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Chang J, Stahlke AR, Chudalayandi S, Rosen BD, Childers AK, Severin AJ. polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies. Genome Biol Evol 2023; 15:7040681. [PMID: 36792366 PMCID: PMC9985148 DOI: 10.1093/gbe/evad020] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) continuous long reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes, including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.
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Affiliation(s)
- Jennifer Chang
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee.,Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames
| | - Amanda R Stahlke
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, Beltsville Maryland
| | | | - Benjamin D Rosen
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Genomics and Improvement Laboratory, Beltsville, Maryland
| | - Anna K Childers
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, Beltsville Maryland
| | - Andrew J Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames
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Stahlke AR, Chang J, Tembrock LR, Sim SB, Chudalayandi S, Geib SM, Scheffler BE, Perera OP, Gilligan TM, Childers AK, Hackett KJ, Coates BS. A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein. Genome Biol Evol 2023; 15:evac131. [PMID: 35959935 PMCID: PMC9990077 DOI: 10.1093/gbe/evac131] [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: 04/06/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.
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Affiliation(s)
- Amanda R Stahlke
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland 20705
| | - Jennifer Chang
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, Mississippi 38776
- USDOE, Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, Tennessee 37831
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50010
| | - Luke R Tembrock
- USDA, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Identification Technology Program, 2301 Research Boulevard, Fort Collins, Colorado 80526
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Sheina B Sim
- USDA, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, 64 Nowelo Street, Hilo, Hawaii 96720
| | - Sivanandan Chudalayandi
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, Iowa 50010
| | - Scott M Geib
- USDA, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Crop and Commodity Protection Research Unit, 64 Nowelo Street, Hilo, Hawaii 96720
| | - Brian E Scheffler
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, Mississippi 38776
| | - Omaththage P Perera
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Southern Insect Management Research Unit, 141 Experiment Station Road, Stoneville, Mississippi 38776
| | - Todd M Gilligan
- USDA, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Identification Technology Program, 2301 Research Boulevard, Fort Collins, Colorado 80526
| | - Anna K Childers
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, Maryland 20705
| | - Kevin J Hackett
- USDA, Agricultural Research Service, Office of National Programs, Crop Production and Protection, 5601 Sunnyside Avenue, Beltsville, Maryland 20705
| | - Brad S Coates
- USDA, Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, 819 Wallace Road, Ames, Iowa 50011
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Stahlke AR, Chang J, Chudalayandi S, Heu CC, Geib SM, Scheffler BE, Childers AK, Fabrick JA. Chromosome-scale genome assembly of the pink bollworm, Pectinophora gossypiella, a global pest of cotton. G3 (Bethesda) 2023; 13:7040364. [PMID: 36790801 PMCID: PMC10085786 DOI: 10.1093/g3journal/jkad040] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/30/2023] [Accepted: 02/04/2023] [Indexed: 02/16/2023]
Abstract
The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae), is a major global pest of cotton. Current management practices include chemical insecticides, cultural strategies, sterile insect releases, and transgenic cotton producing crystalline (Cry) protein toxins of the bacterium Bacillus thuringiensis (Bt). These strategies have contributed to eradication of P. gossypiella from the cotton growing areas of the United States and northern Mexico. However, this pest has evolved resistance to Bt cotton in Asia, where it remains a critical pest, and the benefits of using transgenic Bt crops have been lost. A complete annotated reference genome is needed to improve global Bt resistance management of the pink bollworm. We generated the first chromosome-level genome assembly for pink bollworm from a Bt-susceptible laboratory strain (APHIS-S) using PacBio continuous long reads for contig generation, Illumina Hi-C for scaffolding, and Illumina whole-genome re-sequencing for error-correction. The psuedohaploid assembly consists of 29 autosomes and the Z sex chromosome. The assembly exceeds the minimum Earth BioGenome Project quality standards, has a low error-rate, is highly contiguous at both the contig and scaffold level (L/N50 of 18/8.26 MB and 14/16.44 MB, respectively), and complete, with 98.6% of lepidopteran single-copy orthologs represented without duplication. The genome was annotated with 50% repeat content and 14,107 protein-coding genes, further assigned to 41,666 functional annotations. This assembly represents the first publicly available complete annotated genome of pink bollworm and will serve as the foundation for advancing molecular genetics of this important pest species.
