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Sim SB, Corpuz RL, Simmonds TJ, Geib SM. HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly. BMC Genomics 2022; 23:157. [PMID: 35193521 PMCID: PMC8864876 DOI: 10.1186/s12864-022-08375-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. RESULTS Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. CONCLUSIONS Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.
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Affiliation(s)
- Sheina B Sim
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, 64 Nowelo Street, Hilo, HI, 96720, USA.
| | - Renee L Corpuz
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, 64 Nowelo Street, Hilo, HI, 96720, USA
| | - Tyler J Simmonds
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, 64 Nowelo Street, Hilo, HI, 96720, USA.,Oak Ridge Institute for Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN, 37830, USA
| | - Scott M Geib
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center, 64 Nowelo Street, Hilo, HI, 96720, USA
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Raghavan V, Kraft L, Mesny F, Rigerte L. A simple guide to de novo transcriptome assembly and annotation. Brief Bioinform 2022; 23:6514404. [PMID: 35076693 PMCID: PMC8921630 DOI: 10.1093/bib/bbab563] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome assembly is unnecessary, expensive or difficult. In the absence of a sequenced genome to guide the reconstruction process, the transcriptome must be assembled de novo using only the information available in the RNA-seq reads. Subsequently, the sequences must be annotated in order to identify sequence-intrinsic and evolutionary features in them (for example, protein-coding regions). Although straightforward at first glance, de novo transcriptome assembly and annotation can quickly prove to be challenging undertakings. In addition to familiarizing themselves with the conceptual and technical intricacies of the tasks at hand and the numerous pre- and post-processing steps involved, those interested must also grapple with an overwhelmingly large choice of tools. The lack of standardized workflows, fast pace of development of new tools and techniques and paucity of authoritative literature have served to exacerbate the difficulty of the task even further. Here, we present a comprehensive overview of de novo transcriptome assembly and annotation. We discuss the procedures involved, including pre- and post-processing steps, and present a compendium of corresponding tools.
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Affiliation(s)
- Venket Raghavan
- Corresponding authors: Venket Raghavan, Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany. E-mail: ; Louis Kraft, Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany. E-mail:
| | - Louis Kraft
- Corresponding authors: Venket Raghavan, Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany. E-mail: ; Louis Kraft, Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany. E-mail:
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3
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Lu Y, Boswell M, Boswell W, Salinas RY, Savage M, Reyes J, Walter S, Marks R, Gonzalez T, Medrano G, Warren WC, Schartl M, Walter RB. Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns. BMC Genomics 2020; 21:787. [PMID: 33176680 PMCID: PMC7659085 DOI: 10.1186/s12864-020-07202-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 10/28/2020] [Indexed: 11/25/2022] Open
Abstract
Background Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species, Xiphophorus maculatus, and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period. Results Our results showed 1.3–21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs. Conclusions These observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Raquel Ybanez Salinas
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.,The University of Texas MD Anderson Cancer Center, Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Jose Reyes
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Sean Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Rebecca Marks
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Trevor Gonzalez
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Geraldo Medrano
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.,Developmental Biochemistry, Theodor-Boveri-Institute, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Ronald B Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA
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Abstract
The Bateson–Dobzhansky–Muller (BDM) model describes negative epistatic interactions that occur between genes with a different evolutionary history to account for hybrid incompatibility and is a central theory explaining genetic mechanisms underlying speciation. Since the early 1900 s when the BDM model was forwarded examples of BDM incompatibility have been described in only a few nonvertebrate cases. This study reports the only vertebrate system, with clearly defined interacting loci, that supports the BDM model. In addition, this study also poses that tumorigenesis serves as a novel mechanism that accounts for postzygotic isolation. Mixing genomes of different species by hybridization can disrupt species-specific genetic interactions that were adapted and fixed within each species population. Such disruption can predispose the hybrids to abnormalities and disease that decrease the overall fitness of the hybrids and is therefore named as hybrid incompatibility. Interspecies hybridization between southern platyfish and green swordtails leads to lethal melanocyte tumorigenesis. This occurs in hybrids with tumor incidence following progeny ratio that is consistent with two-locus interaction, suggesting melanoma development is a result of negative epistasis. Such observations make Xiphophorus one of the only two vertebrate hybrid incompatibility examples in which interacting genes have been identified. One of the two interacting loci has been characterized as a mutant epidermal growth factor receptor. However, the other locus has not been identified despite over five decades of active research. Here we report the localization of the melanoma regulatory locus to a single gene, rab3d, which shows all expected features of the long-sought oncogene interacting locus. Our findings provide insights into the role of egfr regulation in regard to cancer etiology. Finally, they provide a molecular explainable example of hybrid incompatibility.
