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The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

A. Bombarely, N. Menda, I. Y. Tecle, R. M. Buels, S. Strickler, T. Fischer-York, A. Pujar, J. Leto, J. Gosselin, L. A. Mueller
2010 Nucleic Acids Research  
The Sol Genomics Network (SGN; http:// solgenomics.net/) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with data types ranging from  ...  SGN hosts several genome maps and sequences, including a pre-release of the tomato (Solanum lycopersicum cv Heinz 1706) reference genome.  ...  ACKNOWLEDGEMENTS The authors would like to gratefully acknowledge Joyce van Eck for her ongoing contribution to the breeders toolbox.  ... 
doi:10.1093/nar/gkq866 pmid:20935049 pmcid:PMC3013765 fatcat:pecgrrxhujcidenzoz2jcue3yq

solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

Isaak Y Tecle, Naama Menda, Robert M Buels, Esther van der Knaap, Lukas A Mueller
2010 BMC Bioinformatics  
Description: The Sol Genomics Network (SGN, http://solgenomics.net) is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids  ...  available on SGN and can be used in private or public mode.  ...  Acknowledgements The project was funded by the USDA CSREES.  ... 
doi:10.1186/1471-2105-11-525 pmid:20964836 pmcid:PMC2984588 fatcat:76jqq2e56bgxzjhj56keb55hgu

Expression of resilience marker genes including nutrient transporters

C Constán-Aguilar, M Chialva, L Lanfranco, F Cardinale
2018 Zenodo  
Acknowledgement The James Hutton Institute (Scotland, UK), leads TOMRES Work Package 4 (Analysis and integration in a decision support system (DSS) of resource use efficiency, and environmental and socio-economic  ...  The Institute is also supported by the Rural and Environmental Science and Analytical Services (RESAS), a Division of the Scottish Government.  ...  The sol genomics network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res 39:D1149. doi:10.1093/nar/gkq866 Fiorilli, V., Catoni, M., Miozzi, L. et al. 2009 .  ... 
doi:10.5281/zenodo.4010696 fatcat:6jdkki5vpnherpadnq6ei2jgfe

Multiplex exome sequencing reveals genome-wide frequency and distribution of mutations in the 'Micro-Tom' Targeting Induced Local Lesions in Genomes (TILLING) mutant library

Ryoichi Yano, Ken Hoshikawa, Yoshihiro Okabe, Ning Wang, Pham Thi Dung, Pulungan Sri Imriani, Hiroshi Shiba, Tohru Ariizumi, Hiroshi Ezura
2019 Plant Biotechnology  
Over 98% of the capture target region could be covered by the short reads with an averaged read depth of 12.8, which enabled us to identify single nucleotide polymorphisms and Indels in a genome-wide manner  ...  While the 'Micro-Tom' TILLING mutant library is used for a wide range of purposes, including both basic research of gene function and breeding of commercial cultivars, genome-wide distribution and frequency  ...  Plant cultivation and genomic DNA extraction in 96 'Micro-Tom' mutants were performed by K.H.  ... 
doi:10.5511/plantbiotechnology.19.0830a pmid:31983876 pmcid:PMC6978505 fatcat:t3nju5w5z5gkvj7fcxa7nvunve

Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook

Hartmut Foerster, James N D Battey, Nicolas Sierro, Nikolai V Ivanov, Lukas A Mueller
2020 Briefings in Bioinformatics  
Manually curated metabolic databases residing at the Sol Genomics Network comprise two taxon-specific databases for the Solanaceae family, i.e. SolanaCyc and the genus Nicotiana, i.e.  ...  Here we describe the curation progress that has been achieved in these databases since the first release version 1.0 in 2016, the curation flow and the curation process using the example metabolic pathway  ...  The latest addition to manually curated taxon-specific databases is hosted at the Sol Genomics Network (SGN) (https://solgenomics.net/) [28, 29] on the SolCyc site (https://solgenomics.net/pages/solcyc  ... 
doi:10.1093/bib/bbaa136 pmid:32662816 pmcid:PMC8138835 fatcat:qgybfnay2rhvdh5w6ff7z2pufm

Citrusgreening.org: An open access and integrated systems biology portal for the Huanglongbing (HLB) disease complex [article]