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Affiliation(s)
- Amanda R Stahlke
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Jennifer Chang
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS 38776, USA.,Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, TN 37831, USA.,Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50010, USA
| | - Sivanandan Chudalayandi
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA 50010, USA
| | - Chan C Heu
- Oak Ridge Institute for Science and Education, P.O. Box 117, Oak Ridge, TN 37831, USA.,USDA, Agricultural Research Service, U.S. Arid Land Agricultural Research Center, 21881 N. Cardon Lane, Maricopa, AZ 85138, USA
| | - Scott M Geib
- USDA, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, 64 Nowelo Street, Hilo, HI 96720, USA
| | - Brian E Scheffler
- USDA, Agricultural Research Service, Jamie Whitten Delta States Research Center, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS 38776, USA
| | - Anna K Childers
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Bee Research Laboratory, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
| | - Jeffrey A Fabrick
- USDA, Agricultural Research Service, U.S. Arid Land Agricultural Research Center, 21881 N. Cardon Lane, Maricopa, AZ 85138, USA
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Muszynski MG, Moss-Taylor L, Chudalayandi S, Cahill J, Del Valle-Echevarria AR, Alvarez-Castro I, Petefish A, Sakakibara H, Krivosheev DM, Lomin SN, Romanov GA, Thamotharan S, Dam T, Li B, Brugière N. The Maize Hairy Sheath Frayed1 ( Hsf1) Mutation Alters Leaf Patterning through Increased Cytokinin Signaling. Plant Cell 2020; 32:1501-1518. [PMID: 32205456 PMCID: PMC7203929 DOI: 10.1105/tpc.19.00677] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/24/2020] [Accepted: 03/13/2020] [Indexed: 05/24/2023]
Abstract
Leaf morphogenesis requires growth polarized along three axes-proximal-distal (P-D) axis, medial-lateral axis, and abaxial-adaxial axis. Grass leaves display a prominent P-D polarity consisting of a proximal sheath separated from the distal blade by the auricle and ligule. Although proper specification of the four segments is essential for normal morphology, our knowledge is incomplete regarding the mechanisms that influence P-D specification in monocots such as maize (Zea mays). Here, we report the identification of the gene underlying the semidominant, leaf patterning maize mutant Hairy Sheath Frayed1 (Hsf1). Hsf1 plants produce leaves with outgrowths consisting of proximal segments-sheath, auricle, and ligule-emanating from the distal blade margin. Analysis of three independent Hsf1 alleles revealed gain-of-function missense mutations in the ligand binding domain of the maize cytokinin (CK) receptor Z. mays Histidine Kinase1 (ZmHK1) gene. Biochemical analysis and structural modeling suggest the mutated residues near the CK binding pocket affect CK binding affinity. Treatment of the wild-type seedlings with exogenous CK phenocopied the Hsf1 leaf phenotypes. Results from expression and epistatic analyses indicated the Hsf1 mutant receptor appears to be hypersignaling. Our results demonstrate that hypersignaling of CK in incipient leaf primordia can reprogram developmental patterns in maize.
