, University of Missouri School of Medicine, Columbia, MO, USA
| | - Teka Khan
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Megan A Sheridan
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Obstetrics and Gynecology, University of Missouri School of Medicine, Columbia, MO, USA
| | - Toshihiko Ezashi
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - R Michael Roberts
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; Department of Biochemistry, University of Missouri, Columbia, MO, USA.
| | - Geetu Tuteja
- Genetics Development and Cell Biology, Iowa State University, Ames, IA, USA; Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA.
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6
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Li J, Singh U, Bhandary P, Campbell J, Arendsee Z, Seetharam AS, Wurtele ES. Foster thy young: enhanced prediction of orphan genes in assembled genomes. Nucleic Acids Res 2021; 50:e37. [PMID: 34928390 PMCID: PMC9023268 DOI: 10.1093/nar/gkab1238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023] Open
Abstract
Proteins encoded by newly-emerged genes ('orphan genes') share no sequence similarity with proteins in any other species. They provide organisms with a reservoir of genetic elements to quickly respond to changing selection pressures. Here, we systematically assess the ability of five gene prediction pipelines to accurately predict genes in genomes according to phylostratal origin. BRAKER and MAKER are existing, popular ab initio tools that infer gene structures by machine learning. Direct Inference is an evidence-based pipeline we developed to predict gene structures from alignments of RNA-Seq data. The BIND pipeline integrates ab initio predictions of BRAKER and Direct inference; MIND combines Direct Inference and MAKER predictions. We use highly-curated Arabidopsis and yeast annotations as gold-standard benchmarks, and cross-validate in rice. Each pipeline under-predicts orphan genes (as few as 11 percent, under one prediction scenario). Increasing RNA-Seq diversity greatly improves prediction efficacy. The combined methods (BIND and MIND) yield best predictions overall, BIND identifying 68% of annotated orphan genes, 99% of ancient genes, and give the highest sensitivity score regardless dataset in Arabidopsis. We provide a light weight, flexible, reproducible, and well-documented solution to improve gene prediction.
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Affiliation(s)
- Jing Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA
| | - Urminder Singh
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Priyanka Bhandary
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Jacqueline Campbell
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agriculture Research Service, Ames, IA 50014, USA
| | - Zebulun Arendsee
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA 50014, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50014, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA 50014, USA.,Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50014, USA.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50014, USA
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7
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Bornowski N, Michel KJ, Hamilton JP, Ou S, Seetharam AS, Jenkins J, Grimwood J, Plott C, Shu S, Talag J, Kennedy M, Hundley H, Singan VR, Barry K, Daum C, Yoshinaga Y, Schmutz J, Hirsch CN, Hufford MB, de Leon N, Kaeppler SM, Buell CR. Genomic variation within the maize stiff-stalk heterotic germplasm pool. Plant Genome 2021; 14:e20114. [PMID: 34275202 DOI: 10.1002/tpg2.20114] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/06/2021] [Indexed: 05/28/2023]
Abstract
The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.
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Affiliation(s)
- Nolan Bornowski
- Dep. of Plant Biology, Michigan State Univ., 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Kathryn J Michel
- Dep. of Agronomy, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - John P Hamilton
- Dep. of Plant Biology, Michigan State Univ., 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Shujun Ou
- Dep. of Ecology, Evolution, and Organismal Biology, Iowa State Univ., 2200 Osborn Drive, Ames, IA, 50011, USA
| | - Arun S Seetharam
- Dep. of Ecology, Evolution, and Organismal Biology, Iowa State Univ., 2200 Osborn Drive, Ames, IA, 50011, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Shengqiang Shu
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, Univ. of Arizona, 1657 E Helen Street, Tucson, AZ, 85721, USA
| | - Megan Kennedy
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Hope Hundley
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Vasanth R Singan
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Chris Daum
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
- U.S. Dep. of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Candice N Hirsch
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
| | - Matthew B Hufford
- Dep. of Ecology, Evolution, and Organismal Biology, Iowa State Univ., 2200 Osborn Drive, Ames, IA, 50011, USA
| | - Natalia de Leon
- Dep. of Agronomy, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Dep. of Energy, Great Lakes Bioenergy Research Center, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Shawn M Kaeppler
- Dep. of Agronomy, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Dep. of Energy, Great Lakes Bioenergy Research Center, Univ. of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Wisconsin Crop Innovation Center, Univ. of Wisconsin - Madison, 8520 University Green, Middleton, WI, 53562, USA
| | - C Robin Buell
- Dep. of Plant Biology, Michigan State Univ., 612 Wilson Road, East Lansing, MI, 48824, USA
- Dep. of Energy, Great Lakes Bioenergy Research Center, Michigan State Univ., 612 Wilson Road, East Lansing, MI, 48824, USA
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8
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Seetharam AS, Yu Y, Bélanger S, Clark LG, Meyers BC, Kellogg EA, Hufford MB. The Streptochaeta Genome and the Evolution of the Grasses. Front Plant Sci 2021; 12:710383. [PMID: 34671369 PMCID: PMC8521107 DOI: 10.3389/fpls.2021.710383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/08/2021] [Indexed: 05/15/2023]
Abstract
In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.
