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Sun M, Zhao Y, Shao X, Ge J, Tang X, Zhu P, Wang J, Zhao T. EST-SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily ( Lilium lancifolium Thunb). Appl Bionics Biomech 2022; 2022:7641048. [PMID: 35126662 PMCID: PMC8816598 DOI: 10.1155/2022/7641048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
The fast advancement and deployment of sequencing technologies after the Human Genome Project have greatly increased our knowledge of the eukaryotic genome sequences. However, due to technological concerns, high-quality genomic data has been confined to a few key organisms. Moreover, our understanding of which portions of genomes make up genes and which transcript isoforms synthesize these genes is scarce. Therefore, the current study has been designed to explore the reliability of the tiger lily (Lilium lancifolium Thunb) transcriptome. The PacBio-SMRT was used for attaining the complete transcriptomic profile. We obtained a total of 815,624 CCS (Circular Consensus Sequence) reads with an average length of 1295 bp. The tiger lily transcriptome has been sequenced for the first time using third-generation long-read technology. Furthermore, unigenes (38,707), lncRNAs (6852), and TF members (768) were determined based on the transcriptome data, followed by evaluating SSRs (3319). It has also been revealed that 105 out of 128 primer pairs effectively amplified PCR products. Around 15,608 transcripts were allocated to 25 distinct KOG Clusters, and 10,706 unigenes were grouped into 52 functional categories in the annotated transcripts. Until now, no tiger lily lncRNAs have been discovered. Results of this study may serve as an extensive set of reference transcripts and help us learn more about the transcriptomes of tiger lilies and pave the path for further research.
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Affiliation(s)
- Mingwei Sun
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | | | - Xiaobin Shao
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Jintao Ge
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Xueyan Tang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Pengbo Zhu
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Jiangying Wang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Tongli Zhao
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
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2
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Brancaccio RN, Robitaille A, Dutta S, Rollison DE, Tommasino M, Gheit T. MinION nanopore sequencing and assembly of a complete human papillomavirus genome. J Virol Methods 2021; 294:114180. [PMID: 33965458 PMCID: PMC8223502 DOI: 10.1016/j.jviromet.2021.114180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/26/2021] [Accepted: 05/03/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to characterize entire viral genome sequences than other time-consuming and low-throughput methodologies. METHODS We report the use of the MinION nanopore sequencer to sequence the full-length genome of human papillomavirus (HPV)-ICB2 (7441 bp), which was previously characterized in our laboratory. Three independent MinION libraries were prepared and sequenced using either three consecutive 12 -h runs (Protocol A) or a single run of 48 h starting from a pool of three barcoded DNA libraries (Protocol B). A fully automated bioinformatics pipeline was developed for the reconstruction of the viral genome. RESULTS Protocols A and B generated 9,354,933 and 3,255,879 reads, respectively. Read length N50 values ranged between 6976 and 7360 nucleotides over the four sequencing runs. Bioinformatics analysis showed that both protocols allowed for the reconstruction of the whole viral genome, with pairwise percentages of identity to HPV-ICB2 of 100 % for protocol A and 99.98 % for protocol B. CONCLUSION Our results show that the use of the MinION nanopore sequencer represents an effective strategy for whole-genome sequencing of HPVs with a minimal error rate.
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Affiliation(s)
- Rosario N Brancaccio
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Alexis Robitaille
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Sankhadeep Dutta
- Chittaranjan National Cancer Institute, Department of Viral Associated Human Cancer, Kolkata, India
| | - Dana E Rollison
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Massimo Tommasino
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France
| | - Tarik Gheit
- Early Detection, Prevention and Infections Branch, International Agency for Research on Cancer, Lyon, France.
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3
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Torma G, Tombácz D, Csabai Z, Moldován N, Mészáros I, Zádori Z, Boldogkői Z. Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus. Viruses 2021; 13:v13040579. [PMID: 33808073 PMCID: PMC8103240 DOI: 10.3390/v13040579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/17/2021] [Accepted: 03/28/2021] [Indexed: 11/16/2022] Open
Abstract
African swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen. Short-read sequencing (SRS) can produce a huge amount of high-precision sequencing reads for transcriptomic profiling, but it is inefficient for comprehensively annotating transcriptomes. Long-read sequencing (LRS) can overcome some of SRS's limitations, but it also has drawbacks, such as low-coverage and high error rate. The limitations of the two approaches can be surmounted by the combined use of these techniques. In this study, we used Illumina SRS and Oxford Nanopore Technologies LRS platforms with multiple library preparation methods (amplified and direct cDNA sequencings and native RNA sequencing) for constructing the ASFV transcriptomic atlas. This work identified many novel transcripts and transcript isoforms and annotated the precise termini of previously described RNAs. This study identified a novel species of ASFV transcripts, the replication origin-associated RNAs. Additionally, we discovered several nested genes embedded into larger canonical genes. In contrast to the current view that the ASFV transcripts are monocistronic, we detected a significant extent of polycistronism. A multifaceted meshwork of transcriptional overlaps was also discovered.
