scholarly journals Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

2019 ◽  
Author(s):  
Ashley Byrne ◽  
Megan A. Supple ◽  
Roger Volden ◽  
Kristin L. Laidre ◽  
Beth Shapiro ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Whole Blood ◽  
Polar Bear ◽  
Ursus Maritimus ◽  
Full Length ◽  
The Arctic ◽  
Model Organisms ◽  
Short Read ◽  
Full Length Cdna ◽  
Long Read

AbstractTranscriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9 based depletion method (Depletion of Abundant Sequences by Hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in-vitro prior to performing any short- and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion we discovered ~6,000 high-confidence isoforms and a number of novel genes. This indicates there is a high diversity of gene isoforms within Ursus maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.

scholarly journals Realizing the potential of full-length transcriptome sequencing

2019 ◽  
Vol 374 (1786) ◽  
pp. 20190097 ◽  
Author(s):  
Ashley Byrne ◽  
Charles Cole ◽  
Roger Volden ◽  
Christopher Vollmers
Keyword(s):  
Single Cell ◽  
Transcriptome Analysis ◽  
Transcriptome Sequencing ◽  
Model Organisms ◽  
Sequencing Technology ◽  
Short Read ◽  
Short Read Sequencing ◽  
Unicellular Eukaryotes ◽  
Long Read ◽  
Future Work

Long-read sequencing holds great potential for transcriptome analysis because it offers researchers an affordable method to annotate the transcriptomes of non-model organisms. This, in turn, will greatly benefit future work on less-researched organisms like unicellular eukaryotes that cannot rely on large consortia to generate these transcriptome annotations. However, to realize this potential, several remaining molecular and computational challenges will have to be overcome. In this review, we have outlined the limitations of short-read sequencing technology and how long-read sequencing technology overcomes these limitations. We have also highlighted the unique challenges still present for long-read sequencing technology and provided some suggestions on how to overcome these challenges going forward. This article is part of a discussion meeting issue ‘Single cell ecology’.

scholarly journals Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing

2021 ◽  
Author(s):  
Valentin Waschulin ◽  
Chiara Borsetto ◽  
Robert James ◽  
Kevin K. Newsham ◽  
Stefano Donadio ◽  
...  
Keyword(s):  
Genome Mining ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Full Length ◽  
Metagenomic Sequencing ◽  
Short Read ◽  
Short Read Sequencing ◽  
Rich Diversity ◽  
Long Read ◽  
The Rich

AbstractThe growing problem of antibiotic resistance has led to the exploration of uncultured bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read sequencing studies of samples from different environments have reported evidence of high biosynthetic gene cluster (BGC) diversity in metagenomes, indicating their potential for producing novel and useful compounds. However, recovering full-length BGC sequences from uncultivated bacteria remains a challenge due to the technological restraints of short-read sequencing, thus making assessment of BGC diversity difficult. Here, long-read sequencing and genome mining were used to recover >1400 mostly full-length BGCs that demonstrate the rich diversity of BGCs from uncultivated lineages present in soil from Mars Oasis, Antarctica. A large number of highly divergent BGCs were not only found in the phyla Acidobacteriota, Verrucomicrobiota and Gemmatimonadota but also in the actinobacterial classes Acidimicrobiia and Thermoleophilia and the gammaproteobacterial order UBA7966. The latter furthermore contained a potential novel family of RiPPs. Our findings underline the biosynthetic potential of underexplored phyla as well as unexplored lineages within seemingly well-studied producer phyla. They also showcase long-read metagenomic sequencing as a promising way to access the untapped genetic reservoir of specialised metabolite gene clusters of the uncultured majority of microbes.

scholarly journals Large-scale collection of full-length cDNA and transcriptome analysis inHevea brasiliensis

DNA Research ◽  
2017 ◽  
pp. dsw056 ◽  
Author(s):  
Yuko Makita ◽  
Kiaw Kiaw Ng ◽  
G. Veera Singham ◽  
Mika Kawashima ◽  
Hideki Hirakawa ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Large Scale ◽  
Full Length ◽  
Full Length Cdna