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Lu Y, Olivas TJ, Boswell M, Boswell W, Warren WC, Schartl M, Walter RB. Intra-Strain Genetic Variation of Platyfish ( Xiphophorus maculatus) Strains Determines Tumorigenic Trajectory. Front Genet 2020; 11:562594. [PMID: 33133148 PMCID: PMC7573281 DOI: 10.3389/fgene.2020.562594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/09/2020] [Indexed: 11/16/2022] Open
Abstract
Xiphophorus interspecies hybrids represent a valuable model system to study heritable tumorigenesis, and the only model system that exhibits both spontaneous and inducible tumors. Types of tumorigenesis depend on the specific pedigree of the parental species, X. maculatus, utilized to produce interspecies hybrids. Although the ancestors of the two currently used X. maculatus parental lines, Jp163 A and Jp163 B, were originally siblings produced by the same mother, backcross interspecies hybrid progeny between X. hellerii and X. maculatus Jp163 A develop spontaneous melanoma initiating at the dorsal fin due to segregation of an oncogene and a regulator encoded by the X. maculatus genome, while the backcross hybrid progeny with X. hellerii or X. couchianus and Jp163 B exhibit melanoma on the flanks of their bodies, especially after treatment with ultraviolet light. Therefore, dissecting the genetic differences between these two closely related lines may lead to better understanding of functional molecular differences associated with tumorigenic mechanisms. For this purpose, comparative genomic analyses were undertaken to establish genetic variants between these two X. maculatus lines. Surprisingly, given the heritage of these two fish lines, we found genetic variants are clustered together in select chromosomal regions. Among these variants are non-synonymous mutations located in 381 genes. The non-random distribution of genetic variants between these two may highlight ancestral chromosomal recombination patterns that became fixed during subsequent inbreeding. Employing comparative transcriptomics, we also determined differences in the skin transcriptional landscape between the two lines. The genetic differences observed are associated with pathways highlighting fundamental cellular functions including inter-cellular and microenvironment-cellular interactions, and DNA repair. These results collectively lead to the conclusion that diverged functional genetic baselines are present between Jp163 A and B strains. Further, disruption of these fixed genetic baselines in the hybrids may give rise to spontaneous or inducible mechanisms of tumorigenesis.
