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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 http://meetings.cshl.edu/courses/2014/c-plan14.shtml.

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.

APPLICATIONS ARE DUE APRIL 15.

Thank you,

Mark Johnson
Brown University
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
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,
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Started by:
Peng Wang
2019-10-16 18:01:45
 
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.
Started by:
john binns
2019-10-11 15:07:04
 
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.
Started by:
Emilio Ortiz
2019-10-02 05:21:32
 
Hi,

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


Thank you,
Is it safe to directly map the gene identifiers (Solyc00g005000.2) using the primary id (Solyc00g005000)?
Started by:
Sridhar Gutam
2019-10-02 05:12:34
 
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
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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
Started by:
C├ęsar Benavidez
2019-09-24 16:22:51
 
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
2019-05-19 11:29:22
 
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:
Erwin Aragon
2019-03-11 09:06:57
 
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
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.
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:
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 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.
Started by:
Lukas Mueller
2009-07-23 12:10:22
 
This topic contains release notes for new SGN website features.