Dear all,

I would like to know how to match the blast Nicotiana gene to its expression data?
I have downloaded the microarray data of tobacco gene expression from the EMBL-EBI ArrayExpress. At the same time, I blast my intsrested gene from N.tabacum TN90. It showed the related information (mRNA_60941 gene_35596|id=AT2G19450.1:evalue=0.0:annot='membrane bound O-acyl transferase (MBOAT) family protein';id=Solyc12g008970.1.1:evalue=0.0:annot='Diacylglycerol acyltransferase'Length=1524).
But how can I match the blast information to the ID in expression data? I searched a lot but I couldn't find it.

Please help.
Thank you very much.

This topic contains release notes for new SGN data releases.

This topic discusses issues in developing controlled-vocabularies for describing Solanaceae phenotypes and traits.
Most should be covered by the 'Solanaceae Phenotype Ontology' (SPO)
(see SGN->Tools->Ontology browser) which is growing by demand of its users community.
Terms which exist in other ontologies (PO, PATO, etc) are mapped to SPO terms.
In some cases it will be advised to use other vocabularies, instead of providing new SPO terms.

Dears friends: I want to Know if Are there microsatellite or other molecular marker that can be used for identify differents species in tomato??? i mean between sculentum and

Dear friends, I am about to begin an investigation of lycopene content in tomato species, as well as identification of microsatellites to identify the gene or genes responsible for the character under study, so I ask if I could help with information on the research topic . Thank you very much

Hi dears,
Is there any possibility that someone can share the cDNA library of benthamiana? Please let me know, if it is possible. Thanks.

Dear All,

I would like to work on phenotyping tomato and brinjal (egg plant) for abiotic stress tolerance traits. For that I would like to know what are the materials and methods needed.

Why I am asking is that if any one in the community had developed a set of protocols for low cost phenotyoing, i would like to use it.

Please connect me with people who are working on phenotyping tomato.

Thanks
Sridhar

Dear Sir/Madam
Hi
I need all of tomato reference and integrated maps such as "Integrated map: Yellow Stuffer X LA1589 and Sun1642 X LA1589".
But when I choose the map, I see "Server error" message.
Please let me know how can I get these maps.
Regards.

The plant biotechnology and molecular breeding laboratory at Mid-Florida Research & Education Center at the University of Florida is seeking a highly motivated scientist to conduct studies of the environmental effect on tomato seed development, which is sponsored by FFAR for three years. The objective of this project is to identify the small RNAs that regulate seed development in response to maternal temperatures. This position requires a person with horticultural practices in growing tomato plants and a strong background in small RNA sequencing and analysis. The majority of research activities will be completed at Mid-Florida Education and Research Center, which is about 15miles from Orlando downtown, Florida; occasional travel to other states such as California may be required.

Applicants should receive a Ph.D. degree within the past 5 years with a solid background in bioinformatics and molecular biology/plant biotechnology, and have at least one first-authored publication in a peer-reviewed journal. Expertise in plant molecular techniques (small RNA delivery, siRNAs manipulation, CRISPR gene-editing) and research experiences in tomato or seed biology will be highly preferred. Candidates should have excellent skills in communications in oral and written English, skills in critical thinking, and are able to work independently in a culture-diverse environment. Applicants with legal visa status in the U.S. will be seriously considered. Salary is competitive and commensurate with background and experience($48000 plus medical benefit etc.). This position will be immediately available and remain open until filled. The term for this position is one year, and renewable contingent on academic performance for at least another 2 years. Qualified applicants should send a CV, and contact information for 3-4 references by email to hhuo@ufl.edu.