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Affiliation(s)
- Arun S. Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Yunqing Yu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | | | - Lynn G. Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | | | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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9
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Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DW, Zeng Y, O'Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, Portwood JL, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 2021; 373:655-662. [PMID: 34353948 PMCID: PMC8733867 DOI: 10.1126/science.abg5289] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/24/2021] [Indexed: 12/24/2022]
Abstract
We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.
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Affiliation(s)
- Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | - Margaret R Woodhouse
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | | | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - William A Ricci
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Tingting Guo
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Silas Tittes
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Asher I Hudson
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | | | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Rebecca D Piri
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Na Wang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Dong Won Kim
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Yibing Zeng
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Christine H O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Amanda M Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Erin Baggs
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - John L Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Ethalinda K S Cannon
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Carson M Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Samantha J Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David E Hufnagel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA
| | - Qiuhan Jiang
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Sarah Pedersen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Michael L Syring
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | | | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Jeffrey Ross-Ibarra
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Doreen Ware
- USDA-ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - R Kelly Dawe
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
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10
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Khan T, Seetharam AS, Zhou J, Bivens NJ, Schust DJ, Ezashi T, Tuteja G, Roberts RM. Single Nucleus RNA Sequence (snRNAseq) Analysis of the Spectrum of Trophoblast Lineages Generated From Human Pluripotent Stem Cells in vitro. Front Cell Dev Biol 2021; 9:695248. [PMID: 34368143 PMCID: PMC8334858 DOI: 10.3389/fcell.2021.695248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/21/2021] [Indexed: 02/03/2023] Open
Abstract
One model to study the emergence of the human trophoblast (TB) has been the exposure of pluripotent stem cells to bone morphogenetic protein 4 (BMP4) in presence of inhibitors of ACTIVIN/TGFB; A83-01 and FGF2; PD173074 (BAP), which generates a mixture of cytotrophoblast, syncytiotrophoblast, and cells with similarities to extravillous trophoblast. Here, H1 human embryonic stem cells were BAP-exposed under two O2 conditions (20% and 5%, respectively). At day 8, single nuclei RNA sequencing was used for transcriptomics analysis, thereby allowing profiling of fragile syncytial structures as well as the more resilient mononucleated cells. Following cluster analysis, two major groupings, one comprised of five (2,4,6,7,8) and the second of three (1,3,5) clusters were evident, all of which displayed recognized TB markers. Of these, two (2 and 3) weakly resembled extravillous trophoblast, two (5 and 6) strongly carried the hallmark transcripts of syncytiotrophoblast, while the remaining five were likely different kinds of mononucleated cytotrophoblast. We suggest that the two populations of nuclei within syncytiotrophoblast may have arisen from fusion events involving two distinct species of precursor cells. The number of differentially expressed genes between O2 conditions varied among the clusters, and the number of genes upregulated in cells cultured under 5% O2 was highest in syncytiotrophoblast cluster 6. In summary, the BAP model reveals an unexpectedly complex picture of trophoblast lineage emergence that will need to be resolved further in time-course studies.