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Affiliation(s)
- Yuan Lu
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
| | - Taryn J Olivas
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States.,Department of Cell Biology, Yale University School of Medicine, New Haven, CT, United States
| | - Mikki Boswell
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
| | - William Boswell
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
| | - Wes C Warren
- Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States.,Developmental Biochemistry, Theodor-Boveri-Institute, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Ronald B Walter
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, United States
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Lu Y, Boswell W, Boswell M, Klotz B, Kneitz S, Regneri J, Savage M, Mendoza C, Postlethwait J, Warren WC, Schartl M, Walter RB. Application of the Transcriptional Disease Signature (TDSs) to Screen Melanoma-Effective Compounds in a Small Fish Model. Sci Rep 2019; 9:530. [PMID: 30679619 PMCID: PMC6345854 DOI: 10.1038/s41598-018-36656-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/22/2018] [Indexed: 12/20/2022] Open
Abstract
Cell culture and protein target-based compound screening strategies, though broadly utilized in selecting candidate compounds, often fail to eliminate candidate compounds with non-target effects and/or safety concerns until late in the drug developmental process. Phenotype screening using intact research animals is attractive because it can help identify small molecule candidate compounds that have a high probability of proceeding to clinical use. Most FDA approved, first-in-class small molecules were identified from phenotypic screening. However, phenotypic screening using rodent models is labor intensive, low-throughput, and very expensive. As a novel alternative for small molecule screening, we have been developing gene expression disease profiles, termed the Transcriptional Disease Signature (TDS), as readout of small molecule screens for therapeutic molecules. In this concept, compounds that can reverse, or otherwise affect known disease-associated gene expression patterns in whole animals may be rapidly identified for more detailed downstream direct testing of their efficacy and mode of action. To establish proof of concept for this screening strategy, we employed a transgenic strain of a small aquarium fish, medaka (Oryzias latipes), that overexpresses the malignant melanoma driver gene xmrk, a mutant egfr gene, that is driven by a pigment cell-specific mitf promoter. In this model, melanoma develops with 100% penetrance. Using the transgenic medaka malignant melanoma model, we established a screening system that employs the NanoString nCounter platform to quantify gene expression within custom sets of TDS gene targets that we had previously shown to exhibit differential transcription among xmrk-transgenic and wild-type medaka. Compound-modulated gene expression was identified using an internet-accessible custom-built data processing pipeline. The effect of a given drug on the entire TDS profile was estimated by comparing compound-modulated genes in the TDS using an activation Z-score and Kolmogorov-Smirnov statistics. TDS gene probes were designed that target common signaling pathways that include proliferation, development, toxicity, immune function, metabolism and detoxification. These pathways may be utilized to evaluate candidate compounds for potential favorable, or unfavorable, effects on melanoma-associated gene expression. Here we present the logistics of using medaka to screen compounds, as well as, the development of a user-friendly NanoString data analysis pipeline to support feasibility of this novel TDS drug-screening strategy.
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Affiliation(s)
- Yuan Lu
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - William Boswell
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Mikki Boswell
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Barbara Klotz
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074, Würzburg, Germany
| | - Susanne Kneitz
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074, Würzburg, Germany
| | - Janine Regneri
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074, Würzburg, Germany
| | - Markita Savage
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - Cristina Mendoza
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | | | - Manfred Schartl
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074, Würzburg, Germany.,Hagler Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, USA
| | - Ronald B Walter
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX, USA.
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Lu Y, Boswell M, Boswell W, Kneitz S, Hausmann M, Klotz B, Regneri J, Savage M, Amores A, Postlethwait J, Warren W, Schartl M, Walter R. Comparison of Xiphophorus and human melanoma transcriptomes reveals conserved pathway interactions. Pigment Cell Melanoma Res 2018; 31:496-508. [PMID: 29316274 PMCID: PMC6013346 DOI: 10.1111/pcmr.12686] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/23/2017] [Indexed: 12/14/2022]
Abstract
Comparative analysis of human and animal model melanomas can uncover conserved pathways and genetic changes that are relevant for the biology of cancer cells. Spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny may be informative in identifying genes and functional pathways that are similarly related to melanoma development in all vertebrates, including humans. To assess functional pathways involved in the Xiphophorus melanoma, we performed gene expression profiling of the melanomas produced in interspecies BC1 and successive backcross generations (i.e., BC5 ) of the cross: X. hellerii × [X. maculatus Jp 163 A × X. hellerii]. Using RNA-Seq, we identified genes that are transcriptionally co-expressed with the driver oncogene, xmrk. We determined functional pathways in the fish melanoma that are also present in human melanoma cohorts that may be related to dedifferentiation based on the expression levels of pigmentation genes. Shared pathways between human and Xiphophorus melanomas are related to inflammation, cell migration, cell proliferation, pigmentation, cancer development, and metastasis. Our results suggest xmrk co-expressed genes are associated with dedifferentiation and highlight these signaling pathways as playing important roles in melanomagenesis.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Michael Hausmann