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Affiliation(s)
- Michael G Muszynski
- Department of Tropical Plant and Soil Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii 96822
| | - Lindsay Moss-Taylor
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Sivanandan Chudalayandi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - James Cahill
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | | | | | - Abby Petefish
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Dmitry M Krivosheev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - Sergey N Lomin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - Georgy A Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - Subbiah Thamotharan
- School of Chemical and Biotechnology, SASTRA University; Thanjavur, 613401, India
| | - Thao Dam
- Corteva Agriscience, Johnston, Iowa 50131
| | - Bailin Li
- Corteva Agriscience, Johnston, Iowa 50131
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Srivastava R, Li Z, Russo G, Tang J, Bi R, Muppirala U, Chudalayandi S, Severin A, He M, Vaitkevicius SI, Lawrence-Dill CJ, Liu P, Stapleton AE, Bassham DC, Brandizzi F, Howell SH. Response to Persistent ER Stress in Plants: A Multiphasic Process That Transitions Cells from Prosurvival Activities to Cell Death. Plant Cell 2018; 30:1220-1242. [PMID: 29802214 PMCID: PMC6048783 DOI: 10.1105/tpc.18.00153] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 05/09/2023]
Abstract
The unfolded protein response (UPR) is a highly conserved response that protects plants from adverse environmental conditions. The UPR is elicited by endoplasmic reticulum (ER) stress, in which unfolded and misfolded proteins accumulate within the ER. Here, we induced the UPR in maize (Zea mays) seedlings to characterize the molecular events that occur over time during persistent ER stress. We found that a multiphasic program of gene expression was interwoven among other cellular events, including the induction of autophagy. One of the earliest phases involved the degradation by regulated IRE1-dependent RNA degradation (RIDD) of RNA transcripts derived from a family of peroxidase genes. RIDD resulted from the activation of the promiscuous ribonuclease activity of ZmIRE1 that attacks the mRNAs of secreted proteins. This was followed by an upsurge in expression of the canonical UPR genes indirectly driven by ZmIRE1 due to its splicing of Zmbzip60 mRNA to make an active transcription factor that directly upregulates many of the UPR genes. At the peak of UPR gene expression, a global wave of RNA processing led to the production of many aberrant UPR gene transcripts, likely tempering the ER stress response. During later stages of ER stress, ZmIRE1's activity declined, as did the expression of survival modulating genes, Bax inhibitor1 and Bcl-2-associated athanogene7, amid a rising tide of cell death. Thus, in response to persistent ER stress, maize seedlings embark on a course of gene expression and cellular events progressing from adaptive responses to cell death.
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Affiliation(s)
- Renu Srivastava
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
| | - Zhaoxia Li
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
| | - Giulia Russo
- MSU-DOE Plant Research Laboratories, Department of Plant Biology, East Lansing, Michigan 48824
| | - Jie Tang
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Ran Bi
- Department of Statistics, Iowa State University, Ames, Iowa 50011
| | - Usha Muppirala
- Genome Informatics Facility, Iowa State University, Ames, Iowa 50011
| | | | - Andrew Severin
- Genome Informatics Facility, Iowa State University, Ames, Iowa 50011
| | - Mingze He
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Samuel I Vaitkevicius
- MSU-DOE Plant Research Laboratories, Department of Plant Biology, East Lansing, Michigan 48824
| | - Carolyn J Lawrence-Dill
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, Iowa 50011
| | - Ann E Stapleton
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, North Carolina 28403
| | - Diane C Bassham
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Federica Brandizzi
- MSU-DOE Plant Research Laboratories, Department of Plant Biology, East Lansing, Michigan 48824
| | - Stephen H Howell
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011
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Abstract
Advances in sequencing technology have led to the availability of complete genome sequences of many different plant species. In order to make sense of this deluge of information, functional genomics efforts have been intensified on many fronts. With improvements in plant transformation technologies, T-DNA and/or transposon-based gene and enhancer-tagged populations in various crop species are being developed to augment functional annotation of genes and also to help clone important genes. State-of-the-art cloning and sequencing technologies, which would help identify T-DNA or transposon junction sequences in large genomes, have also been initiated. This chapter gives a brief history of enhancer trapping and then proceeds to describe gene and enhancer tagging in plants. The significance of reporter gene fusion populations in plant genomics, especially in important cereal crops, is discussed.
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Abstract
Heterosis refers to the phenomenon that progeny of diverse varieties of a species or crosses between species exhibit greater biomass, speed of development, and fertility than both parents. Various models have been posited to explain heterosis, including dominance, overdominance, and pseudo-overdominance. In this Perspective, we consider that it might be useful to the field to abandon these terms that by their nature constrain data interpretation and instead attempt a progression to a quantitative genetic framework involving interactions in hierarchical networks. While we do not provide a comprehensive model to explain the phenomenology of heterosis, we provide the details of what needs to be explained and a direction of pursuit that we feel should be fruitful.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, 65211, USA.
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