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Gupta P, Dholaniya PS, Princy K, Madhavan AS, Sreelakshmi Y, Sharma R. Augmenting tomato functional genomics with a genome-wide induced genetic variation resource. FRONTIERS IN PLANT SCIENCE 2024; 14:1290937. [PMID: 38328621 PMCID: PMC10848261 DOI: 10.3389/fpls.2023.1290937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/22/2023] [Indexed: 02/09/2024]
Abstract
Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Department of Biological Sciences, SRM University-AP, Amaravati, Andhra Pradesh, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Kunnappady Princy
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Athira Sethu Madhavan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Ortiz-Cortés LY, Aréchiga-Carvajal ET, Ventura-Canseco LMC, Ruíz-Valdiviezo VM, Gutiérrez-Miceli FA, Alvarez-Gutiérrez PE. Analysis of phenotypic changes in high temperature and low pH extreme conditions of Alicyclobacillus sendaiensis PA2 related with the cell wall and sporulation genes. Arch Microbiol 2024; 206:53. [PMID: 38180563 DOI: 10.1007/s00203-023-03735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/01/2023] [Accepted: 11/04/2023] [Indexed: 01/06/2024]
Abstract
The A. sendaiensis PA2 is a polyextremophile bacterium. In this study, we analyze the A. sendaiensis PA2 genome. The genome was assembled and annotated. The A. sendaiensis PA2 genome structure consists of a 2,956,928 bp long chromosome and 62.77% of G + C content. 3056 CDSs were predicted, and 2921 genes were assigned to a putative function. The ANIm and ANIb value resulted in 97.17% and 96.65%, the DDH value was 75.5%, and the value of TETRA (Z-score) was 0.98. Comparative genomic analyses indicated that three systems are enriched in A. sendaiensis PA2. This strain has phenotypic changes in cell wall during batch culture at 65 °C, pH 5.0 and without carbon and nitrogen source. The presence of unique genes of cell wall and sporulation subsystem could be related to the adaptation of A. sendaiensis PA2 to hostile conditions.
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Affiliation(s)
- Lourdes Yaret Ortiz-Cortés
- Tecnológico Nacional de México/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México
| | | | | | - Victor Manuel Ruíz-Valdiviezo
- Tecnológico Nacional de México/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México
| | - Federico Antonio Gutiérrez-Miceli
- Tecnológico Nacional de México/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México
| | - Peggy Elizabeth Alvarez-Gutiérrez
- Tecnológico Nacional de México/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México.
- CONAHCYT/IT de Tuxtla Gutiérrez, Carretera Panamericana Km 1080, Col. Terán, 29050, Tuxtla Gutiérrez, Chiapas, México.
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3
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Shecori S, Kher MM, Tyagi K, Lerno L, Netzer Y, Lichter A, Ebeler SE, Drori E. A Field Collection of Indigenous Grapevines as a Valuable Repository for Applied Research. PLANTS (BASEL, SWITZERLAND) 2022; 11:2563. [PMID: 36235429 PMCID: PMC9570891 DOI: 10.3390/plants11192563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
The grapevine is an economically important plant, with a historical connection to the development of human culture. Currently, over 6000 accessions are known as individual grapevine varieties, some of which are important to national heritage, valuable for current viticultural practices, and as genetic resources to maintain plasticity under changing climatic conditions, environmental sustainability, and market demands. Recently, the diversity of cultivated grapevines has declined significantly, due to the increased focus of global wine industries on a few major cultivars. Moreover, due to biotic and abiotic stresses, the wild V. vinifera germplasm's genetic diversity has declined, with some varieties on the verge of extinction. Vitis germplasm conservation can be achieved via either in situ (e.g., protected areas) or Ex situ (e.g., field collections, seed banks, and tissue culture collections) methods. This study aims to highlight the importance of Vitis field bank collections. We demonstrate the research done in the Israeli indigenous Vitis vinifera collection. The multi-layer analysis of the varieties enabled the identification of drought stress-resistant varieties, and suggested a mechanism for this resistance through noting the dramatic phenological differences in foliage development between resistant and sensitive varieties. In addition, we show a general characterization of the varieties via major grape characteristics, including bunch and berry shape, as well as their possible utilization based on their aromatic and phenolic profiles.