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Affiliation(s)
- Gábor Torma
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - Dóra Tombácz
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - Zsolt Csabai
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - Norbert Moldován
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
| | - István Mészáros
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143 Budapest, Hungary; (I.M.); (Z.Z.)
| | - Zoltán Zádori
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt. 21, H-1143 Budapest, Hungary; (I.M.); (Z.Z.)
| | - Zsolt Boldogkői
- Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4., 6720 Szeged, Hungary; (G.T.); (D.T.); (Z.C.); (N.M.)
- Correspondence:
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4
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Faizuloev E, Mintaev R, Petrusha O, Marova A, Smirnova D, Ammour Y, Meskina E, Sergeev O, Zhavoronok S, Karaulov A, Svitich O, Zverev V. New approach of genetic characterization of group A rotaviruses by the nanopore sequencing method. J Virol Methods 2021; 292:114114. [PMID: 33662411 DOI: 10.1016/j.jviromet.2021.114114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/17/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
Nanopore sequencing of virus genomes represented by segmented RNA (e.g. rotaviruses) requires the development of specific approaches. Due to the massive use of rotavirus vaccines, the relevance of monitoring the genetic diversity of circulating strains of group A rotaviruses (RVA) increased. The WHO recommended method of multiplex type-specific PCR does not allow genotyping of all clinically significant strains of RVA and identifying inter-strain differences within the genotype. We have described a new principle of amplification of RVA gene segments using six primers for reverse transcription and one universal primer for PCR for nanopore sequencing. The amplification of RVA genome was tested on clinical samples and three phylogenetically distant laboratory RVA strains, Wa (G1P[8]), DS-1 (G2P[4]) and 568 (G3P[3]). The developed protocol of sample preparation and nanopore sequencing allowed obtaining full-length sequences for gene segments of RVA, including the diagnostically significant segments 9 (VP7), 4 (VP4) and 6 (VP6) with high accuracy and coverage. The accuracy of sequencing of the rotavirus genome exceeded 99.5 %, and the genome coverage varied for different strains from 59.0 to 99.6 % (on average 86 %). The developed approach of nanopore sequencing of RVA genome could be a prospective tool for epidemiological studies and surveillance of rotavirus infection.
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Affiliation(s)
- Evgeny Faizuloev
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia.
| | - Ramil Mintaev
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia; FSBI «Center for Strategic Planning and Management of Medical and Biological Health Risks», Laboratory of Gene Therapy, Moscow, Russia
| | - Olga Petrusha
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia
| | - Anna Marova
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia
| | - Daria Smirnova
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia
| | - Yulia Ammour
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia
| | - Elena Meskina
- M. Vladimirsky Moscow Regional Research Clinical Institute (MONIKI), Department of Children's Infections, Moscow, Russia
| | - Oleg Sergeev
- Sechenov First Moscow State Medical University, Faculty of Preventive Medicine, Moscow, Russia
| | - Sergey Zhavoronok
- Belarusian State Medical University, Department of Infectious Diseases, Minsk, Belarus
| | - Alexander Karaulov
- Sechenov First Moscow State Medical University, Department of Clinical Immunology and Allergy, Moscow, Russia
| | - Oxana Svitich
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia; Sechenov First Moscow State Medical University, Faculty of Preventive Medicine, Moscow, Russia
| | - Vitaly Zverev
- I. Mechnikov Research Institute of Vaccines and Sera, Department of Virology, Moscow, Russia; Sechenov First Moscow State Medical University, Faculty of Preventive Medicine, Moscow, Russia
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5
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Gao Q, Liu W, Wang JL, Wang XP, Zhou XM. PacBio Long-Read Sequencing Transcriptome Dataset of Adult Harmonia axyridis Under Diapause Inducing and Reproductive Inducing Photoperiod. Front Genet 2020; 11:1010. [PMID: 33061940 PMCID: PMC7518098 DOI: 10.3389/fgene.2020.01010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/07/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Qiao Gao
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wen Liu
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jia-Lu Wang
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiao-Ping Wang
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xing-Miao Zhou
- Hubei Key Laboratory of Insect Resources Utilization and Sustainable Pest Management, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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6
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Long-read assays shed new light on the transcriptome complexity of a viral pathogen. Sci Rep 2020; 10:13822. [PMID: 32796917 PMCID: PMC7427789 DOI: 10.1038/s41598-020-70794-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
Characterization of global transcriptomes using conventional short-read sequencing is challenging due to the insensitivity of these platforms to transcripts isoforms, multigenic RNA molecules, and transcriptional overlaps. Long-read sequencing (LRS) can overcome these limitations by reading full-length transcripts. Employment of these technologies has led to the redefinition of transcriptional complexities in reported organisms. In this study, we applied LRS platforms from Pacific Biosciences and Oxford Nanopore Technologies to profile the vaccinia virus (VACV) transcriptome. We performed cDNA and direct RNA sequencing analyses and revealed an extremely complex transcriptional landscape of this virus. In particular, VACV genes produce large numbers of transcript isoforms that vary in their start and termination sites. A significant fraction of VACV transcripts start or end within coding regions of neighbouring genes. This study provides new insights into the transcriptomic profile of this viral pathogen.
