Solgenomics

Congratulations to BTI's Zhangjun Fei, Jim Giovannoni, Lukas Mueller, and board member Susan McCouch for being among the most highly cited researchers during the last decade!

BTI's Lukas Mueller worked with an international team of 57 people to create Breedbase, a database software to help plant breeders speed crop improvement around the world.
https://btiscience.org/explore-bti/news/post/breedbase-software-to-help-speed-crop-improvement/

The authors assembled 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution

Genome evolution and diversity of wild and cultivated potatoes - Nature High-quality diploid assemblies of potato genomes from 24 wild and 20 cultivated potatoes provide insights into the complex evolution and diversity of potatoes, and could have applications in the breeding of hybrid potatoes.

The authors report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits.

Graph pangenome captures missing heritability and empowers tomato breeding - Nature A precise catalogue of more than 19 million variants from 838 tomato genomes, including 32 new reference-level genome assemblies, advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.

The Mueller lab at the Boyce Thompson Institute (https://btiscience.org/), which maintains several advanced databases, including the Solgenomics (https://solgenomics.net/), Cassavabase (https://cassavabase.org/) and Citrusgreening.org (https://citrusgreening.org/), has an open position for a Research Associate in the field of bioinformatics, genomic and breeding databases,omics analysis, and genome sequencing and annotation.

Major responsibilities will include leading genomics and transcriptomics analysis, genome annotation, code development and maintenance of genomics databases and websites.

http://bti.hrmdirect.com/employment/job-opening.php?req=1765948&&

Here's a really neat story about a new software package that helps plant breeders analyze crops in the field, and how BTI's Nick Morales of the Mueller lab created an interface that makes it easier to use:
https://acsess.onlinelibrary.wiley.com/doi/10.1002/csan.20438.

Give - Boyce Thompson Institute Gary Blissard Carmen Catalá Zhangjun Fei Jim Giovannoni Maria Harrison Michelle Heck Georg Jander Magdalena Julkowska Daniel Klessig Fay-WeiLi Greg Martin Lukas Mueller Andrew Nelson Eric Richards Frank Schroeder Aleksandra Skirycz David Stern Joyce Van Eck

SOL Meeting 2020 will be a virtual conference hosted SOL Genomics Nov 9-11th 14:00 to 17:30 CET. More details https://solgenomics.net/sol2020
Registration is free! https://forms.gle/YagGUagfdi25W6oZ7
But abstract submission deadline is Oct 15th
Flyer:https://solgenomics.net/static_content/SOL_INTERNATIONAL_Flyer.pdf

New tomato reference SL4.0 and annotation ITAG4.0 released in time for the XVI Conference
Highlights: https://solgenomics.net/organism/Solanum_lycopersicum/genome/
Download: ftp://ftp.solgenomics.net/tomato_genome/assembly/build_4.00/ and ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG4.0_release/

Build highlights SL4.0
- Only 44Kb of N's (unknown bases) compared to 81.7Mb in SL3.0
- Only 152 unplaced contigs in Chr 00 compared to 4,374 in SL3.0
- Better annotation of repeat regions in SL4.0

Annotation highlights ITAG4.0
- 34,075 protein coding genes in ITAG4.0
- Functional descriptions assigned to 29,532 genes
- ITAG4.0 has 4,794 novel genes
- 29,281 genes preserved from ITAG2.3

Sol Genomics Network The International Tomato Genome Sequencing Project was begun in 2004 by an international consortium including participants from Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States. The initial approach was to sequence only the euchromatic seque...

BTI recently welcomed Patrick Adebola and Asrat Amele of the AfricaYam Project to Ithaca. The AfricaYam Project is funded by the Gates Foundation. The project and its partners aim to increase yam productivity, while also reducing production costs and environmental impact by developing and deploying preferred varieties with higher yield, greater resistance to pests and diseases, and improved quality.

BTI has been involved in the project since its inception, creating the YamBase database. BTI has also conducted numerous trainings for YamBase user groups. BTI communicates with breeders on a regular basis and gets feedback on how to further improve the database's features.

“Our visit to BTI was very fruitful," said Adebola, Project Leader AfricaYam. "We were able to meet with the BTI group and made useful suggestions on how to better improve the usability of the database. Additional traits to be added to yam ontology were suggested. It is our hope that YamBase will be a one stop shop for farmers and project partners where requests for advanced clones and released yam varieties can be ordered on a click of a button."

Learn more about AfricaYam here: http://africayam.org/