Create Release 4---2022-05-11.md

Author: marcelakarey

sorghum/Release 4---2022-05-11.md

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+## SorghumBase Release 4.0
+### Released: May 2022
+## Summary
+
+For the first time, this release includes the genome of the poplar tree, a dicot model plant that like sorghum, is also studied for drought tolerance and bioenergy production. Poplar is the eighth outgroup species that together with the genomes of 18 sorghum varieties was used to generate 31,210 protein-coding gene family trees to support phylogenetic analyses and cross-species comparisons.
+
+The fourth release of SorghumBase also features a [mapping file](https://ftp.sorghumbase.org/release-4/Sorghum_BTx623_gene_id_mapping_v3.1.1.txt) for interconversion of sorghum gene identifiers of the forms Sobic.nnn, SORBI_3nnn, and SbNNN, and which is available at [SorghumBase’s FTP site](https://ftp.sorghumbase.org/).
+
+ Our publications database has grown to 348 papers, three of which have been highlighted in recent [News](https://www.sorghumbase.org/posts?categories=news) posts, together with relevant [Events](https://www.sorghumbase.org/events) for the sorghum research community.
+
+Core funding for the project is provided by the Agricultural Research Service of the [U.S. Department of Agriculture](http://www.usda.gov/) (USDA ARS 8062-21000-041-00D).
+
+## Release Information
+- [Overall Highlights](#overall-highlights)
+- [Databases](#databases)
+- [References](#references)
+
+## Overall Highlights
+
+**New Genomes**
+
+- [_Populus trichocarpa_](https://ensembl.sorghumbase.org/Populus_trichocarpa) (poplar tree)
+
+**New Data**
+
+- [Mapping file](https://ftp.sorghumbase.org/release-4/Sorghum_BTx623_gene_id_mapping_v3.1.1.txt) to interconvert sorghum gene identifiers of the forms Sobic.nnn, SORBI_3nnn, and SbNNN.
+
+**Other Updates and Highlights**
+
+- The link to [SorghumBase’s FTP site](https://ftp.sorghumbase.org/) has been made more prominent in the [Homepage](https://www.sorghumbase.org).
+
+- A modest increase (n=23) in relevant sorghum papers in our [Publications](https://www.sorghumbase.org/publications) database. Three of those are described in more detailed in news items that include author quotes, images and links to relevant websites.
+
+
+## Databases
+### Comparative Genomics
+
+[**Gene Trees.**](https://ensembl.sorghumbase.org/prot_tree_stats.html) A total of
+31,210 protein-coding gene family trees were constructed using the peptide encoded by
+the canonical transcript (i.e., a representative transcript for a given gene) for each
+of 829,431 individual genes (870,922 input proteins) from 26 plant genomes.
+
+### Variation
+
+No updates since release 3. Genetic variation data sets are available for over 17 million sorghum variants including almost 13 million single nucleotide
+polymorphisms (SNPs) [(Lozano _et al_, 2021)](https://sorghumbase.org/paper/comparative-evolutionary-genetics-of-deleterious-load-in-sorghum-and-maize) and a combined 4.3 million chemically induced by ethyl methanesulfonate (EMS) point mutations [(Addo-Quaye _et al_, 2018)](https://www.sorghumbase.org/paper/19942) and [(Jiao _et al_, 2016)](https://sorghumbase.org/paper/a-sorghum-mutant-resource-as-an-efficient-platform-for-gene-discovery-in-grasses); and nearly 6,000 QTLs from the [Sorghum QTL Atlas](https://aussorgm.org.au/).
+
+### Expression
+
+Gene expression data for the _S. bicolor_ BTx623 genome reference was curated and
+processed through the [EMBL-EBI Expression Atlas](https://www.ebi.ac.uk/gxa/plant/experiments). No other updates since release 2.
+
+### Pathways
+
+Orthology-based sorghum pathways for _S. bicolor_ BTx623 projected from curated Japonica rice pathways by [Gramene’s Plant Reactome](https://plantreactome.gramene.org/). No other updates since release 2.
+
+### Curated Publications
+
+Our database of sorghum research papers has grown to 348 publications. The integrated search interface includes matching papers when searching by author, keywords, pubmed ID, or any other text within the title or abstract. Publications in the database can be linked to news items and funding sources, for example: [(Lozano _et al_, 2021)](https://sorghumbase.org/paper/comparative-evolutionary-genetics-of-deleterious-load-in-sorghum-and-maize).
+
+
+## References
+
+Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al. 2006. _The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)_. Science. 313:1596-1604. 
+PMID: 16973872. doi: [10.1126/science.1128691](https://doi.org/10.1126/science.1128691).