Trichinella and polar bears: a limited risk for humans

2017 ◽  
Vol 91 (4) ◽  
pp. 440-446 ◽  
Author(s):  
J. Dupouy-Camet ◽  
P. Bourée ◽  
H. Yera
Keyword(s):  
World War Ii ◽  
Polar Bear ◽  
Ursus Maritimus ◽  
The Arctic ◽  
Polar Bears ◽  
World War ◽  
Protected Species ◽  
Brown Bears ◽  
Limited Access ◽  
Human Trichinellosis

AbstractIn this review, we identified 63 cases reported since World War II of human trichinellosis linked to the consumption of parasitized polar bear (Ursus maritimus) meat. This low number contrasts to the numerous cases of human trichinellosis related to consumption of the meat of black (U. americanus) or brown bears (U. arctos). The prevalence of Trichinella infection is high in bears, but larval muscular burden is usually lower in polar bears compared to other bear species. Polar bears, therefore, seem to play a limited role in the transmission of trichinellosis to humans, as native residents living in the Arctic traditionally consume well-cooked bear meat, and travellers and foreign hunters have only limited access to this protected species due to the declining polar bear population.

Hydroxylated and methyl sulfone PCB metabolites in adipose and whole blood of polar bear (Ursus maritimus) from East Greenland

2004 ◽  
Vol 331 (1-3) ◽  
pp. 125-141 ◽  
Author(s):  
G SANDALA ◽  
C SONNEHANSEN ◽  
R DIETZ ◽  
D MUIR ◽  
K VALTERS ◽  
...  
Keyword(s):  
Whole Blood ◽  
Polar Bear ◽  
Ursus Maritimus ◽  
East Greenland ◽  
Pcb Metabolites

scholarly journals Testing the hypothesis that routine sea ice coverage of 3-5 mkm2 results in a greater than 30% decline in population size of polar bears (Ursus maritimus)

2017 ◽  
Author(s):  
Susan J Crockford
Keyword(s):  
Sea Ice ◽  
Population Size ◽  
Habitat Loss ◽  
Polar Bear ◽  
Population Decline ◽  
Ursus Maritimus ◽  
The Arctic ◽  
Polar Bears ◽  
Population Declines ◽  
Sea Ice Decline

The polar bear (Ursus maritimus) was the first species to be classified as threatened with extinction based on predictions of future conditions rather than current status. These predictions were made using expert-opinion forecasts of population declines linked to modeled habitat loss – first by the International Union for the Conservation of Nature (IUCN)’s Red List in 2006, and then by the United States Fish and Wildlife Service (USFWS) in 2008 under the Endangered Species Act (ESA), based on data collected to 2005 and 2006, respectively. Both assessments predicted significant population declines of polar bears would result by mid-century as a consequence of summer sea ice extent rapidly reaching 3-5 mkm2 on a regular basis: the IUCN predicted a >30% decline in total population, while the USFWS predicted the global population would decline by 67% (including total extirpation of ten subpopulations within two vulnerable ecoregions). Biologists involved in these conservation assessments had to make several critical assumptions about how polar bears might be affected by future habitat loss, since sea ice conditions predicted to occur by 2050 had not occurred prior to 2006. However, summer sea ice declines have been much faster than expected: low ice levels not expected until mid-century (about 3-5 mkm2) have occurred regularly since 2007. Realization of predicted sea ice levels allows the ‘rapid sea ice decline = population decline’ assumption for polar bears to be treated as a testable hypothesis. Data collected between 2007 and 2015 reveal that polar bear numbers have not declined as predicted and no subpopulation has been extirpated. Several subpopulations expected to be at high risk of decline remained stable and five showed increases in population size. Another at-risk subpopulation was not counted but showed marked improvement in reproductive parameters and body condition with less summer ice. As a consequence, the hypothesis that repeated summer sea ice levels of below 5 mkm2 will cause significant population declines in polar bears is rejected, a result that indicates the ESA and IUCN judgments to list polar bears as threatened based on future risks of habitat loss were scientifically unfounded and that similar predictions for Arctic seals and walrus may be likewise flawed. The lack of a demonstrable ‘rapid sea ice decline = population decline’ relationship for polar bears also potentially invalidates updated survival model outputs that predict catastrophic population declines should the Arctic become ice-free in summer.

