MERS coronavirus
Mining metagenomes for coronavirus sequences has become particularly topical in 2020 (see the Pangolin 2019-nCoV-like coronavirus example https://doi.org/10.1101/2020.02.08.939660)
1,017 Matching Annotations
- Mar 2020
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academic.oup.com academic.oup.com
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RNA viruses
As this works with RNA viruses it has been made part of the "Free access to OUP resources on coronavirus and related topics" collection on the Oxford University Press website https://academic.oup.com/journals/pages/coronavirus
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direct RNA sequencing. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome to date.
This approach of using Oxford Nanopore direct-RNA sequencing for viruses has now been carried out on the SARSCov2/COVID19 causing coronavirus. See https://doi.org/10.1101/2020.03.05.976167
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galaxy-based viral genome assembly pipeline
This galaxy + viral genome assembly approach has been updated in 2020 to analyze and store COVID19/SARSCov2 data https://covid19.galaxyproject.org/
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swine flu
Jennifer Gardy discusses the groundbreaking H1N1 crowdsourcing efforts in her TEDx talk here (with lots of lessons for the coronavirus outbreak a decade later) https://www.youtube.com/watch?v=LmAugMSJ1-Y
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Escherichia coli O104: H4
See more in GigaBlog about the novel "tweenome" method of datasharing for this project http://gigasciencejournal.com/blog/notes-from-an-e-coli-tweenome-lessons-learned-from-our-first-data-doi/
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excessively exploited
Despite being the reason Hong Kong was known as the "fragrant harbour" these tree's are heavily poached and nearly extinct in the wild in Hong Kong http://www.bbc.com/travel/story/20170306-the-scent-thats-pricier-than-gold
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- Feb 2020
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Taylor J Noble
Taylor Noble video abstract: https://youtu.be/NQjmxE4Frxo
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Ocean Sampling Day
One of the authors has presented a talk on the Citizen Science offshoot of this project here https://youtu.be/t6WpLbd0Nf8
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Critical Assessment of Metagenome Interpretation (CAMI) initiative
See the CAMI website https://data.cami-challenge.org/
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Since 1996
The Fort Lauderdale agreement followed these up in 2003, but there has been a long gap since then https://www.genome.gov/10506537/reaffirmation-and-extension-of-nhgri-rapid-data-release-policies
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- Oct 2019
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www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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detections in surrounding states
And it has just been reported in Connecticut https://www.nbcconnecticut.com/news/local/Destructive-Spotted-Lanternfly-Spotted-in-Connecticut-563208361.html
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Here, we present a 2.3 Gb de novo genome assembly of a field-collected adult female spotted lanternfly (Lycorma delicatula) using a single Pacific Biosciences SMRT Cell.
See the press release here discussing the novelty of this data https://www.eurekalert.org/pub_releases/2019-10/udoa-fgo101619.php
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Eudyptes moseleyi Northern rockhopper Wild Amsterdam Island NRP 118–1 May 2016
Data in GigaDB here: http://dx.doi.org/10.5524/102171
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europepmc.org europepmc.org
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Saccharomyces cerevisiae
See https://www.ncbi.nlm.nih.gov/genome/?term=Saccharomyces%20cerevisiae[Organism]&cmd=DetailsSearch
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African eggplant
Also know as the scarlet eggplant or bitter tomato.
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“orphan crop”
The African eggplant is a good example of the work of the Africa Orphan Crop consortium and many of the authors are consortium members. You can read more on the first genomes released in GigaBlog here: http://gigasciencejournal.com/blog/democratising-data-aocc/
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