Abstract
This has been recommended and reviewed by F1000 here https://f1000.com/prime/735958664
1,027 Matching Annotations
- Mar 2020
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academic.oup.com academic.oup.com
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Abstract
This has been highlighted and reviewed by F1000 https://f1000.com/prime/718180400
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europepmc.org europepmc.org
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hypothes.is (use the hashtag/tag #chromosomenomenclature)
Please add comments directly on the key parts of the commentary you would like to raise any issues with.
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forensic investigations
Some examples of forensic entomology highlighted here https://www.wired.com/2013/10/when-crime-scene-evidence-crawls-away/
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academic.oup.com academic.oup.com
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Access to OUP resources on COVID-19, other coronaviruses, and related topics
30 leading publishers have all made their coronavirus related content open access in this manner https://wellcome.ac.uk/press-release/publishers-make-coronavirus-covid-19-content-freely-available-and-reusable
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gigasciencejournal.com gigasciencejournal.com
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Guest Blog: Data in the time of Coronavirus
This follows on from previous infectious disease modelling guest blogs from Dr Mike Dean on Ebola http://gigasciencejournal.com/blog/guest-blog-the-2014-ebola-epidemic-approaches-and-resources-to-slow-the-spread-of-infection/ and Zika http://gigasciencejournal.com/blog/guest-blog-mind-zika-data-gap/
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Table S3. Representative applications of genome editing. A summary of the representative applications in different organisms.
Using hypothes.is this information can also be updated via annotations here. e.g. adding mention of Twist biosciences, whose Oligo pools are utilized in many CRISPR applications including generation of CRISPR guide RNA (sgRNA) libraries. See https://www.twistbioscience.com/products/oligopools
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Table S1. Online tools for TALEN and CRISPR/Cas9. Collected online tools for TALEN and CRISPR/Cas9 are presented in this table. Updates can be accessed in GitHub [107]. Table S2. Commercial service for TALEN and CRISPR/Cas9. Collected commercial service for TALEN and CRISPR/Cas9 are presented in this table. Updates could can accessed in GitHub [107]. Table S3. Representative applications of genome editing. A summary of the representative applications in different organisms.
Given that new methods, kits, and services continue to be rapidly developed and updated, an editable version we set up on Github wiki, and readers encourage to update it. See https://github.com/gigascience/paper-chen2014/wiki
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Here, we present the first chromosome-level genome assembly and gene annotation of A. sinensis.
See some media coverage of this work here https://news.cgtn.com/news/2020-03-24/Scientists-release-genome-of-agarwood-tree-Aquilaria-sinensis-P7q0PlxXmo/index.html
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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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This must be achieved by sequencing and archiving huge numbers of microbial genomes, both from clinical cases and known environmental reservoirs, on a continual basis.
Even without reference genomes, 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
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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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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)
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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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- 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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