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Affiliation(s)
- Shani Shecori
- Chemical Engineering Department, Ariel University, Ariel 40700, Israel
| | | | - Kamal Tyagi
- Horticulture Section, SIPS, Cornell University, Ithaca, NY 14853, USA
| | - Larry Lerno
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Yishai Netzer
- Chemical Engineering Department, Ariel University, Ariel 40700, Israel
- Eastern Regional R&D Center, Ariel 40700, Israel
| | - Amnon Lichter
- Department of Postharvest Science, The Volcani Institute, Rishon LeZion 7528809, Israel
| | - Susan E. Ebeler
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Elyashiv Drori
- Chemical Engineering Department, Ariel University, Ariel 40700, Israel
- Eastern Regional R&D Center, Ariel 40700, Israel
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4
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Méndez M, Guimerà M, Corral J, Cívico S. Sperm origin impact on early human embryo kinetics. CLINICA E INVESTIGACION EN GINECOLOGIA Y OBSTETRICIA 2022. [DOI: 10.1016/j.gine.2022.100750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Cortaga CQ, Lachica JAP, Lantican DV, Ocampo ETM. Genome-wide SNP and InDel analysis of three Philippine mango species inferred from whole-genome sequencing. J Genet Eng Biotechnol 2022; 20:46. [PMID: 35275322 PMCID: PMC8917249 DOI: 10.1186/s43141-022-00326-3] [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: 11/03/2021] [Accepted: 02/27/2022] [Indexed: 11/16/2022]
Abstract
Background The Philippines is among the top 10 major exporters of mango worldwide. However, genomic studies of Philippine mangoes remain largely unexplored and lacking. Here, we sequenced the whole genome of the three Philippine mango species, namely, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica “Carabao” variety using Illumina HiSeq 2500, to identify and analyze their genome-wide variants (SNPs and InDels). Results The high confidence variants were identified by successfully mapping 93–95% of the quality-filtered reads to the Alphonso and Tommy Atkins mango reference genomes. Using these two currently available mango genomes, most variants were observed in M. odorata (4,353,063 and 4,277,287), followed by M. altissima (3,392,763 and 3,449,917), and lastly, M. indica Carabao (2,755,267 and 2,852,480). Approximately 50, 46, and 38% of the variants were unique in the three Philippine mango genomes. The analysis of variant effects and functional annotation across the three mango species revealed 56,982 variants with high-impact effects mapped onto 37,746 genes, of which 25% were found to be novel. The affected mango genes include those with potential economic importance such as 6945 genes for defense/resistance/immune response, 323 genes for fruit development, and 338 genes for anthocyanin production. Conclusions To date, this is the first sequencing effort to comprehensively analyze genome-wide variants essential for the development of genome-wide markers specific to these mango species native to the Philippines. This study provides an important genomic resource that can be used for the genetic improvement of mangoes. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00326-3.
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Affiliation(s)
- Cris Q Cortaga
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines. .,Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines.
| | - John Albert P Lachica
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines.,Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Darlon V Lantican
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
| | - Eureka Teresa M Ocampo
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines.,Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, 4031, Laguna, Philippines
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6
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Genomic characteristics of a novel strain Lactiplantibacillus plantarum X7021 isolated from the brine of stinky tofu for the application in food fermentation. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.113054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Zhang Y, Li J, Cui Q, Hu P, Hu S, Qian Y. Circular RNA hsa_circ_0006091 as a novel biomarker for hepatocellular carcinoma. Bioengineered 2022; 13:1988-2003. [PMID: 35068348 PMCID: PMC8973770 DOI: 10.1080/21655979.2021.2006952] [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] [Indexed: 12/30/2022] Open
Abstract
Circular RNAs (circRNAs) are stable and extensively distributed non-coding RNA molecules that are differentially expressed in liver cancer tissues in the human body. In this study, we aimed to investigate circRNA as a novel candidate biomarker for hepatocellular carcinoma (HCC). For three groups of HCC and neighboring healthy tissues, the differentially expressed circRNAs were identified through high-throughput sequencing analysis. Reverse transcription PCR (RT-PCR) and quantitative polymerase chain reaction (qPCR) were employed for the evaluation of circRNAs that show an elevated expression level in HCC. The obtained results revealed the significantly differential expression of hsa_circ_0006091 in HCC. Then we obtained their target genes through biological analysis, followed by verifying the underlined target genes, and the regulator of G-protein signaling 12 (RGS12) showed an elevated expression level in HCC tissues. Finally, receiver operating characteristic (ROC) curve analysis was conducted on AFP, RGS12, and hsa_circ_0006091, and combined analysis was performed. Furthermore, hsa_circ_0006091 is a novel candidate biomarker for HCC and could improve the diagnostic strategies, prediction, and follow-up of HCC patients. The joint diagnosis of the hsa_circ_0006091&AFP and hsa_circ_0006091&RGS12 has diagnostic significance and can be used as a molecular marker for HCC diagnosis. Abbreviations: AUC:area under the ROC curve; ROC:Receptor Operating Characteristics; bp:base pair;mRNA:Messenger Ribonucleic acid;ceRNA:Competing endogenous RNA; RT-qPCR: Real time-quantitativen PCR technology; circRNA: circular RNA; HCC:Hepatocellular carcinoma;miRNA:microRNA;KEGG:Kyoto Encyclopedia of Genes and Genomes; RGS12:regulator of G-protein signaling 12; AFP:alpha fetoprotein; ncRNAs:non-coding RNAs; GEO:Gene Expression Omnibus; FDR:false discovery rate