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Affiliation(s)
- Teka Khan
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Arun S. Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Jie Zhou
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Obstetrics and Gynecology, University of Missouri School of Medicine, Columbia, MO, United States
| | - Nathan J. Bivens
- DNA Core Facility, University of Missouri, Columbia, MO, United States
| | - Danny J. Schust
- Department of Obstetrics and Gynecology, University of Missouri School of Medicine, Columbia, MO, United States
| | - Toshihiko Ezashi
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Geetu Tuteja
- Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - R. Michael Roberts
- Christopher S Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Division of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
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11
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Murugan K, Suresh SK, Seetharam AS, Severin AJ, Sashital DG. Systematic in vitro specificity profiling reveals nicking defects in natural and engineered CRISPR-Cas9 variants. Nucleic Acids Res 2021; 49:4037-4053. [PMID: 33744974 PMCID: PMC8053117 DOI: 10.1093/nar/gkab163] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022] Open
Abstract
Cas9 is an RNA-guided endonuclease in the bacterial CRISPR-Cas immune system and a popular tool for genome editing. The commonly used Streptococcus pyogenes Cas9 (SpCas9) is relatively non-specific and prone to off-target genome editing. Other Cas9 orthologs and engineered variants of SpCas9 have been reported to be more specific. However, previous studies have focused on specificity of double-strand break (DSB) or indel formation, potentially overlooking alternative cleavage activities of these Cas9 variants. In this study, we employed in vitro cleavage assays of target libraries coupled with high-throughput sequencing to systematically compare cleavage activities and specificities of two natural Cas9 variants (SpCas9 and Staphylococcus aureus Cas9) and three engineered SpCas9 variants (SpCas9 HF1, HypaCas9 and HiFi Cas9). We observed that all Cas9s tested could cleave target sequences with up to five mismatches. However, the rate of cleavage of both on-target and off-target sequences varied based on target sequence and Cas9 variant. In addition, SaCas9 and engineered SpCas9 variants nick targets with multiple mismatches but have a defect in generating a DSB, while SpCas9 creates DSBs at these targets. Overall, these differences in cleavage rates and DSB formation may contribute to varied specificities observed in genome editing studies.
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Affiliation(s)
- Karthik Murugan
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Molecular, Cellular, and Developmental Biology Interdepartmental Program, Iowa State University, Ames, IA 50011, USA
| | - Shravanti K Suresh
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USA
| | - Andrew J Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Molecular, Cellular, and Developmental Biology Interdepartmental Program, Iowa State University, Ames, IA 50011, USA
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12
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Hufnagel DE, Hufford MB, Seetharam AS. SequelTools: a suite of tools for working with PacBio Sequel raw sequence data. BMC Bioinformatics 2020; 21:429. [PMID: 33004007 PMCID: PMC7532105 DOI: 10.1186/s12859-020-03751-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/11/2020] [Indexed: 12/20/2022] Open
Abstract
Background PacBio sequencing is an incredibly valuable third-generation DNA sequencing method due to very long read lengths, ability to detect methylated bases, and its real-time sequencing methodology. Yet, hitherto no tool was available for analyzing the quality of, subsampling, and filtering PacBio data. Results Here we present SequelTools, a command-line program containing three tools: Quality Control, Read Subsampling, and Read Filtering. The Quality Control tool quickly processes PacBio Sequel raw sequence data from multiple SMRTcells producing multiple statistics and publication-quality plots describing the quality of the data including N50, read length and count statistics, PSR, and ZOR. The Read Subsampling tool allows the user to subsample reads by one or more of the following criteria: longest subreads per CLR or random CLR selection. The Read Filtering tool provides options for normalizing data by filtering out certain low-quality scraps reads and/or by minimum CLR length. SequelTools is implemented in bash, R, and Python using only standard libraries and packages and is platform independent. Conclusions SequelTools is a program that provides the only free, fast, and easy-to-use quality control tool, and the only program providing this kind of read subsampling and read filtering for PacBio Sequel raw sequence data, and is available at https://github.com/ISUgenomics/SequelTools.