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7
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Meta-analytic approach for transcriptome profiling of herpes simplex virus type 1. Sci Data 2020; 7:223. [PMID: 32647284 PMCID: PMC7347551 DOI: 10.1038/s41597-020-0558-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/09/2020] [Indexed: 11/09/2022] Open
Abstract
In this meta-analysis, we re-analysed and compared herpes simplex virus type 1 transcriptomic data generated by eight studies using various short- and long-read sequencing techniques and different library preparation methods. We identified a large number of novel mRNAs, non-coding RNAs and transcript isoforms, and validated many previously published transcripts. Here, we present the most complete HSV-1 transcriptome to date. Furthermore, we also demonstrate that various sequencing techniques, including both cDNA and direct RNA sequencing approaches, are error-prone, which can be circumvented by using integrated approaches. This work draws attention to the need for using multiple sequencing approaches and meta-analyses in transcriptome profiling studies to obtain reliable results.
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8
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O’Donnell ST, Ross RP, Stanton C. The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach. Front Microbiol 2020; 10:3084. [PMID: 32047482 PMCID: PMC6997344 DOI: 10.3389/fmicb.2019.03084] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.
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Affiliation(s)
- Shane Thomas O’Donnell
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - R. Paul Ross
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- Department of Microbiology, University College Cork – National University of Ireland, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
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9
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Lejars M, Kobayashi A, Hajnsdorf E. Physiological roles of antisense RNAs in prokaryotes. Biochimie 2019; 164:3-16. [PMID: 30995539 DOI: 10.1016/j.biochi.2019.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/12/2019] [Indexed: 12/16/2022]
Abstract
Prokaryotes encounter constant and often brutal modifications to their environment. In order to survive, they need to maintain fitness, which includes adapting their protein expression patterns. Many factors control gene expression but this review focuses on just one, namely antisense RNAs (asRNAs), a class of non-coding RNAs (ncRNAs) characterized by their location in cis and their perfect complementarity with their targets. asRNAs were considered for a long time to be trivial and only to be found on mobile genetic elements. However, recent advances in methodology have revealed that their abundance and potential activities have been underestimated. This review aims to illustrate the role of asRNA in various physiologically crucial functions in both archaea and bacteria, which can be regrouped in three categories: cell maintenance, horizontal gene transfer and virulence. A literature survey of asRNAs demonstrates the difficulties to characterize and assign a role to asRNAs. With the aim of facilitating this task, we describe recent technological advances that could be of interest to identify new asRNAs and to discover their function.
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Affiliation(s)
- Maxence Lejars
- CNRS UMR8261, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
| | - Asaki Kobayashi
- SABNP, INSERM U1204, Université d'Evry Val-d'Essonne, Bâtiment Maupertuis, Rue du Père Jarlan, 91000, Évry Cedex, France.