scholarly journals Testing the hypothesis that routine sea ice coverage of 3-5 mkm2 results in a greater than 30% decline in population size of polar bears (Ursus maritimus)

2017 ◽  
Author(s):  
Susan J Crockford
Keyword(s):  
Sea Ice ◽  
Population Size ◽  
Habitat Loss ◽  
Polar Bear ◽  
Population Decline ◽  
Ursus Maritimus ◽  
The Arctic ◽  
Polar Bears ◽  
Population Declines ◽  
Sea Ice Decline

The polar bear (Ursus maritimus) was the first species to be classified as threatened with extinction based on predictions of future conditions rather than current status. These predictions were made using expert-opinion forecasts of population declines linked to modeled habitat loss – first by the International Union for the Conservation of Nature (IUCN)’s Red List in 2006, and then by the United States Fish and Wildlife Service (USFWS) in 2008 under the Endangered Species Act (ESA), based on data collected to 2005 and 2006, respectively. Both assessments predicted significant population declines of polar bears would result by mid-century as a consequence of summer sea ice extent rapidly reaching 3-5 mkm2 on a regular basis: the IUCN predicted a >30% decline in total population, while the USFWS predicted the global population would decline by 67% (including total extirpation of ten subpopulations within two vulnerable ecoregions). Biologists involved in these conservation assessments had to make several critical assumptions about how polar bears might be affected by future habitat loss, since sea ice conditions predicted to occur by 2050 had not occurred prior to 2006. However, summer sea ice declines have been much faster than expected: low ice levels not expected until mid-century (about 3-5 mkm2) have occurred regularly since 2007. Realization of predicted sea ice levels allows the ‘rapid sea ice decline = population decline’ assumption for polar bears to be treated as a testable hypothesis. Data collected between 2007 and 2015 reveal that polar bear numbers have not declined as predicted and no subpopulation has been extirpated. Several subpopulations expected to be at high risk of decline remained stable and five showed increases in population size. Another at-risk subpopulation was not counted but showed marked improvement in reproductive parameters and body condition with less summer ice. As a consequence, the hypothesis that repeated summer sea ice levels of below 5 mkm2 will cause significant population declines in polar bears is rejected, a result that indicates the ESA and IUCN judgments to list polar bears as threatened based on future risks of habitat loss were scientifically unfounded and that similar predictions for Arctic seals and walrus may be likewise flawed. The lack of a demonstrable ‘rapid sea ice decline = population decline’ relationship for polar bears also potentially invalidates updated survival model outputs that predict catastrophic population declines should the Arctic become ice-free in summer.

Polar Bear tagging in Alaska, 1968

Polar Record ◽  
1969 ◽  
Vol 14 (91) ◽  
pp. 459-462 ◽  
Author(s):  
J. W. Lentfer
Keyword(s):  
Life History ◽  
Air Force ◽  
Research Laboratory ◽  
Polar Bear ◽  
Ursus Maritimus ◽  
The Arctic ◽  
Polar Bears ◽  
The Us ◽  
History Information ◽  
Sport Fisheries

The Alaska Department of Fish and Game started marking Polar Bears (Ursus maritimus) in 1967 to obtain life history information (Lentfer, 1968), and continued in 1968 with the assistance of the US Bureau of Sport Fisheries and Wildlife. Special thanks for use of facilities are given to the Arctic Research Laboratory at Barrow and to the Tin City and Cape Lisburne Air Force stations. Participating biologists were J. W. Lentfer, L. H. Miller, S. H. Eide, and G. N. Bos of the Alaska Department of Fish and Game and J. W. Brooks of the US Bureau of Sport Fisheries and Wildlife.

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