AgBase: a functional genomics resource for agriculture

McCarthy, Fiona M.; Wang, Nan; Magee, G Bryce; Nanduri, Bindu; Lawrence, Mark L.; Camon, Evelyn; Barrell, Daniel; Hill, David P.; Dolan, M. Eileen; Williams, W. Paul; Luthe, Dawn S.; Bridges, Susan M.; Burgess, Shane C.

doi:10.1186/1471-2164-7-229

Cited by 258 publications

(203 citation statements)

References 35 publications

Supporting

Mentioning

202

Contrasting

Unclassified

Order By: Relevance

“…The annotated GO terms were further classified with the plant set of the GO Slim Viewer (McCarthy et al, 2006) (summarized in Supplemental Figure S3, full list in Supplemental Table S6). …”

Section: Resultsmentioning

confidence: 99%

A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens

et al. 2014

View full text Add to dashboard Cite

Noccaea caerulescens is an extremophile plant species belonging to the Brassicaceae family. It has adapted to grow on soils containing high, normally toxic, concentrations of metals such as nickel, zinc, and cadmium. Next to being extremely tolerant to these metals, it is one of the few species known to hyperaccumulate these metals to extremely high concentrations in their aboveground biomass. In order to provide additional molecular resources for this model metal hyperaccumulator species to study and understand the mechanism of adaptation to heavy metal exposure, we aimed to provide a comprehensive database of transcript sequences for N. caerulescens. In this study, 23,830 transcript sequences (isotigs) with an average length of 1025 bp were determined for roots, shoots and inflorescences of N. caerulescens accession “Ganges” by Roche GS-FLEX 454 pyrosequencing. These isotigs were grouped into 20,378 isogroups, representing potential genes. This is a large expansion of the existing N. caerulescens transcriptome set consisting of 3705 unigenes. When translated and compared to a Brassicaceae proteome set, 22,232 (93.2%) of the N. caerulescens isotigs (corresponding to 19,191 isogroups) had a significant match and could be annotated accordingly. Of the remaining sequences, 98 isotigs resembled non-plant sequences and 1386 had no significant similarity to any sequence in the GenBank database. Among the annotated set there were many isotigs with similarity to metal homeostasis genes or genes for glucosinolate biosynthesis. Only for transcripts similar to Metallothionein3 (MT3), clear evidence for an additional copy was found. This comprehensive set of transcripts is expected to further contribute to the discovery of mechanisms used by N. caerulescens to adapt to heavy metal exposure.

show abstract

“…The annotated GO terms were further classified with the plant set of the GO Slim Viewer (McCarthy et al, 2006) (summarized in Supplemental Figure S3, full list in Supplemental Table S6). …”

Section: Resultsmentioning

confidence: 99%

A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens

et al. 2014

View full text Add to dashboard Cite

show abstract

“…GOSlim terms were extracted from the AgBase web site (http://agbase.msstate.edu/cgi-bin/tools/GOanna.cgi) 17 using GOSlim Viewer after summarizing GO data. For Botrytis proteins with no assigned function homology searches were performed using the BlastP program against all nonredundant protein sequences in the NCBI database released on September 2009 (http://blast.ncbi.nlm.nih.gov/).…”

Section: Methodsmentioning

confidence: 99%

Proteomic Analysis of Ripening Tomato Fruit Infected by Botrytis cinerea

et al. 2012

View full text Add to dashboard Cite

Botrytis cinerea, a model necrotrophic fungal pathogen that causes gray mold as it infects different organs on more than 200 plant species, is a significant contributor to postharvest rot in fresh fruit and vegetables, including tomatoes. By describing host and pathogen proteomes simultaneously in infected tissues, the plant proteins that provide resistance and allow susceptibility and the pathogen proteins that promote colonization and facilitate quiescence can be identified. This study characterizes fruit and fungal proteins solubilized in the B. cinerea−tomato interaction using shotgun proteomics. Mature green, red ripe wild type and ripening inhibited (rin) mutant tomato fruit were infected with B. cinerea B05.10, and the fruit and fungal proteomes were identified concurrently 3 days postinfection. One hundred eighty-six tomato proteins were identified in common among red ripe and red ripe-equivalent ripening inhibited (rin) mutant tomato fruit infected by B. cinerea. However, the limited infections by B. cinerea of mature green wild type fruit resulted in 25 and 33% fewer defense-related tomato proteins than in red and rin fruit, respectively. In contrast, the ripening stage of genotype of the fruit infected did not affect the secreted proteomes of B. cinerea. The composition of the collected proteins populations and the putative functions of the identified proteins argue for their role in plant−pathogen interactions.

show abstract

“…To assess the coverage of the assembled PUTs, we further compared PUTs against the predicted gene primary transcripts using BLASTN with a cut off E-value of 1e-10, ≥95% identity and minimum aligned length of 80 bp, the results were summarized in Table 1. Gene Ontology (GO) information was extracted from the UniProt ID mapping table based on the BLASTP of gene model protein sequences against the UniProtKB/Swiss-Prot (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/).The GO categories were further analyzed using GO SlimViewer using plant specific GO terms (McCarthy et al, 2006). …”

Section: Functional Annotation Of Putsmentioning

confidence: 99%

Comprehensive Cataloging and Analysis of Alternative Splicing in Maize

Min

2017

cmb

View full text Add to dashboard Cite

Gene expression is a key step in developmental regulation and responses in changing environments in plants. Alternative splicing (AS) is a process generating multiple RNA isoforms from a single gene pre-mRNA transcript that increases the diversity of functional proteins and RNAs. Identification and analysis of alternatively splicing events are critical for crop improvement and understanding regulatory mechanisms. In maize large numbers of transcripts generated by RNA-seq technology are available, we incorporated these data with data assembled with ESTs and mRNAs to comprehensively catalog all genes having pre-mRNAs undergoing AS. A total of 192 624 AS events were detected and classified, including 103 566 (53.8%) basic events and 89 058 (46.2%) complex events which were formed by combination of various types of basic events. Intron retention was the dominant type of basic AS event, accounting for 24.1%. These AS events were identified from 91 128 transcripts which were generated from 26 669 genomic loci, of which consisted of 20 860 gene models. It was estimated that 55.3% maize genes may be subjected to AS. The transcripts mapping information can be used to improve the predicted gene models in maize. The data can be accessed at Plant Alternative Splicing Database

show abstract

AgBase: a functional genomics resource for agriculture

Cited by 258 publications

References 35 publications

A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens

A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens

Proteomic Analysis of Ripening Tomato Fruit Infected by Botrytis cinerea

Comprehensive Cataloging and Analysis of Alternative Splicing in Maize

Contact Info

Product

Resources

About