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Affiliation(s)
- David E Hufnagel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA. .,Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, IA, 50010, USA.
| | - Matthew B Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
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13
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Liu J, Seetharam AS, Chougule K, Ou S, Swentowsky KW, Gent JI, Llaca V, Woodhouse MR, Manchanda N, Presting GG, Kudrna DA, Alabady M, Hirsch CN, Fengler KA, Ware D, Michael TP, Hufford MB, Dawe RK. Gapless assembly of maize chromosomes using long-read technologies. Genome Biol 2020; 21:121. [PMID: 32434565 PMCID: PMC7238635 DOI: 10.1186/s13059-020-02029-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements.
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Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Victor Llaca
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | | | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gernot G Presting
- Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Magdy Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Georgia Genomics and Bioinformatics Core Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Kevin A Fengler
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, 14853, USA
| | - Todd P Michael
- Informatics Department, J. Craig Venter Institute, La Jolla, CA, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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14
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Liu J, Seetharam AS, Chougule K, Ou S, Swentowsky KW, Gent JI, Llaca V, Woodhouse MR, Manchanda N, Presting GG, Kudrna DA, Alabady M, Hirsch CN, Fengler KA, Ware D, Michael TP, Hufford MB, Dawe RK. Gapless assembly of maize chromosomes using long-read technologies. Genome Biol 2020. [PMID: 32434565 DOI: 10.1101/2020.01.14.906230v1.full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize genome (B73-Ab10) composed of 63 contigs and a contig N50 of 162 Mb. This genome includes gapless assemblies of chromosome 3 (236 Mb) and chromosome 9 (162 Mb), and 53 Mb of the Ab10 meiotic drive haplotype. The data also reveal the internal structure of seven centromeres and five heterochromatic knobs, showing that the major tandem repeat arrays (CentC, knob180, and TR-1) are discontinuous and frequently interspersed with retroelements.
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Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kyle W Swentowsky
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Jonathan I Gent
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Victor Llaca
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | | | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gernot G Presting
- Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Magdy Alabady
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Georgia Genomics and Bioinformatics Core Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Kevin A Fengler
- Corteva Agriscience™, 8325 NW 62nd Ave, Johnston, IA, 50131, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY, 14853, USA
| | - Todd P Michael
- Informatics Department, J. Craig Venter Institute, La Jolla, CA, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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15
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Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam AS, Stein JC, Llaca V, Manchanda N, Gilbert AM, Wei S, Chin CS, Hufnagel DE, Pedersen S, Snodgrass SJ, Fengler K, Woodhouse M, Walenz BP, Koren S, Phillippy AM, Hannigan BT, Dawe RK, Hirsch CN, Hufford MB, Ware D. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nat Commun 2020; 11:2288. [PMID: 32385271 PMCID: PMC7211024 DOI: 10.1038/s41467-020-16037-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 04/09/2020] [Indexed: 01/23/2023] Open
Abstract
Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11-21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.
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Affiliation(s)
- Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Jianing Liu
- Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
| | - Kapeel M Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | | | - Arun S Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
- Genome Informatics Facility, Iowa State University, Ames, Iowa, 50011, USA
| | - Joshua C Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Victor Llaca
- Genomics Technologies, Applied Science and Technology, Corteva Agriscience TM, Johnston, Iowa, 50131, USA
| | - Nancy Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Amanda M Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA
| | - Chen-Shan Chin
- DNAnexus, Inc., Mountain View, San Francisco, California, 94040, USA
| | - David E Hufnagel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Sarah Pedersen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Samantha J Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA
| | - Kevin Fengler
- Genomics Technologies, Applied Science and Technology, Corteva Agriscience TM, Johnston, Iowa, 50131, USA
| | - Margaret Woodhouse
- USDA ARS Corn Insects and Crop Genetics Research Unit, Ames, Iowa, 50011, USA
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Brett T Hannigan
- DNAnexus, Inc., Mountain View, San Francisco, California, 94040, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA.
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108, USA.
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011, USA.
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724, USA.
- USDA ARS Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, New York, 14853, USA.