Mirella Flores-Gonzalez, Prashant S Hosmani, Noe Fernandez-Pozo, Marina Mann, Jodi Lynn Humann, Doreen Main, Michelle Heck, Susan J Brown, Lukas A Mueller, Surya Saha
2019 bioRxiv   pre-print
To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease.  ...  Bulk downloads are available for all genome and annotation datasets from the FTP site (ftp://ftp.citrusgreening.org). The portal can be accessed at https://citrusgreening.org/.  ...  It . https://doi.org/10.1101/868364 doi: bioRxiv preprint Methods Database implementation The Citrusgreening.org platform is based on the Sol Genomics Network (solgenomics.net) architecture implemented  ... 
doi:10.1101/868364 fatcat:xdos3c4v4rhetfbit7pfp6556y

Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies

David N. Kuhn, Don Livingstone, Dorrie Main, Ping Zheng, Chris Saski, F. Alex Feltus, Keithanne Mockaitis, Andrew D. Farmer, Gregory D. May, Raymond J. Schnell, Juan C. Motamayor
2011 Tree Genetics & Genomes  
For the first strategy, SNPs were identified using cacao expressed sequence tags homologous to COSII sequences.  ...  Strategy II utilized a leaf transcriptome of cacao genotype "Matina 1-6" and Strategy III the genomic sequence of a 3-Mb region of "Matina 1-6" linkage group 5 associated with an important quantitative  ...  Belinda Martineau for editing the manuscript, and Dr. J. Michael Moore for assistance with the statistical analysis of the synteny data.  ... 
doi:10.1007/s11295-011-0424-0 fatcat:vkub2wnh7zez7n2k3ni2r2hdy4

Genomic analysis of the native European Solanum species, S. dulcamara

Nunzio D'Agostino, Tomek Golas, Henri van de Geest, Aureliano Bombarely, Thikra Dawood, Jan Zethof, Nicky Driedonks, Erik Wijnker, Joachim Bargsten, Jan-Peter Nap, Celestina Mariani, Ivo Rieu
2013 BMC Genomics  
Using the SNP markers in combination with genomic AFLP and CAPS markers, the first genome-wide genetic linkage map of bittersweet was generated.  ...  Based on gene orthology, the markers were anchored to the genome of related Solanum species (tomato, potato and eggplant), revealing both conserved and novel chromosomal rearrangements.  ...  The project was supported by CBSG2012 (projects PG11 and BB17), part of the Dutch Genomics Initiative (NGI).  ... 
doi:10.1186/1471-2164-14-356 pmid:23713999 pmcid:PMC3680029 fatcat:7ta4exb7hvhgvffy5eewgehj7i

Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-Based Curation

Hajime Ohyanagi, Tomoyuki Takano, Shin Terashima, Masaaki Kobayashi, Maasa Kanno, Kyoko Morimoto, Hiromi Kanegae, Yohei Sasaki, Misa Saito, Satomi Asano, Soichi Ozaki, Toru Kudo (+9 others)
2014 Plant and Cell Physiology  
public short read archive, digitally profiled the entire set of gene expression profiles, and drawn GENs by using correspondence analysis (CA) to take advantage of gene expression similarities.  ...  Comprehensive integration of large-scale omics resources such as genomes, transcriptomes and metabolomes will provide deeper insights into broader aspects of molecular biology.  ...  /) (Ohyanagi et al. 2006 , Tanaka et al. 2008 , Sakai et al. 2013 , the Sol Genome Network (http://solgenomics.net/) (Bombarely et al. 2011) , the Grape Genome Database (http://genomes.cribi.unipd. it  ... 
doi:10.1093/pcp/pcu188 pmid:25505034 pmcid:PMC4301748 fatcat:oeejcnumn5gdtm4jf6mogvq2py

A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines

D. H. Chitwood, R. Kumar, L. R. Headland, A. Ranjan, M. F. Covington, Y. Ichihashi, D. Fulop, J. M. Jimenez-Gomez, J. Peng, J. N. Maloof, N. R. Sinha
2013 The Plant Cell  
Introgression lines (ILs), in which genetic material from wild tomato species is introgressed into a domesticated background, have been used extensively in tomato (Solanum lycopersicum) improvement.  ...  Here, we genotype an IL population derived from the wild desert tomato Solanum pennellii at ultrahigh density, providing the exact gene content harbored by each line.  ...  To remove reads originating from repeat-rich genomic regions, RESCAN sequencing reads were initially mapped to the Sol Genomic Network's tomato repeat database using BWA (BWA parameters: -e 15 -i 10 -k  ... 
doi:10.1105/tpc.113.112391 pmid:23872539 pmcid:PMC3753377 fatcat:ofzmbmkq3jca3bhg4kr2jhmx6m

'Candidatus Phytoplasma solani' interferes with the distribution and uptake of iron in tomato