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Barbara Klotz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Janine Regneri
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, USA
| | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
- Texas A&M Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, USA
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
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Boswell M, Boswell W, Lu Y, Savage M, Mazurek Z, Chang J, Muster J, Walter R. The transcriptional response of skin to fluorescent light exposure in viviparous (Xiphophorus) and oviparous (Danio, Oryzias) fishes. Comp Biochem Physiol C Toxicol Pharmacol 2018; 208:77-86. [PMID: 29017858 PMCID: PMC5889750 DOI: 10.1016/j.cbpc.2017.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 01/14/2023]
Abstract
Differences in light sources are common in animal facilities and potentially can impact experimental results. Here, the potential impact of lighting differences on skin transcriptomes has been tested in three aquatic animal models commonly utilized in biomedical research, (Xiphophorus maculatus (platyfish), Oryzias latipes (medaka) and Danio rerio (zebrafish). Analysis of replicate comparative RNA-Seq data showed the transcriptional response to commonly utilized 4100K or "cool white" fluorescent light (FL) is much greater in platyfish and medaka than in zebrafish. FL induces genes associated with inflammatory and immune responses in both medaka and zebrafish; however, the platyfish exhibit suppression of genes involved with immune/inflammation, as well as genes associated with cell cycle progression. Furthermore, comparative analyses of gene expression data from platyfish UVB exposures, with medaka and zebrafish after exposure to 4100K FL, show comparable effects on the same stress pathways. We suggest the response to light is conserved, but that long-term adaptation to species specific environmental niches has resulted in a shifting of the wavelengths required to incite similar "genetic" responses in skin. We forward the hypothesis that the "genetic perception" of light may have evolved differently than ocular perception and suggest that light type (i.e., wavelengths emitted) is an important parameter to consider in experimental design.
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Affiliation(s)
- Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666, USA.
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666, USA.
| | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666, USA.
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666, USA.
| | - Zachary Mazurek
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666, USA.
| | - Jordan Chang
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666, USA.
| | - Jeanot Muster
- Howard Hughes Medical Institute, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, San Marcos, TX 78666, USA.
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Klotz B, Kneitz S, Regensburger M, Hahn L, Dannemann M, Kelso J, Nickel B, Lu Y, Boswell W, Postlethwait J, Warren W, Kunz M, Walter RB, Schartl M. Expression signatures of early-stage and advanced medaka melanomas. Comp Biochem Physiol C Toxicol Pharmacol 2018; 208:20-28. [PMID: 29162497 PMCID: PMC5936653 DOI: 10.1016/j.cbpc.2017.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 01/07/2023]
Abstract
Melanoma is one of the most aggressive tumors with a very low survival rate once metastasized. The incidence of newly detected cases increases every year suggesting the necessity of development and application of innovative treatment strategies. Human melanoma develops from melanocytes localized in the epidermis of the skin to malignant tumors because of deregulated effectors influencing several molecular pathways. Despite many advances in describing the molecular changes accompanying melanoma formation, many critical and clinically relevant molecular features of the transformed pigment cells and the underlying mechanisms are largely unknown. To contribute to a better understanding of the molecular processes of melanoma formation, we use a transgenic medaka melanoma model that is well suited for the investigation of melanoma tumor development because fish and human melanocytes are both localized in the epidermis. The purpose of our study was to gain insights into melanoma development from the first steps of tumor formation up to melanoma progression and to identify gene expression patterns that will be useful for monitoring treatment effects in drug screening approaches. Comparing transcriptomes from juvenile fish at the tumor initiating stage with nevi and advanced melanoma of adults, we identified stage specific expression signatures and pathways that are characteristic for the development of medaka melanoma, and are also found in human malignancies.
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Affiliation(s)
- Barbara Klotz
- Physiological Chemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.
| | - Martina Regensburger
- Physiological Chemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.
| | - Lena Hahn
- Physiological Chemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.
| | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Birgit Nickel
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon, OR 97401, USA
| | - Wesley Warren
- Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA
| | - Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, Philipp-Rosenthal-Str. 23, 04103 Leipzig, Germany
| | - Ronald B. Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Manfred Schartl
- Physiological Chemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany.
- Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
- Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, Texas, 77843, USA
- Corresponding author: Prof. Dr. Manfred Schartl, Tel.: +49 931 31 84148; fax: +49 931 31 84150. (M. Schartl)
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Boswell WT, Boswell M, Walter DJ, Navarro KL, Chang J, Lu Y, Savage MG, Shen J, Walter RB. Exposure to 4100K fluorescent light elicits sex specific transcriptional responses in Xiphophorus maculatus skin. Comp Biochem Physiol C Toxicol Pharmacol 2018; 208:96-104. [PMID: 28965926 PMCID: PMC5876067 DOI: 10.1016/j.cbpc.2017.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 02/06/2023]
Abstract
It has been reported that exposure to artificial light may affect oxygen intake, heart rate, absorption of vitamins and minerals, and behavioral responses in humans. We have reported specific gene expression responses in the skin of Xiphophorus fish after exposure to ultraviolet light (UV), as well as, both broad spectrum and narrow waveband visible light. In regard to fluorescent light (FL), we have shown that male X. maculatus exposed to 4100K FL (i.e. "cool white") rapidly suppress transcription of many genes involved with DNA replication and repair, chromosomal segregation, and cell cycle progression in skin. We have also detailed sex specific transcriptional responses of Xiphophorus skin after exposure to UVB. However, investigation of gender differences in global gene expression response after exposure to 4100K FL has not been reported, despite common use of this FL source for residential, commercial, and animal facility illumination. Here, we compare RNA-Seq results analyzed to assess changes in the global transcription profiles of female and male X. maculatus skin in response to 4100K FL exposure. Our results suggest 4100K FL exposure incites a sex-biased genetic response including up-modulation of inflammation in females and down modulation of DNA repair/replication in males. In addition, we identify clusters of genes that become oppositely modulated in males and females after FL exposure that are principally involved in cell death and cell proliferation.
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Affiliation(s)
- William T Boswell
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Mikki Boswell
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Dylan J Walter
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Kaela L Navarro
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Jordan Chang
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Yuan Lu
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Markita G Savage
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA.
| | - Ronald B Walter
- Department of Chemistry and Biochemistry, Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
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11
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Gonzalez TJ, Lu Y, Boswell M, Boswell W, Medrano G, Walter S, Ellis S, Savage M, Varga ZM, Lawrence C, Sanders G, Walter RB. Fluorescent light exposure incites acute and prolonged immune responses in zebrafish (Danio rerio) skin. Comp Biochem Physiol C Toxicol Pharmacol 2018; 208:87-95. [PMID: 28965927 PMCID: PMC5876079 DOI: 10.1016/j.cbpc.2017.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 01/13/2023]
Abstract
Artificial light produces an emission spectrum that is considerably different than the solar spectrum. Artificial light has been shown to affect various behavior and physiological processes in vertebrates. However, there exists a paucity of data regarding the molecular genetic effects of artificial light exposure. Previous studies showed that one of the commonly used fluorescent light source (FL; 4100K or "cool white") can affect signaling pathways related to maintenance of circadian rhythm, cell cycle progression, chromosome segregation, and DNA repair/recombination in the skin of male Xiphophorus maculatus. These observations raise questions concerning the kinetics of the FL induced gene expression response, and which biological functions become modulated at various times after light exposure. To address these questions, we exposed zebrafish to 4100K FL and utilized RNA-Seq to assess gene expression changes in skin at various times (1 to 12h) after FL exposure. We found 4100K FL incites a robust early (1-2h) transcriptional response, followed by a more protracted late response (i.e., 4-12h). The early transcriptional response involves genes associated with cell migration/infiltration and cell proliferation as part of an overall increase in immune function and inflammation. The protracted late transcriptional response occurs within gene sets predicted to maintain and perpetuate the inflammatory response, as well as suppression of lipid, xenobiotic, and melatonin metabolism.