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16
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Murugan K, Seetharam AS, Severin AJ, Sashital DG. CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects. J Biol Chem 2020; 295:5538-5553. [PMID: 32161115 PMCID: PMC7186167 DOI: 10.1074/jbc.ra120.012933] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/04/2020] [Indexed: 12/26/2022] Open
Abstract
Cas12a (Cpf1) is an RNA-guided endonuclease in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome editing. Cas12a can bind and cut dsDNA targets with high specificity in vivo, making it an ideal candidate for expanding the arsenal of enzymes used in precise genome editing. However, this reported high specificity contradicts Cas12a's natural role as an immune effector against rapidly evolving phages. Here, we employed high-throughput in vitro cleavage assays to determine and compare the native cleavage specificities and activities of three different natural Cas12a orthologs (FnCas12a, LbCas12a, and AsCas12a). Surprisingly, we observed pervasive sequence-specific nicking of randomized target libraries, with strong nicking of DNA sequences containing up to four mismatches in the Cas12a-targeted DNA-RNA hybrid sequences. We also found that these nicking and cleavage activities depend on mismatch type and position and vary with Cas12a ortholog and CRISPR RNA sequence. Our analysis further revealed robust nonspecific nicking of dsDNA when Cas12a is activated by binding to a target DNA. Together, our findings reveal that Cas12a has multiple nicking activities against dsDNA substrates and that these activities vary among different Cas12a orthologs.
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Affiliation(s)
- Karthik Murugan
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011; Molecular, Cellular, and Developmental Biology Interdepartmental Program, Iowa State University, Ames, Iowa 50011
| | - Arun S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50011
| | - Andrew J Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50011
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011; Molecular, Cellular, and Developmental Biology Interdepartmental Program, Iowa State University, Ames, Iowa 50011.
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17
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Manchanda N, Portwood JL, Woodhouse MR, Seetharam AS, Lawrence-Dill CJ, Andorf CM, Hufford MB. GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations. BMC Genomics 2020; 21:193. [PMID: 32122303 PMCID: PMC7053122 DOI: 10.1186/s12864-020-6568-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/07/2020] [Indexed: 11/28/2022] Open
Abstract
Background Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types. Results Our application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies. Conclusions The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.
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Affiliation(s)
- Nancy Manchanda
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - John L Portwood
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | | | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Ames, IA, 50011, USA
| | - Carolyn J Lawrence-Dill
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA.,Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Carson M Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
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18
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Masonbrink R, Maier TR, Muppirala U, Seetharam AS, Lord E, Juvale PS, Schmutz J, Johnson NT, Korkin D, Mitchum MG, Mimee B, den Akker SEV, Hudson M, Severin AJ, Baum TJ. The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC Genomics 2019; 20:119. [PMID: 30732586 PMCID: PMC6367775 DOI: 10.1186/s12864-019-5485-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations. The parasitic success of H. glycines relies on the comprehensive re-engineering of an infection site into a syncytium, as well as the long-term suppression of host defense to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms of effector acquisition, diversification, and selection need to be understood before effective control strategies can be developed, but the lack of an annotated genome has been a major roadblock. RESULTS Here, we use PacBio long-read technology to assemble a H. glycines genome of 738 contigs into 123 Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7 Mb), and horizontal gene transfer events (151 genes). A large number of putative effectors (431 genes) were identified in the genome, many of which were found in transposons. CONCLUSIONS This advance provides a glimpse into the host and parasite interplay by revealing a diversity of mechanisms that give rise to virulence genes in the soybean cyst nematode, including: tandem duplications containing over a fifth of the total gene count, virulence genes hitchhiking in transposons, and 107 horizontal gene transfers not reported in other plant parasitic nematodes thus far. Through extensive characterization of the H. glycines genome, we provide new insights into H. glycines biology and shed light onto the mystery underlying complex host-parasite interactions. This genome sequence is an important prerequisite to enable work towards generating new resistance or control measures against H. glycines.
