Release Notes

This page details updates to Service Usage. You can periodically check this page for announcements about new or updated features, bug fixes, known issues, and deprecated functionality.

July 2023

Datasets

4 new chromosome-scale genomes were added:

• Musella lasiocarpa (early advance before publication)
• Ensete ventricosum (retrieved and transformed from NCBI)
• Musa Textilis 'abaca' and Musa Fe'i Utafun (early advance before publication)

Feature

• Blast search updated and New blast server
• Gene editing tool, Crispor: please don't hesitate to send feedback
• Jbrowse and Synvisio updated with new chromosome-scale genomes

January 2023

Feature

• Translocation : Musa chromosome structure database

Datasets

• Martin et al 2022 : Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea. Plant Journal

September 2022

Features

• Gene search tool was upgraded with the latest version of Tripal MegaSearch
• Blast search supports now multiple species selection and was extended with additional banks (other Musaceae, Ginger, Rice and Arabidopsis genomes).
• GO enrichment tool was updated with GO annotation from new genomes.
• Synteny viewer was updated with 2 new chromosomes scales genomes (Fe'i and beccarii)
• JBrowse instance added for 3 new genomes (Ensete ventricosum, Fe'i and beccarii)

Datasets

2 new chromosome scale genomes were added

• Musa Fe'i
• Musa beccarii (early advance before publication)

June 2022

Features

• A GO enrichment tool was added
• A RNA-seq count display was added with 3 transcriptomics studies

Datasets

Public RNA-seq added to transcriptomics data viewer

• Cenci A et al. 2019. Effect of paleopolyploidy and allopolyploidy on gene expression in banana. BMC Genomics 20: 244.
• Zorrilla-Fontanesi, Y., Rouard, M., Cenci, A. et al. Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. Sci Rep 6, 22583 (2016).
• Zhang, L., Cenci, A., Rouard, M. et al. Transcriptomic analysis of resistant and susceptible banana corms in response to infection by Fusarium oxysporum f. sp. cubense tropical race 4. Sci Rep 9, 8199 (2019).
   

May 2022

Features

• GeMo is now available to explore genome ancestry mosaics of published related studies
• MusaCyc, supported by pathwaytools was added
• Synvisio was updated for easier multiple comparisons between genomes
• Diane, a tool to perform Differential gene expression analyses, was added

Datasets

• List of corresponding gene between DH Pahang v2 and v4 is available

April 2022

• Jbrowse tracks restored
• Liftoffs tracks added
• Panache updated with new software version

May 2021

• Servers experienced technical difficulties preventing users to perform BLAST searches, Primer design or file download
• Display of multiple alignment and phylogenetic trees and some Jbrowse tracks were affected.
• Download section is still uncomplete.

April 2021

Datasets

• Release of the M. acuminata malaccensis DH Pahang v4
  • Belser et al. 2021 Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing. BioRxiv
• Release of the first Pangenome in musaceae (Musa and Ensete)
  • Rijzaani et al. 2021 The pangenome of banana highlights differences between genera and genomes. The plant genome (in press)

Features

• Panache is now available to explore the Musaceae pangenome
• JBrowse instance for the Musaceae pangenome and DH Pahang v4
• Blast search extended to the Musaceae pangenome and DH Pahang v4

February 2021

Datasets

• InterPro ang Gene ontology annotations updated for Musa acuminata 'DH Pahang' and made available as text and GFF file in download

December 2020

Public v3 release: A major new release was set on line with the followling elements:

Features

• Synvisio is now available to compare chromosome scale assemblies.
• GIGWA is available with multiple genotyping studies
• Blast and Jbrowse extended to 9 genomes
• New section for gene families (example)
• Cross-links to GreenPhylDB and South green instances of Genomics added
• New page for list of contributors created
• The Term of service was updated

Datasets

• Public RNAseq mapped to A and/or B genomes and added as Jbrowse tracks
  • Wang Z et al. 2019. Musa balbisiana genome reveals subgenome evolution and functional divergence. Nature Plants: 1.
  • Cenci A et al. 2019. Effect of paleopolyploidy and allopolyploidy on gene expression in banana. BMC Genomics 20: 244.
• Public Resquencing data mapped to A and/or B genomes and added as Jbrowse tracks
  • Sambles C et al. 2020. Genome sequencing data for wild and cultivated bananas, plantains and abacá. Data in Brief
  • Busche M et al. 2020. Genome Sequencing of Musa acuminata Dwarf Cavendish Reveals a Duplication of a Large Segment of Chromosome 2. G3: Genes, Genomes, Genetics 10: 37–42.
  • Wang Z et al. 2019. Musa balbisiana genome reveals subgenome evolution and functional divergence. Nature Plants: 1.
• Public genotyping data inserted in Gigwa
  • Martin G et al. 2020. Chromosome reciprocal translocations have accompanied subspecies evolution in bananas. The Plant Journal.
  • Martin G et al. 2020. Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana. The Plant Journal 102: 1008–1025.
  • Nyine M et al. 2019. Association genetics of bunch weight and its component traits in East African highland banana (Musa spp. AAA group). Theoretical and Applied Genetics 132: 3295–3308.
• Ensete Glaucum Genome is available before publication
• New Download sections with access to sequence, BAM, CRAM, VCF and other files including transcriptomes assemblies from
  • Sarah G et al. 2017. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Resources 17: 565–580