Create PanOryza Genomes Release 3.1---2022-03-09.md

Author: marcelakarey

oryza/PanOryza Genomes Release 3.1---2022-03-09.md

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+## Oryza PanGenome Release 3.1
+### Released: March 2022
+## Summary
+
+Gramene's Oryza Pan-Genome (https://oryza.gramene.org) is a web portal for comparative plant genomics focused on rice varieties. In its release 3.1, the gene family trees were rebuilt using the same species included in release 3.0 but with superior quality. 
+
+A total of 37,423 GeneTree families were constructed comprising 1,134,514 individual genes (1,187,461 input proteins). See updated stats [here](https://oryza-ensembl.gramene.org/prot_tree_stats.html). 
+
+The new trees include the same species as the prior release 3.0: 25 Oryza genomes, _Leersia perrieri_ (the most closely related species to the Oryza in the Oryzeae tribe), 6 plant outgroups (B73 maize, sorghum, Arabidopsis thaliana, grapevine, a vascular plant, and a single-celled green algae) and Drosophila, in order to allow comparisons between higher eukaryotes, lower plants, and the model Arabidopsis in the Oryza pan-genome. 
+
+Core funding for the project was provided by the National Science Foundation (NSF IOS-1127112) and the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 8062-21000-041-00D).  
+
+## Release Information
+- [Overall Highlights](#overall-highlights)
+- [Databases](#databases)
+- [Statistics](#statistics)
+- [References](#references)
+
+## Overall Highlights {#overall-highlights}
+
+Our comparative genomics collection was updated to include a total of 37,423 protein-coding gene family trees using Ensembl Compara software (Herrero _et al_, 2016). The new trees were constructed with 1,187,461 input proteins from 1,134,514 individual genes from the 25 Oryza genomes, _L. perrieri_, and 7 outgroup species (Arabidopsis thaliana, sorghum, grapevine, Chlamydomonas, Selaginella, B73 maize in assembly versions 4 and 5, and Drosophila) in the Oryza pan-genome.
+
+
+## Databases {#databases}
+### Comparative Genomics
+
+[**Gene Trees.**](https://oryza-ensembl.gramene.org/prot_tree_stats.html) A total of 37,423 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 1,134,514 individual genes (1,187,461 input proteins) from 33 genomes.
+
+[**Whole-Genome Alignments**](https://oryza-ensembl.gramene.org/compara_analyses.html). Please see [release notes for version 3.0](https://oryza.gramene.org/news).
+
+[**Synteny**](https://oryza-ensembl.gramene.org/compara_analyses.html). Please see [release notes for version 3.0](https://oryza.gramene.org/news).
+
+### Variation
+
+Please see [release notes for version 3.0](https://oryza.gramene.org/news).
+
+### Expression
+
+Please see [release notes for version 3.0](https://oryza.gramene.org/news).
+
+### Pathways
+
+Please see [release notes for version 3.0](https://oryza.gramene.org/news).
+
+## References {#references}
+
+- Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, et al. "Ensembl comparative genomics resources." Database. 2016;2016. doi:10.1093/database/bav096
+