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Affiliation(s)
- Rick Masonbrink
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Tom R. Maier
- Department of Plant Pathology, Iowa State University, Ames, IA USA
| | - Usha Muppirala
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Arun S. Seetharam
- Department of Plant Pathology, Iowa State University, Ames, IA USA
- Genome Informatics Facility, Iowa State University, Ames, IA USA
| | - Etienne Lord
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC Canada
| | | | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Nathan T. Johnson
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA USA
- Department of Computer Science, Worcester Polytechnic Institute, Worcester, MA USA
| | | | - Benjamin Mimee
- Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC Canada
| | | | - Matthew Hudson
- Department of Crop Sciences University of Illinois, Urbana, IL USA
| | | | - Thomas J. Baum
- Department of Plant Pathology, Iowa State University, Ames, IA USA
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19
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Masonbrink RE, Purcell CM, Boles SE, Whitehead A, Hyde JR, Seetharam AS, Severin AJ. An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species. Genome Biol Evol 2019; 11:431-438. [PMID: 30657886 PMCID: PMC6373831 DOI: 10.1093/gbe/evz006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2019] [Indexed: 11/13/2022] Open
Abstract
Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2. This assembly approach resulted in 8,371 scaffolds and total length of 1.498 Gb; the N50 was 1.895 Mb, and the longest scaffold was 13.2 Mb. Gene models were predicted, using MAKER2, from RNA-Seq data and all related expressed sequence tags and proteins from NCBI; this resulted in 57,785 genes with an average length of 8,255 bp. In addition, single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone. Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms. Among the six abalone species examined, the endangered white abalone appears to harbor the lowest levels of heterozygosity. This draft genome assembly and the sequencing data provide a foundation for genome-enabled aquaculture improvement for red abalone, and for genome-guided conservation efforts for the other five species and, in particular, for the endangered white and black abalone.
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Affiliation(s)
| | - Catherine M Purcell
- Ocean Associates, Inc. Under Contract to NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California
| | - Sara E Boles
- Department of Environmental Toxicology, University of California, Davis
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis
| | - John R Hyde
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California
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20
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Masonbrink R, Maier TR, Seetharam AS, Juvale PS, Baber L, Baum TJ, Severin AJ. SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines). Database (Oxford) 2019; 2019:baz111. [PMID: 31680133 PMCID: PMC6853641 DOI: 10.1093/database/baz111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/22/2019] [Accepted: 08/09/2019] [Indexed: 11/25/2022]
Abstract
Soybean is an important worldwide crop, and farmers continue to experience significant yield loss due to the soybean cyst nematode (SCN), Heterodera glycines. This soil-borne roundworm parasite is rated the most important pathogen problem in soybean production. The infective nematodes enter into complex interactions with their host plant by inducing the development of specialized plant feeding cells that provide the parasites with nourishment. Addressing the SCN problem will require the development of genomic resources and a global collaboration of scientists to analyze and use these resources. SCNBase.org was designed as a collaborative hub for the SCN genome. All data and analyses are downloadable and can be analyzed with three integrated genomic tools: JBrowse, Feature Search and BLAST. At the time of this writing, a number of genomic and transcriptomic data sets are already available, with 43 JBrowse tracks and 21 category pages describing SCN genomic analyses on gene predictions, transcriptome and read alignments, effector-like genes, expansion and contraction of genomic repeats, orthology and synteny with related nematode species, Single Nucleotide Polymorphism (SNPs) from 15 SCN populations and novel splice sites. Standard functional gene annotations were supplemented with orthologous gene annotations using a comparison to nine related plant-parasitic nematodes, thereby enabling functional annotations for 85% of genes. These annotations led to a greater grasp on the SCN effectorome, which include over 3324 putative effector genes. By designing SCNBase as a hub, future research findings and genomic resources can easily be uploaded and made available for use by others with minimal needs for further curation. By providing these resources to nematode research community, scientists will be empowered to develop novel, more effective SCN management tools.
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Affiliation(s)
- Rick Masonbrink
- Genome Informatics Facility, Iowa State University, Osborne Dr, Ames, IA 50011, USA
| | - Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Pammel Dr, Ames, IA 50011, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Iowa State University, Osborne Dr, Ames, IA 50011, USA
| | - Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Pammel Dr, Ames, IA 50011, USA
| | - Levi Baber
- Research IT, Iowa State University, Osborne Dr, Ames, IA 50011, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Pammel Dr, Ames, IA 50011, USA
| | - Andrew J Severin
- Genome Informatics Facility, Iowa State University, Osborne Dr, Ames, IA 50011, USA
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21
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Abstract
Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.