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Affiliation(s)
- Trevor J Gonzalez
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Yuan Lu
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Mikki Boswell
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - William Boswell
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Geraldo Medrano
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Sean Walter
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Samuel Ellis
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Markita Savage
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
| | - Zoltan M Varga
- Zebrafish International Resource Center (ZIRC), 5274 University of Oregon Eugene, OR 97403, USA.
| | - Christian Lawrence
- Children's Hospital Boston Karp Family Research Laboratories, 4th Floor One Blackfan Circle Boston, MA 02115, USA.
| | - George Sanders
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA 98195-7340, USA.
| | - Ronald B Walter
- Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
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Lu Y, Klimovich CM, Robeson KZ, Boswell W, Ríos-Cardenas O, Walter RB, Morris MR. Transcriptome assembly and candidate genes involved in nutritional programming in the swordtail fish Xiphophorus multilineatus. PeerJ 2017; 5:e3275. [PMID: 28480144 PMCID: PMC5417068 DOI: 10.7717/peerj.3275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 04/04/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Nutritional programming takes place in early development. Variation in the quality and/or quantity of nutrients in early development can influence long-term health and viability. However, little is known about the mechanisms of nutritional programming. The live-bearing fish Xiphophorus multilineatus has the potential to be a new model for understanding these mechanisms, given prior evidence of nutritional programming influencing behavior and juvenile growth rate. We tested the hypotheses that nutritional programming would influence behaviors involved in energy homeostasis as well gene expression in X. multilineatus. METHODS We first examined the influence of both juvenile environment (varied in nutrition and density) and adult environment (varied in nutrition) on behaviors involved in energy acquisition and energy expenditure in adult male X. multilineatus. We also compared the behavioral responses across the genetically influenced size classes of males. Males stop growing at sexual maturity, and the size classes of can be identified based on phenotypes (adult size and pigment patterns). To study the molecular signatures of nutritional programming, we assembled a de novo transcriptome for X. multilineatus using RNA from brain, liver, skin, testis and gonad tissues, and used RNA-Seq to profile gene expression in the brains of males reared in low quality (reduced food, increased density) and high quality (increased food, decreased density) juvenile environments. RESULTS We found that both the juvenile and adult environments influenced the energy intake behavior, while only the adult environment influenced energy expenditure. In addition, there were significant interactions between the genetically influenced size classes and the environments that influenced energy intake and energy expenditure, with males from one of the four size classes (Y-II) responding in the opposite direction as compared to the other males examined. When we compared the brains of males of the Y-II size class reared in a low quality juvenile environment to males from the same size class reared in high quality juvenile environment, 131 genes were differentially expressed, including metabolism and appetite master regulator agrp gene. DISCUSSION Our study provides evidence for nutritional programming in X. multilineatus, with variation across size classes of males in how juvenile environment and adult diet influences behaviors involved in energy homeostasis. In addition, we provide the first transcriptome of X. multilineatus, and identify a group of candidate genes involved in nutritional programming.