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Affiliation(s)
- Yongwei Zhang
- Department of Gastrointestinal surgery, Anqing First People’s Hospital Affiliated to Anhui Medical University, Anhui 246004, China
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230001, China
| | - Jun Li
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230001, China
| | - Quanwei Cui
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230001, China
| | - Panyi Hu
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230001, China
| | - Shuangjiu Hu
- Department of Gastrointestinal surgery, Anqing First People’s Hospital Affiliated to Anhui Medical University, Anhui 246004, China
| | - Yeben Qian
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230001, China
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8
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Rahimi O, Ohana‐Levi N, Brauner H, Inbar N, Hübner S, Drori E. Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range. Ecol Evol 2021; 11:6657-6671. [PMID: 34141248 PMCID: PMC8207413 DOI: 10.1002/ece3.7519] [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] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
The spatial distribution of plants is constrained by demographic and ecogeographic factors that determine the range and abundance of the species. Wild grapevine (Vitis vinifera ssp. sylvestris) is distributed from Switzerland in the north to Israel in the south. However, little is known about the ecogeographic constraints of this species and its genetic and phenotypic characteristics, especially at the southern edge of its distribution range in the Levant region. In this study, we explore the population structure of southern Levantine wild grapevines and the correlation between demographic and ecogeographic characteristics. Based on our genetic analysis, the wild grapevine populations in this region can be divided into two major subgroups in accordance with a multivariate spatial and ecogeographical clustering model. The identified subpopulations also differ in morphological traits, mainly leaf hairiness which may imply adaptation to environmental stress. The findings suggest that the Upper Jordan River population was spread to the Sea of Galilee area and that a third smaller subpopulation at the south of the Golan Heights may represent a distinguished gene pool or a recent establishment of a new population. A spatial distribution model indicated that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V. v. sylvestris distribution at its southern distribution range. These factors in addition to limited gene flow between populations prevent further spread of wild grapevines southwards to semi-arid regions.
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Affiliation(s)
- Oshrit Rahimi
- Department of Chemical EngineeringAriel UniversityArielIsrael
| | | | - Hodaya Brauner
- The Samson Family Grape and Wine Research CenterEastern Regional R&D CenterArielIsrael
| | - Nimrod Inbar
- Department of Civil EngineeringAriel UniversityArielIsrael
- The Department of Geophysics and Space ScienceEastern Regional R&D CenterArielIsrael
| | - Sariel Hübner
- Galilee Research Institute (Migal)Tel‐Hai Academic CollegeUpper GalileeIsrael
| | - Elyashiv Drori
- Department of Chemical EngineeringAriel UniversityArielIsrael
- The Samson Family Grape and Wine Research CenterEastern Regional R&D CenterArielIsrael
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9
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Bruscadin JJ, de Souza MM, de Oliveira KS, Rocha MIP, Afonso J, Cardoso TF, Zerlotini A, Coutinho LL, Niciura SCM, de Almeida Regitano LC. Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus. Sci Rep 2021; 11:7321. [PMID: 33795794 PMCID: PMC8016890 DOI: 10.1038/s41598-021-86782-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Marcela Maria de Souza
- grid.34421.300000 0004 1936 7312Post-Doctoral Fellow, Department of Animal Science, Iowa State University, Ames, IA USA
| | - Karina Santos de Oliveira
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Marina Ibelli Pereira Rocha
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Juliana Afonso
- grid.11899.380000 0004 1937 0722Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, SP Brazil
| | - Tainã Figueiredo Cardoso
- grid.460200.00000 0004 0541 873XEmbrapa Pecuária Sudeste, P. O. Box 339, São Carlos, SP 13564-230 Brazil
| | - Adhemar Zerlotini
- grid.460200.00000 0004 0541 873XEmbrapa Informática Agropecuária, Campinas, SP Brazil
| | - Luiz Lehmann Coutinho
- grid.11899.380000 0004 1937 0722Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, SP Brazil
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10
