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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 have a list of tomato gene model ids. I would like to know how can I map tomato gene model ids (for ex, Solyc09g009710.2) to Affymetrix GeneChip Tomato Genome Array (for ex, Les.4492.2.S1_at)?
Where Can I get the mapping file?

In FAQ, I found a mapping file, but it is ITAG model to SGN.
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.

Recently, researchers from the Institution of Belgium VIB and Ghent University have noted that they found a new step in the complex regulation of plant stem cells. Data show that some tissue stem cells in plant roots are less sensitive to DNA damage. These cells preserve original integrated DNA copy and can be used to replace damaged cells when necessary.

Read the full text and tell us your opinion:
Dear Sol genomics network,

Shin-Han Shiu, Marja Timmermans, and I are organizing this summer's Cold Spring Harbor "Frontiers and Techniques in Plant Sciences" (June 27 - July 17).

The course provides foundational work in plant sciences as well as practical laboratory experience in techniques like RNA-seq, proteomics, mapping-by-sequencing, genome editing, and imaging. In recent years the course has stressed the quantitative nature of plant biology and students will be introduced to computational techniques required for analyzing large datasets.

As you may know, this course has been going strong for >30 years and has been taken by many successful plant scientists. I encourage you to let students, postdocs and faculty colleagues know about the course, which will be taught be a fantastic group of investigators

CSH can provide limited financial support for US students to cover their tuition room and board through an NSF grant and other sources of funding. Thus, I strongly encourage you to consider sending your new students and/or post-docs to the course, which has had a very strong positive impact on the trajectory of participants.


Thank you,

Mark Johnson
Brown University
Is it safe to directly map the gene identifiers (Solyc00g005000.2) using the primary id (Solyc00g005000)?
Transitions are base mutations of purine to purine (A <-> G) or pyrimidine to pyrimidine (C <-> T). Transversions are purine to pyrimidine or vice versa (A <-> C, A <-> T, G <-> C, G <-> T). And it is well-known that transitions are more common than transversions in the populations.

So what is the condition in the evolution of duplicated genes? Suppose a gene A is duplicated with two copies A1 and A2 in the same genome (not two alleles in different sets of chromosomes, or the same gene in two different cells/organisms). At first A1 and A2 had the same sequence, but then they went through an evolution process and each got some mutations. Now let's check the sequence of A1 and A2 again, are the differences between A1 and A2 mainly transitions instead of transversions?

Although I think it would not be surprising to find that transitions are more common in this condition, I've searched some papers focusing on the evolution of duplicated genes to look for some support. However, they mainly discuss what happened to their functions instead of sequences.
Hi dears,
Is there any possibility that someone can share the cDNA library of benthamiana? Please let me know, if it is possible. Thanks.
Started by:
Peng Wang

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.
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
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
In the life cycle of a mammalian cell, about one-third of proteins are phosphorylated. In vertebrate genes, about 5% of genes encode proteins are protein kinase and phosphatase involved in phosphorylation and dephosphorylation. It can be involved in regulating the growth, development, response to stress, disease occurrence and other life processes by stimulating and regulating many signaling pathways. It has always been the focus and hotspot of biological research.

Protein Phosphorylation

Protein phosphorylation refers to the process of promoting protein post-translational modification, which transfers ATP or GTP phosphate group (P04) to different kinds of amino acids (mainly include serine S, threonine T, tyrosine Y) under the catalysis of kinase.

Types of Phosphorylation Modification

Phosphorylated proteins can be classified into four classes depending on the amino acid residues of the phosphate, namely, O-phosphate protein, N-phosphate protein, acyl phosphate protein, and S-phosphate protein.

O-phosphate protein is formed by phosphorylation of hydroxy amino acids such as serine, threonine or tyrosine. N-phosphate protein is formed by phosphorylation of arginine, lysine or histidine. Acyl phosphate protein is formed by phosphorylation of aspartic acid or glutamic acid. S-phosphate protein is formed by cysteine phosphorylation.

Started by:
Naama Menda
2018-09-28 12:20:26
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.
Started by:
john binns
2018-01-09 05:45:44
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.
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.
Started by:
Emilio Ortiz
2014-01-19 23:11:32

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

Thank you,
Started by:
Lukas Mueller
2013-02-20 23:31:36
This topic contains release notes for new SGN data releases.
Started by:
Lukas Mueller
2011-12-14 10:49:32
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 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.
Started by:
Lukas Mueller
2009-07-23 12:10:22
This topic contains release notes for new SGN website features.