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Affiliation(s)
- Yuan Lu
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | | | - Kalen Z Robeson
- Department of Biological Sciences, Ohio University, Athens, OH, USA
| | - William Boswell
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Oscar Ríos-Cardenas
- Red de Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Mexico
| | - Ronald B Walter
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA
| | - Molly R Morris
- Department of Biological Sciences, Ohio University, Athens, OH, USA
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Lu Y, Boswell M, Boswell W, Kneitz S, Hausmann M, Klotz B, Regneri J, Savage M, Amores A, Postlethwait J, Warren W, Schartl M, Walter R. Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus interspecies hybrids. Mol Carcinog 2017; 56:1935-1944. [PMID: 28345808 DOI: 10.1002/mc.22651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 03/07/2017] [Accepted: 03/23/2017] [Indexed: 01/10/2023]
Abstract
Development of spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny, (X. hellerii × [X. maculatus Jp 163 A × X. hellerii]) is due to Mendelian segregation of a oncogene (xmrk) and a molecularly uncharacterized locus, called R(Diff), on LG5. R(Diff) is thought to suppresses the activity of xmrk in healthy X. maculatus Jp 163 A parental species that rarely develop melanoma. To better understand the molecular genetics of R(Diff), we utilized RNA-Seq to study allele-specific gene expression of spontaneous melanoma tumors and corresponding normal skin samples derived from 15 first generation backcross (BC1 ) hybrids and 13 fifth generation (BC5 ) hybrids. Allele-specific expression was determined for all genes and assigned to parental allele inheritance for each backcross hybrid individual. Results showed that genes residing in a 5.81 Mbp region on LG5 were exclusively expressed from the X. hellerii alleles in tumor-bearing BC1 hybrids. This observation indicates this region is consistently homozygous for X. hellerii alleles in tumor bearing animals, and therefore defines this region to be the R(Diff) locus. The R(Diff) locus harbors 164 gene models and includes the previously characterized R(Diff) candidate, cdkn2x. Twenty-one genes in the R(Diff) region show differential expression in the tumor samples compared to normal skin tissue. These results further characterize the R(Diff) locus and suggest tumor suppression may require a multigenic region rather than a single gene variant. Differences in gene expression between tumor and normal skin tissue in this region may indicate interactions among several genes are required for backcross hybrid melanoma development.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Michael Hausmann
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Barbara Klotz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Janine Regneri
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.,Texas A&M Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, Texas
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
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Lu Y, Bowswell M, Bowswell W, Yang K, Schartl M, Walter RB. Molecular genetic response of Xiphophorus maculatus-X. couchianus interspecies hybrid skin to UVB exposure. Comp Biochem Physiol C Toxicol Pharmacol 2015; 178:86-92. [PMID: 26254713 PMCID: PMC4662913 DOI: 10.1016/j.cbpc.2015.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 12/13/2022]
Abstract
The phenotypic and genetic similarities between Xiphophorus and human melanoma render Xiphophorus a useful animal model for studying the genetic basis of melanoma etiology. In the Xiphophorus model, melanoma has been shown to be inducible by ultraviolet light (UVB) exposure among interspecies hybrids, but not in parental line fish similarly treated. This leads to questions of what genes are responsive to UVB exposure in the skin of the interspecies hybrids, as well as how parental alleles in hybrids may be differentially regulated and the potential roles they may play in induced melanomagenesis. To address these questions, we produced X. maculatus Jp 163 B×X. couchianus (Sp-Couch) F1 hybrid fish, exposed both hybrid and parental fish to UVB, and performed gene expression profiling of the skin using RNA-Seq methodology. We characterized a group of unique UVB-responsive genes in Sp-Couch hybrid including dct, pmela, tyr, tyrp1a, slc2a11b, rab38a, rab27, tspan10, slc45a2, oca2, slc24a5, ptn and mitfa. These genes are associated with melanin production and melanocyte proliferation. They were also up-regulated in Sp-Couch hybrid, indicating that their UVB response is hybridization initiated. In the hybrid, several melanin production and pigmentation related genes, including slc45a2, tspan10, dct, slc2a11b and ptn showed either X. couchianus or X. maculatus allele specific expression. The finding that these genes exhibit allele specific expression regulatory mechanisms in Sp-Couch hybrids, but do not exhibit a corresponding UVB response in either one of the parental fishes, may suggest UVB targets and imply mechanisms regarding the susceptibility of Sp-Couch to induced melanomagenesis.