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Maya I, Smirin-Yosef P, Kahana S, Morag S, Yacobson S, Agmon-Fishman I, Matar R, Bitton E, Shohat M, Basel-Salmon L, Salmon-Divon M. A study of normal copy number variations in Israeli population. Hum Genet 2020; 140:553-563. [PMID: 32980975 DOI: 10.1007/s00439-020-02225-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/19/2020] [Indexed: 10/23/2022]
Abstract
The population of Israel is ethnically diverse, and individuals from different ethnic groups share specific genetic variations. These variations, which have been passed on from common ancestors, are usually reported in public databases as rare variants. Here, we aimed to identify ethnicity-based benign copy number variants (CNVs) and generate the first Israeli CNV database. We applied a data-mining approach to the results of 10,193 chromosomal microarray tests, of which 2150 tests were from individuals of 13 common ethnic backgrounds (n ≥ 10). We found 165 CNV regions (> 50 kbp) that are unique to specific ethnic groups (uCNVRs). The frequency of more than 19% of these uCNVRs is between 1 and 20% of the common ethnic origin, while their frequency in the overall cohort is between 0.5 and 1.6%. Of these 165 uCNVRs, 98 are reported as variants of unknown significance or as not available in dbVar; we postulate that these uCNVRs should be annotated as either "likely benign" or "benign". The ethnic-specific CNVs extracted in this study will allow geneticists to distinguish between relevant pathogenic genomic aberrations and benign ethnicity-related variations, thus preventing variant misinterpretation that may lead to unnecessary pregnancy terminations.
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Affiliation(s)
- Idit Maya
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Pola Smirin-Yosef
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Sarit Kahana
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Sne Morag
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Shiri Yacobson
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Ifaat Agmon-Fishman
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Reut Matar
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Elisheva Bitton
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Mordechai Shohat
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel.,Maccabi Health Services, Rehovot, Israel
| | - Lina Basel-Salmon
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel. .,The Adelson School of Medicine, Ariel University, Ariel, Israel.
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11
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Ejigu GF, Jung J. Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. BIOLOGY 2020; 9:E295. [PMID: 32962098 PMCID: PMC7565776 DOI: 10.3390/biology9090295] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022]
Abstract
Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to decode the information contained in nucleotide sequences. This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders. Here, we present a summary of both structural and functional annotations, as well as the associated comparative annotation tools and pipelines. We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation. Further, we discuss quality-control practices and the need for re-annotation, and highlight the future of annotation.
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Affiliation(s)
| | - Jaehee Jung
- Department of Information and Communication Engineering, Myongji University, Yongin-si 17058, Gyeonggi-do, Korea;
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12
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Olivieri F, Calafiore R, Francesca S, Schettini C, Chiaiese P, Rigano MM, Barone A. High-Throughput Genotyping of Resilient Tomato Landraces to Detect Candidate Genes Involved in the Response to High Temperatures. Genes (Basel) 2020; 11:genes11060626. [PMID: 32517343 PMCID: PMC7349060 DOI: 10.3390/genes11060626] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/04/2022] Open
Abstract
The selection of tolerant varieties is a powerful strategy to ensure highly stable yield under elevated temperatures. In this paper, we report the phenotypic and genotypic characterization of 10 tomato landraces to identify the best performing under high temperatures. The phenotyping of five yield-related traits allowed us to select one genotype that exhibits highly stable yield performances in different environmental conditions. Moreover, a Genotyping-by-Sequencing approach allowed us to explore the genetic variability of the tested genotypes. The high and stable yielding landrace E42 was the most polymorphic one, with ~49% and ~47% private SNPs and InDels, respectively. The effect of 26,113 mutations on proteins’ structure was investigated and it was discovered that 37 had a high impact on the structure of 34 proteins of which some are putatively involved in responses to high temperatures. Additionally, 129 polymorphic sequences aligned against tomato wild species genomes revealed the presence in the genotype E42 of several introgressed regions deriving from S. pimpinellifolium. The position on the tomato map of genes affected by moderate and high impact mutations was also compared with that of known markers/QTLs (Quantitative Trait Loci) associated with reproductive and yield-related traits. The candidate genes/QTLs regulating heat tolerance in the selected landrace E42 could be further investigated to better understand the genetic mechanisms controlling traits for high and stable yield trait under high temperatures.