Hi everyone, I have a list of petunia gene IDs that I'd like to blast on the Tomato genome. Can someone suggest how I can do that? I don't want to do it individually, eg geting all the sequences of my petunia genes and blasting them. thanks in advance

With the discovering of new microRNAs and the uncovering of their importance various biological functions as small regulatory elements, miRNA research is rapidly evolving. miRNA sequencing is used to discover novel miRNAs, examine the dierential expression of all miRNAs and to characterize variations with single-base resolution.

https://integraterna.creative-biogene.com/service/microrna-sequencing-service.html

I'm in Tanzania as an intern at a seed producing farm working with various tomato varieties. In a few months, I will be sequencing the genome on these varieties with the MinION from Oxford Nanopore Technology.

I am looking for a complete and comprehensive list of the most promising genes that have been linked to drought tolerance. While searching for genes and loci on the solgenomics website I have found 56 entries when searching for ''drought'' in ''tomato''. I will need to select the most promising genes to perform a comparative analysis once I've sequenced the genome of various tomato varieties here in Tanzania. How complete do you think these 56 entries are and are there other sources I should consider?

I would love to hear your suggestions,

Lorenzo

Hi,
I am very confused browsing literature because I can not find a clear statement about the ploidy of N. benthamiana.
N. tabacum is clearly an allotetraploid, and tetraploid (2n = 4x = 48), with 4 copies of n=12. Genome size over 4.5 Gb, however,
N benthamiana it is reported to be an "ancient" allotetraploid, but currently it is n=19, and 38 total number of chromosomes, so it seems that from the ancient allotetraploid (48 chromosomes), genome fractionation has occurred and 38 remains, and that currently the genome is "diploid" (2n = 2x = 38). Is this correct?. Is N benthamiana diploid?.
Thank you very much.
Best regards,

I would like to know whether Triticum aestivum database is updated and is there any reference where I researchers have designed construct for VIGS in wheat

Hello
I would like to access the potato annotation file in iTAG nomenclature with their respective TAIR nomenclature codes equivalent to each gene. Is that possible? I can not find the annotation file that includes that information. I need to match the nomenclature accepted in DAVID (The Database for Annotation).

Example in PGSC annotation available in Phytozome

PGSC0003DMG400000001 = AT1G12600.1

I am a college student engaged in plant breeding. I want to study the genome-wide analysis of cassava disease-related gene families. Any suggestions?

Hi, I would like to know if there is a straightforward way to translate the one nomenclature to the other.
Both refer to genes/loci/protein, right... but if I have to compare to see coincidences from one list in one format and one list in the other (having hundreds of proteins/genes in each list), I can die doing searches and endless alignments, and still not accomplishing the job...
Please help.
Thank you very much.

This topic is for members of the SOL community from around the world to publish job openings. If interested, please reply directly to the poster. Job postings submitters please note that the postings will be removed by default 8 months after posting.

This topic contains release notes for new SGN website features.

Is it safe to directly map the gene identifiers (Solyc00g005000.2) using the primary id (Solyc00g005000)?

Here we report a serious problem with tobacco gene models. We tried to map the gene models of Nitociana tabacum (TN90), which you provide in your ftp, to the TN90 genome assembly sequences. Unfortunately, a lot of gene models could not be mapped. Of the 122388 gene models you provided in the gene model file,only 53714 could be mapped to the genome assembly. We do not know what method you used to identify gene models. Could you check all the datasets of the three tobacco varieties(TN90, K326 and Bathma)? Thank you.

Dear all,
I need your help here. Does anyone know how to convert ITAG gene tomato annotations to KEGG (or UniProt) ID?

Thanks in advance!

Irene

Hi,

Is there any way to download the 2860 COSII sequences? Please let me know.


Thank you,

In the next few years, hundreds of Solanaceae will be sequenced using next generation sequencing methods. If you intend to sequence a Solanaceae, please provide information on the species to avoid duplicate sequencing of accessions on the SGN SOL-100 page http://solgenomics.net/organism/sol100/view. This topic is for the discussion of SOL-100 related questions.

This topics is for the researchers of the SOL community around the world who need some specific materials for their experiments and express some request to those who could provide them with the expected materials or resources.