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Affiliation(s)
- Yuan Lu
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry Texas State University, San Marcos, TX, 78666
| | - Mikki Bowswell
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry Texas State University, San Marcos, TX, 78666
| | - William Bowswell
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry Texas State University, San Marcos, TX, 78666
| | - Kuan Yang
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry Texas State University, San Marcos, TX, 78666
| | - Manfred Schartl
- Physiologische Chemie, Universität Würzburg Biozentrum, Am Hubland, and Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Ronald B. Walter
- Molecular Bioscience Research Group, Department of Chemistry and Biochemistry Texas State University, San Marcos, TX, 78666
- Corresponding author:
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15
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Amores A, Catchen J, Nanda I, Warren W, Walter R, Schartl M, Postlethwait JH. A RAD-tag genetic map for the platyfish (Xiphophorus maculatus) reveals mechanisms of karyotype evolution among teleost fish. Genetics 2014; 197:625-41. [PMID: 24700104 PMCID: PMC4063920 DOI: 10.1534/genetics.114.164293] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 03/20/2014] [Indexed: 11/18/2022] Open
Abstract
Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3-40 among deer alone); in contrast, teleost fish genomes are stable (24-25 in 58% of teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged ∼120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish ∼195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years.
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Affiliation(s)
- Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Julian Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403
| | - Indrajit Nanda
- Institute of Human Genetics, University of Würzburg, D-97074 Würzburg, Germany
| | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Ron Walter
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666
| | - Manfred Schartl
- Physiological Chemistry, University of Würzburg, Biozentrum, Am Hubland, and Comprehensive Cancer Center, University Clinic Würzburg, 97074 Würzburg, Germany
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Chen C, Khaleel SS, Huang H, Wu CH. Software for pre-processing Illumina next-generation sequencing short read sequences. SOURCE CODE FOR BIOLOGY AND MEDICINE 2014; 9:8. [PMID: 24955109 PMCID: PMC4064128 DOI: 10.1186/1751-0473-9-8] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 04/22/2014] [Indexed: 01/08/2023]
Abstract
Background When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets. Methods We developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7. Results Several combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference-based assembly as measured by assembly contiguity and correctness. Conclusions Trimming of short read sequences can improve the quality of de novo and reference-based assembly and assembler performance. The parallel processing capability of ngsShoRT reduces trimming time and improves the memory efficiency when dealing with large datasets. We recommend combining sequencing artifacts removal, and quality score based read filtering and base trimming as the most consistent method for improving sequence quality and downstream assemblies. ngsShoRT source code, user guide and tutorial are available at http://research.bioinformatics.udel.edu/genomics/ngsShoRT/. ngsShoRT can be incorporated as a pre-processing step in genome and transcriptome assembly projects.
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Affiliation(s)
- Chuming Chen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA
| | - Sari S Khaleel
- Geisel School of Medicine, Dartmouth College, Hanover, NH USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE USA
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Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2012. [PMID: 23201534 DOI: 10.1016/j.cbd.2012.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In recent years RNA-Seq technology has been used not only to quantify differences in gene expression but also to understand the underlying mechanisms that lead to these differences. Nucleotide sequence variation arising through evolution may differentially affect the expression profiles of divergent species. RNA-Seq technology, combined with techniques to differentiate parental alleles and quantify their abundance, have recently become popular methods for allele specific gene expression (ASGE) analyses. However, analysis of gene expression within interspecies hybrids may be difficult when one of the two parental genomes represented in the hybrid does not have robust genomic resources or available transcriptome data. Herein, we compare two strategies for analyzing allele specific expression within interspecies hybrids produced from crossing two Xiphophorus fish species. The first strategy relies upon a robust reference transcriptome assembly from one species followed by identification of SNPs and creation of an in silico reference transcriptome for the second species. The second strategy employs de novo assembly of reference transcriptomes for both parental species followed by identification of homologous transcripts prior to mapping hybrid reads to a combined hybrid reference. Our results show that, although both methods are able to achieve balanced allelic distribution upon read mapping of F(1) hybrid fish transcriptomes, the second "de novo" assembly approach is superior for ASGE analyses and leads to results more consistent with those found from quantitative real time PCR assessment of gene expression. In addition, our analysis indicates that indels between the two parental alleles are the major cause of the differences in results observed when employing these two methods.
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Fieber LA, Tanguay RL, Walter RB, Williams DE. Aquatic animal models of human disease: selected papers from the 5th conference. Comp Biochem Physiol C Toxicol Pharmacol 2012; 155:9-10. [PMID: 21729766 DOI: 10.1016/j.cbpc.2011.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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