Sara Buoso, Laura Pagliari, Rita Musetti, Marta Martini, Fabio Marroni, Wolfgang Schmidt, Simonetta Santi
2019 BMC Genomics  
'Candidatus Phytoplasma solani' infection changes the Fe distribution in tomato leaves, affects the photosynthetic machinery and perturbs the orchestration of root-mediated transport processes by compromising  ...  To infer a possible involvement of Fe in the host-phytoplasma interaction, we investigated the effects of 'Candidatus Phytoplasma solani' infection on tomato plants (Solanum lycopersicum cv.  ...  Acknowledgements We are grateful to Alberto Loschi for his help in plant rearing and infection, and Carla Calligaro for technical support in the sample preparation for Perls'-DAB staining.  ... 
doi:10.1186/s12864-019-6062-x pmid:31500568 pmcid:PMC6734453 fatcat:y7pqd552u5dfpkbkh36yhupd3q

New insights into tomato microRNAs

Thaís Cunha de Sousa Cardoso, Tamires Caixeta Alves, Carolina Milagres Caneschi, Douglas dos Reis Gomes Santana, Christiane Noronha Fernandes-Brum, Gabriel Lasmar Dos Reis, Matheus Martins Daude, Thales Henrique Cherubino Ribeiro, Miguel Maurício Díaz Gómez, André Almeida Lima, Luiz Antônio Augusto Gomes, Marcos de Souza Gomes (+5 others)
2018 Scientific Reports  
Current progress in sequencing the tomato genome has generated useful information to assist in the study of their genetic diversity 12,23 .  ...  Due to the specific characteristics and growing conditions, tomato varieties are constantly improved 14 .  ...  Acknowledgements The authors thank UFU, FAPEMIG, CAPES and CNPq for fellowships and financial support. Author Contributions  ... 
doi:10.1038/s41598-018-34202-3 fatcat:a77lhuo7pncdtfshfagrhqfgry

Major Quantitative Trait Loci and Putative Candidate Genes for Powdery Mildew Resistance and Fruit-Related Traits Revealed by an Intraspecific Genetic Map for Watermelon (Citrullus lanatus var. lanatus)

Kwang-Hwan Kim, Ji-Hyun Hwang, Dong-Yeup Han, Minkyu Park, Seungill Kim, Doil Choi, Yongjae Kim, Gung Pyo Lee, Sun-Tae Kim, Young-Hoon Park, Yong Pyo Lim
2015 PLoS ONE  
An intraspecific genetic map for watermelon was constructed using an F 2 population derived from 'Arka Manik' × 'TS34' and transcript sequence variants and quantitative trait loci (QTL) for resistance  ...  The results PLOS ONE |  ...  Candidate fruit morphology genes were identified using BLASTP searches with tomato SUN, OVATE, LOCULE NUMBER, and FAS-CIATED (FAS) protein sequences achieved from the Sol Genome Network (SGN) (http://  ... 
doi:10.1371/journal.pone.0145665 pmid:26700647 pmcid:PMC4689417 fatcat:37mybqvghff4hk65vefonqh364

The genome sequence of the wild tomatoSolanum pimpinellifoliumprovides insights into salinity tolerance [article]

Rozaimi Razali, Salim Bougouffa, Mitchell J. L. Morton, Damien J. Lightfoot, Intikhab Alam, Magbubah Essack, Stefan T. Arold, Allan Kamau, Sandra M. Schmöckel, Yveline Pailles, Mohammed Shahid, Craig T. Michell (+5 others)
2017 bioRxiv   pre-print
The LA0480 genome size (811 Mb) and the number of annotated genes (25,970) are within the range observed for other sequenced tomato species.  ...  Additionally, we used DEAP to compare protein function betweenS. pimpinellifoliumand cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses.  ...  Protein datasets for S. pennellii and S. lycopersicum were obtained from the Sol Genomics Network (https://solgenomics.net/).  ... 
doi:10.1101/215517 fatcat:45qp2h4l45bq5mywq6ytdf42ze

Identification and Functional Analysis of Tomato CIPK Gene Family

Yao Zhang, Xi'nan Zhou, Siyuan Liu, Anzhou Yu, Chuanming Yang, Xiuling Chen, Jiayin Liu, Aoxue Wang
2019 International Journal of Molecular Sciences  
In this study, 22 members of the tomato CIPK gene family were successfully identified by using a combination of bioinformatics techniques and molecular analyses.  ...  This is the first study to uncover the nucleotide sequence for tomato CIPK family members and systematically study the changes of tomato CIPK family members under abiotic stress.  ...  We would like to thank the anonymous reviewers for their constructive comments. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms21010110 pmid:31877938 pmcid:PMC6981861 fatcat:5octcvk7hzcs7l4ape23okrslm
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