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Affiliation(s)
- Fabrizio Olivieri
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | - Roberta Calafiore
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | - Silvana Francesca
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | | | - Pasquale Chiaiese
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | - Maria Manuela Rigano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Napoli, Italy; (F.O.); (R.C.); (S.F.); (P.C.); (M.M.R.)
- Correspondence: ; Tel.: +39-0812539491
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13
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Piombo E, Bosio P, Acquadro A, Abbruscato P, Spadaro D. Different Phenotypes, Similar Genomes: Three Newly Sequenced Fusarium fujikuroi Strains Induce Different Symptoms in Rice Depending on Temperature. PHYTOPATHOLOGY 2020; 110:656-665. [PMID: 31721656 DOI: 10.1094/phyto-09-19-0359-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bakanae, caused by the hemibiotrophic fungus Fusarium fujikuroi, is one of the most important diseases of rice and is attributed to up to 75% of losses, depending on the strain and environmental conditions. Some strains cause elongation and thin leaves, whereas others induce stunting and chlorotic seedlings. Differences in symptoms are attributed to genetic differences in the strains. F. fujikuroi strains Augusto2, CSV1, and I1.3 were sequenced with Illumina MiSeq, and pathogenicity trials were conducted on rice cultivar Galileo, which is susceptible to bakanae. By performing gene prediction, single nucleotide polymorphism (SNP) calling, and structural variant analysis with a reference genome, we show how an extremely limited number of polymorphisms in genes not commonly associated with bakanae disease can cause strong differences in phenotype. CSV1 and Augusto2 were particularly close, with only 21,887 SNPs between them, but they differed in virulence, reaction to temperature, induced symptoms, colony morphology and color, growth speed, fumonisin, and gibberellin production. Genes potentially involved in the shift in phenotype were identified. Furthermore, we show how temperature variation may result in different symptoms even in rice plants inoculated with the same F. fujikuroi strain. Moreover, all of the F. fujikuroi strains became more virulent at higher temperatures. Significant differences were likewise observed in gibberellic acid production and in the expression of both fungal and plant gibberellin biosynthetic genes.
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Affiliation(s)
- Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Grugliasco, Turin 10095, Italy
- Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, Grugliasco, Turin 10095, Italy
| | - Pietro Bosio
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Grugliasco, Turin 10095, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Grugliasco, Turin 10095, Italy
| | | | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Grugliasco, Turin 10095, Italy
- Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, Grugliasco, Turin 10095, Italy
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14
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Sanjurjo-Soriano C, Erkilic N, Baux D, Mamaeva D, Hamel CP, Meunier I, Roux AF, Kalatzis V. Genome Editing in Patient iPSCs Corrects the Most Prevalent USH2A Mutations and Reveals Intriguing Mutant mRNA Expression Profiles. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2019; 17:156-173. [PMID: 31909088 PMCID: PMC6938853 DOI: 10.1016/j.omtm.2019.11.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
Inherited retinal dystrophies (IRDs) are characterized by progressive photoreceptor degeneration and vision loss. Usher syndrome (USH) is a syndromic IRD characterized by retinitis pigmentosa (RP) and hearing loss. USH is clinically and genetically heterogeneous, and the most prevalent causative gene is USH2A. USH2A mutations also account for a large number of isolated autosomal recessive RP (arRP) cases. This high prevalence is due to two recurrent USH2A mutations, c.2276G>T and c.2299delG. Due to the large size of the USH2A cDNA, gene augmentation therapy is inaccessible. However, CRISPR/Cas9-mediated genome editing is a viable alternative. We used enhanced specificity Cas9 of Streptococcus pyogenes (eSpCas9) to successfully achieve seamless correction of the two most prevalent USH2A mutations in induced pluripotent stem cells (iPSCs) of patients with USH or arRP. Our results highlight features that promote high target efficacy and specificity of eSpCas9. Consistently, we did not identify any off-target mutagenesis in the corrected iPSCs, which also retained pluripotency and genetic stability. Furthermore, analysis of USH2A expression unexpectedly identified aberrant mRNA levels associated with the c.2276G>T and c.2299delG mutations that were reverted following correction. Taken together, our efficient CRISPR/Cas9-mediated strategy for USH2A mutation correction brings hope for a potential treatment for USH and arRP patients.