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Affiliation(s)
- Joshua T Trujillo
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ
| | | | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Mark A Beilstein
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ
- The School of Plant Sciences, The University of Arizona, Tucson, AZ
| | - Rebecca A Mosher
- Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ
- The School of Plant Sciences, The University of Arizona, Tucson, AZ
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22
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Bhandary P, Seetharam AS, Arendsee ZW, Hur M, Wurtele ES. Raising orphans from a metadata morass: A researcher's guide to re-use of public 'omics data. Plant Sci 2018; 267:32-47. [PMID: 29362097 DOI: 10.1016/j.plantsci.2017.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/07/2017] [Accepted: 10/15/2017] [Indexed: 05/19/2023]
Abstract
More than 15 petabases of raw RNAseq data is now accessible through public repositories. Acquisition of other 'omics data types is expanding, though most lack a centralized archival repository. Data-reuse provides tremendous opportunity to extract new knowledge from existing experiments, and offers a unique opportunity for robust, multi-'omics analyses by merging metadata (information about experimental design, biological samples, protocols) and data from multiple experiments. We illustrate how predictive research can be accelerated by meta-analysis with a study of orphan (species-specific) genes. Computational predictions are critical to infer orphan function because their coding sequences provide very few clues. The metadata in public databases is often confusing; a test case with Zea mays mRNA seq data reveals a high proportion of missing, misleading or incomplete metadata. This metadata morass significantly diminishes the insight that can be extracted from these data. We provide tips for data submitters and users, including specific recommendations to improve metadata quality by more use of controlled vocabulary and by metadata reviews. Finally, we advocate for a unified, straightforward metadata submission and retrieval system.
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Affiliation(s)
- Priyanka Bhandary
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USA
| | - Zebulun W Arendsee
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Manhoi Hur
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- Dept. of Genetics Development and Cell Biology, Iowa State University, Ames IA 50010, USA; Center for Metabolic Biology, Iowa State University, Ames, IA 50011, USA.
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23
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Cullen JN, Lithio A, Seetharam AS, Zheng Y, Li G, Nettleton D, O'Connor AM. Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis. Vet Microbiol 2017; 207:267-279. [PMID: 28757034 DOI: 10.1016/j.vetmic.2017.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 12/25/2022]
Abstract
Infectious bovine keratoconjunctivitis (IBK) is an important production limiting disease in cattle. Moraxella bovis has historically been considered the primary causal agent; however, vaccines have not been consistently shown as effective in controlling disease incidence. The purpose of this study was to examine the bacterial community of calf eyes prior to disease onset using high-throughput sequencing of 16S ribosomal RNA and determine if it was associated with IBK occurrence. The study was designed as a case-control nested within a randomized controlled trial (RCT). Eye swabs were collected from all spring-born calves without clinical signs of IBK (t0 swabs) on a research farm with a previous history of IBK disease outbreaks. At follow-up or weaning, calves were diagnosed as IBK positive or negative. The lag time between enrollment swabs (t0) and IBK diagnosis ranged from approximately one to three months. Cases were randomly selected from IBK positive calves and controls were selected from IBK negative calves (i.e. calves that did not exhibit clinical signs of IBK throughout the course of the RCT). Analysis of the fold-change differences between cases and controls did not reveal large-scale distinctions in bacterial composition. However, principal component analysis suggested bacterial composition differences between calf management groups, which were based on dam parity. Moraxella was found to be among the top ten most abundant genera in our population; however, the difference in abundance was not significant between the cases and controls. No large-scale differences in the bacterial communities of calves that did or did not develop IBK were observed in our population. Nevertheless, it remains unclear whether the "natural" bacterial population of the calf might ultimately impact disease status. Further study is warranted to examine bacterial taxa that were observed to be significantly more abundant in the cases or controls as potential vaccines/therapeutic targets.
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Affiliation(s)
- J N Cullen
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, United States.
| | - A Lithio
- Department of Statistics, College of Liberal Arts and Sciences, College of Agriculture and Life Sciences, Iowa State University, Ames, IA, 50011, United States.
| | - A S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, United States.
| | - Y Zheng
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, United States.
| | - G Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, United States.
| | - D Nettleton
- Department of Statistics, College of Liberal Arts and Sciences, College of Agriculture and Life Sciences, Iowa State University, Ames, IA, 50011, United States.
| | - A M O'Connor
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, United States.