| | - Eliane Hajnsdorf
- CNRS UMR8261, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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10
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Spatz SJ, Garcia M, Riblet S, Ross TA, Volkening JD, Taylor TL, Kim T, Afonso CL. MinION sequencing to genotype US strains of infectious laryngotracheitis virus. Avian Pathol 2019; 48:255-269. [PMID: 30722676 DOI: 10.1080/03079457.2019.1579298] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Over the last decade the US broiler industry has fought long-lasting outbreaks of infectious laryngotracheitis (ILTV). Previously, nine genotypes (I-IX) of ILTVs have been recognized using the polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) method with three viral alleles (gB, gM and UL47/gG). In this study, the genotyping system was simplified to six genotypes by amplicon sequencing and examining discriminating single nucleotide polymorphisms (SNPs) within these open reading frames. Using phylogenomic analysis of 27 full genomes of ILTV, a single allele (ORF A/ORF B) was identified containing SNPs that could differentiate ILTVs into genotypes congruent with the phylogenetic partitioning. The allelic variations allowed for the cataloging of the 27 strains into 5 genotypes: vaccinal TCO, vaccinal CEO, virulent CEO-like, virulent US and virulent US backyard flocks from 1980 to 1990, correlating with the PCR-RFLP genotypes I/ II/ III (TCO), IV (CEO), V (virulent CEO-like), VI (virulent US) and VII/VIII/IX (virulent US backyard flock isolates). With the unique capabilities of third generation sequencing, we investigated the application of Oxford Nanopore MinION technology for rapid sequencing of the amplicons generated in the single-allele assay. This technology was an improvement over Sanger-based sequencing of the single allele amplicons due to a booster amplification step in the MinION sequencing protocol. Overall, there was a 90% correlation between the genotyping results of the single-allele assay and the multi-allele assay. Surveillance of emerging ILTV strains could greatly benefit from real-time amplicon sequencing using the single-allele assay and MinION sequencing. RESEARCH HIGHLIGHTS A multi-allelic assay identified nine ILTV genotypes circulating in the US Single-allele genotyping is congruent with whole genome phylogenetic partitioning US ILTV strains can be grouped into five genotypes using the single-allele assay The single-allele assay can be done using MinION sequencing of barcoded amplicons.
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Affiliation(s)
- Stephen J Spatz
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
| | - Maricarmen Garcia
- b Department of Population Health , College of Veterinary Medicine, Poultry Diagnostic and Research Center, University of Georgia , Athens , GA , USA
| | - Sylva Riblet
- b Department of Population Health , College of Veterinary Medicine, Poultry Diagnostic and Research Center, University of Georgia , Athens , GA , USA
| | - Teresa A Ross
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
| | | | - Tonya L Taylor
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
| | - Taejoong Kim
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
| | - Claudio L Afonso
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
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11
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Wai H, Douglas AGL, Baralle D. RNA splicing analysis in genomic medicine. Int J Biochem Cell Biol 2018; 108:61-71. [PMID: 30594648 DOI: 10.1016/j.biocel.2018.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/03/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
High-throughput next-generation sequencing technologies have led to a rapid increase in the number of sequence variants identified in clinical practice via diagnostic genetic tests. Current bioinformatic analysis pipelines fail to take adequate account of the possible splicing effects of such variants, particularly where variants fall outwith canonical splice site sequences, and consequently the pathogenicity of such variants may often be missed. The regulation of splicing is highly complex and as a result, in silico prediction tools lack sufficient sensitivity and specificity for reliable use. Variants of all kinds can be linked to aberrant splicing in disease and the need for correct identification and diagnosis grows ever more crucial as novel splice-switching antisense oligonucleotide therapies start to enter clinical usage. RT-PCR provides a useful targeted assay of the splicing effects of identified variants, while minigene assays, massive parallel reporter assays and animal models can also be used for more detailed study of a particular splicing system, given enough time and resources. However, RNA-sequencing (RNA-seq) has the potential to be used as a rapid diagnostic tool in genomic medicine. By utilising data science approaches and machine learning, it may prove possible to finally understand and interpret the 'splicing code' and apply this knowledge in human disease diagnostics.
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Affiliation(s)
- Htoo Wai
- Human Development and Health, Faculty of Medicine, University of Southampton, UK
| | - Andrew G L Douglas
- Human Development and Health, Faculty of Medicine, University of Southampton, UK; Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, UK; Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
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Proteogenomic Identification of a Novel Protein-Encoding Gene in Bovine Herpesvirus 1 That Is Expressed during Productive Infection. Viruses 2018; 10:v10090499. [PMID: 30223481 PMCID: PMC6164122 DOI: 10.3390/v10090499] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 12/12/2022] Open
Abstract
Bovine herpesvirus 1 (BoHV-1) is one of several microbes that contributes to the development of the bovine respiratory disease (BRD) and can also induce abortions in cattle. As other alpha-herpesvirinae subfamily members, BoHV-1 efficiently replicates in many cell types and subsequently establishes a life-long latent infection in sensory neurons. BoHV-1 encodes more than 70 proteins that are expressed in a well-defined manner during productive infection. However, in silico open reading frame (ORF) prediction of the BoHV-1 genome suggests that the virus may encode more than one hundred proteins. In this study we used mass spectrometry followed by proteogenomic mapping to reveal the existence of 92 peptides that map to previously un-annotated regions of the viral genome. Twenty-one of the newly termed “intergenic peptides” were predicted to have a viable ORF around them. Twelve of these produced an mRNA transcript as demonstrated by strand-specific RT-PCR. We further characterized the 5′ and 3′ termini of one mRNA transcript, ORF-A, and detected a 55 kDa protein produced during active infection using a custom-synthesized antibody. We conclude that the coding potential of BoHV-1 is underestimated.
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