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Affiliation(s)
- Carla Sanjurjo-Soriano
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
| | - Nejla Erkilic
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
| | - David Baux
- University of Montpellier, 34095 Montpellier, France.,Medical Genetics Laboratory, CHU, 34093 Montpellier, France
| | - Daria Mamaeva
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
| | - Christian P Hamel
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France.,National Reference Centre for Inherited Sensory Disorders, CHU, 34295 Montpellier, France
| | - Isabelle Meunier
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France.,National Reference Centre for Inherited Sensory Disorders, CHU, 34295 Montpellier, France
| | - Anne-Françoise Roux
- University of Montpellier, 34095 Montpellier, France.,Medical Genetics Laboratory, CHU, 34093 Montpellier, France
| | - Vasiliki Kalatzis
- Inserm U1051, Institute for Neurosciences of Montpellier, 34091 Montpellier, France.,University of Montpellier, 34095 Montpellier, France
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15
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Parveen A, Khurana S, Kumar A. Overview of Genomic Tools for Circular Visualization in the Next-generation Genomic Sequencing Era. Curr Genomics 2019; 20:90-99. [PMID: 31555060 PMCID: PMC6728899 DOI: 10.2174/1389202920666190314092044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022] Open
Abstract
After human genome sequencing and rapid changes in genome sequencing methods, we have entered into the era of rapidly accumulating genome-sequencing data. This has derived the development of several types of methods for representing results of genome sequencing data. Circular genome visual-ization tools are also critical in this area as they provide rapid interpretation and simple visualization of overall data. In the last 15 years, we have seen rapid changes in circular visualization tools after the de-velopment of the circos tool with 1-2 tools published per year. Herein we have summarized and revisited all these tools until the third quarter of 2018.
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Affiliation(s)
- Alisha Parveen
- 1Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany; 2Pharmacology Department, Central Drug Research Institute - Lucknow, Uttar Pradesh, India; 3Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
| | - Sukant Khurana
- 1Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany; 2Pharmacology Department, Central Drug Research Institute - Lucknow, Uttar Pradesh, India; 3Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
| | - Abhishek Kumar
- 1Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany; 2Pharmacology Department, Central Drug Research Institute - Lucknow, Uttar Pradesh, India; 3Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany
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16
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Piombo E, Sela N, Wisniewski M, Hoffmann M, Gullino ML, Allard MW, Levin E, Spadaro D, Droby S. Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases. Front Microbiol 2018; 9:593. [PMID: 29666611 PMCID: PMC5891927 DOI: 10.3389/fmicb.2018.00593] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 03/15/2018] [Indexed: 01/08/2023] Open
Abstract
The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product "Shemer." Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. We assembled the whole genome sequence of two strains of M. fructicola using PacBio and Illumina shotgun sequencing technologies. Using the PacBio, a high-quality draft genome consisting of 93 contigs, with an estimated genome size of approximately 26 Mb, was obtained. Comparative analysis of M. fructicola proteins with the other three available closely related genomes revealed a shared core of homologous proteins coded by 5,776 genes. Comparing the genomes of the two M. fructicola strains using a SNP calling approach resulted in the identification of 564,302 homologous SNPs with 2,004 predicted high impact mutations. The size of the genome is exceptionally high when compared with those of available closely related organisms, and the high rate of homology among M. fructicola genes points toward a recent whole-genome duplication event as the cause of this large genome. Based on the assembled genome, sequences were annotated with a gene description and gene ontology (GO term) and clustered in functional groups. Analysis of CAZymes family genes revealed 1,145 putative genes, and transcriptomic analysis of CAZyme expression levels in M. fructicola during its interaction with either grapefruit peel tissue or Penicillium digitatum revealed a high level of CAZyme gene expression when the yeast was placed in wounded fruit tissue.
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Affiliation(s)
- Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Turin, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Michael Wisniewski
- United States Department of Agriculture – Agricultural Research Service, Kernersville, WV, United States
| | - Maria Hoffmann
- Division of Microbiology, United States Food and Drug Administration, College Park, MD, United States
| | - Maria L. Gullino
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Turin, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
| | - Marc W. Allard
- Division of Microbiology, United States Food and Drug Administration, College Park, MD, United States
| | - Elena Levin
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Turin, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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