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24
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Seetharam AS, Kawaler E, Du ZQ, Rothschild MF, Severin AJ. Microbiome analyses of pacific white shrimp (Litopenaeus vannamei) collected from disparate geographical locations. Genom Data 2015; 6:67-9. [PMID: 26697337 PMCID: PMC4664682 DOI: 10.1016/j.gdata.2015.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 08/04/2015] [Accepted: 08/07/2015] [Indexed: 11/28/2022]
Abstract
In this study, the tail muscle microbiota of pacific white shrimp (Litopenaeus vannamei) sourced from five countries across Central and South America and Southeast Asia were determined and compared. The genomic DNA was sequenced at around 10 × coverage for each geographical location and was assembled de novo for comparative analysis. The assembled sequences for all the lines were classified based on their similarity to the sequences in the public database. We found that there is high correlation among the microbiota of shrimp from disparate regions, as well as the presence of some DNA from bacteria known to cause food poisoning in humans. Sequencing data has been deposited at NCBI-SRA database and can be found under the BioProject ID PRJNA282154.
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Affiliation(s)
- Arun S. Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USA
| | - Emily Kawaler
- Department of Animal Sciences, Iowa State University, Ames, IA 50011, USA
| | - Zhi-Qiang Du
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Max F. Rothschild
- Department of Animal Sciences, Iowa State University, Ames, IA 50011, USA
| | - Andrew J. Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50011, USA
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25
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Xue C, Seetharam AS, Musharova O, Severinov K, Brouns SJJ, Severin AJ, Sashital DG. CRISPR interference and priming varies with individual spacer sequences. Nucleic Acids Res 2015; 43:10831-47. [PMID: 26586800 PMCID: PMC4678831 DOI: 10.1093/nar/gkv1259] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 10/30/2015] [Indexed: 12/21/2022] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid 'primed' adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR-Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed 'naïve' adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection.
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Affiliation(s)
- Chaoyou Xue
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Arun S Seetharam
- Genome Informatics Facility, Office of Biotechnology, Iowa State University Ames, IA 50011, USA
| | - Olga Musharova
- Institutes of Gene Biology and Molecular Genetics, Russian Academy of Sciences, Moscow 119991, Russia Skolkovo Institute of Science and Technology, Skolkovo, Russia, Moscow, Russia Peter the Great Polytechnical University, St. Petersburg, Russia
| | - Konstantin Severinov
- Institutes of Gene Biology and Molecular Genetics, Russian Academy of Sciences, Moscow 119991, Russia Skolkovo Institute of Science and Technology, Skolkovo, Russia, Moscow, Russia Peter the Great Polytechnical University, St. Petersburg, Russia Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, the Netherlands
| | - Andrew J Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University Ames, IA 50011, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
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26
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Abstract
Type IIB restriction endonucleases are site-specific endonucleases that cut both strands of double-stranded DNA upstream and downstream of their recognition sequences. These restriction enzymes have recognition sequences that are generally interrupted and range from 5 to 7 bases long. They produce DNA fragments which are uniformly small, ranging from 21 to 33 base pairs in length (without cohesive ends). The fragments are generated from throughout the entire length of a genomic DNA providing an excellent fractional representation of the genome. In this study we simulated restriction enzyme digestions on 21 sequenced genomes of various Drosophila species using the predicted targets of 16 Type IIB restriction enzymes to effectively produce a large and arbitrary selection of loci from these genomes. The fragments were then used to compare organisms and to calculate the distance between genomes in pair-wise combination by counting the number of shared fragments between the two genomes. Phylogenetic trees were then generated for each enzyme using this distance measure and the consensus was calculated. The consensus tree obtained agrees well with the currently accepted tree for the Drosophila species. We conclude that multi-locus sub-genomic representation combined with next generation sequencing, especially for individuals and species without previous genome characterization, can accelerate studies of comparative genomics and the building of accurate phylogenetic trees.
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Affiliation(s)
- Arun S Seetharam
- Bioinformatics Core, Purdue University , West Lafayette, IN , USA
| | - Gary W Stuart
- Department of Biology, Indiana State University , Terre Haute, IN , USA
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