Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing ...
Antarctica poses numerous challenges to life such as cold shock, low nutrient concentrations and periodic desiccation over a wide range of extreme temperatures. Cyanobacteria survive this harsh environment having evolved adaptive metabolic plasticity to become the dominant primary producers. The typ...
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Dryad
2023
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Online Access: | https://dx.doi.org/10.5061/dryad.k98sf7mb1 https://datadryad.org/stash/dataset/doi:10.5061/dryad.k98sf7mb1 |
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ftdatacite:10.5061/dryad.k98sf7mb1 2024-02-04T09:53:30+01:00 Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing ... Dextro, Rafael B. Delbaje, Endrews Freitas, Paloma N. N. Geraldes, Vanessa Pinto, Ernani Long, Paul F. Fiore, Marli F. 2023 https://dx.doi.org/10.5061/dryad.k98sf7mb1 https://datadryad.org/stash/dataset/doi:10.5061/dryad.k98sf7mb1 en eng Dryad https://dx.doi.org/10.1099/ijs.0.070078-0 https://dx.doi.org/10.5281/zenodo.7650767 Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 FOS Biological sciences cyanobacterium phylogeny Antarctica HPLC-MS chlorophyll a Carotenoids genome Dataset dataset 2023 ftdatacite https://doi.org/10.5061/dryad.k98sf7mb110.1099/ijs.0.070078-010.5281/zenodo.7650767 2024-01-05T04:51:50Z Antarctica poses numerous challenges to life such as cold shock, low nutrient concentrations and periodic desiccation over a wide range of extreme temperatures. Cyanobacteria survive this harsh environment having evolved adaptive metabolic plasticity to become the dominant primary producers. The type strain cyanobacterium Halotia branconii CENA392 was isolated from an Antarctic intertidal seashore. The complete circular genome of this strain is presented herein, which was assembled using long sequence reads. The genome encoded some stress-related genes associated with low-temperature adaptation and biosynthesis of mycosporine-like amino acid (MAA) photoprotective compounds. Empirical experimentation demonstrated constitutive production of the MAA porphyra-334 and total carotenoids without exposure to low temperatures or ultraviolet radiation stress. Phylogenetic analysis provided insights on the taxonomic placement and the evolutionary history of some annotated genes. These data exemplify the importance of ... : Obtaining the genome: Bacteria growing over the surface of H. branconii CENA392 were removed by serial washing following a procedure reported by Delbaje et al. (2021). Total gDNA was extracted from washed cyanobacterial cells using an All-Prep DNA/RNA Mini kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. DNA stable Plus (Biomatrica, San Diego, USA) was added at a final volume of 25 %(v/v) to preserve integrity of the gDNA during lyophilization. The lyophilized gDNA was sent for whole-genome sequencing to the Joint Genome Institute (Berkley, CA, USA; JGI Project ID: 1338759). A PacBio SMRTbell library was prepared for circular consensus sequencing using a PacBio RS platform. The reads were filtered using BBMap v38.90 (Bushnell et al. 2017) with the icecreamfinder.sh program using default parameters. De novo genome assembly was performed with default parameters using Flye v2.9 (Kolmogorov et al. 2019). The assembled scaffolds were classified with Kaiju v1.7.2 (Menzel et al., 2016) to ... Dataset Antarc* Antarctic Antarctica DataCite Metadata Store (German National Library of Science and Technology) Antarctic Bushnell ENVELOPE(-150.800,-150.800,-85.600,-85.600) Menzel ENVELOPE(-96.083,-96.083,-72.067,-72.067) |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
English |
topic |
FOS Biological sciences cyanobacterium phylogeny Antarctica HPLC-MS chlorophyll a Carotenoids genome |
spellingShingle |
FOS Biological sciences cyanobacterium phylogeny Antarctica HPLC-MS chlorophyll a Carotenoids genome Dextro, Rafael B. Delbaje, Endrews Freitas, Paloma N. N. Geraldes, Vanessa Pinto, Ernani Long, Paul F. Fiore, Marli F. Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing ... |
topic_facet |
FOS Biological sciences cyanobacterium phylogeny Antarctica HPLC-MS chlorophyll a Carotenoids genome |
description |
Antarctica poses numerous challenges to life such as cold shock, low nutrient concentrations and periodic desiccation over a wide range of extreme temperatures. Cyanobacteria survive this harsh environment having evolved adaptive metabolic plasticity to become the dominant primary producers. The type strain cyanobacterium Halotia branconii CENA392 was isolated from an Antarctic intertidal seashore. The complete circular genome of this strain is presented herein, which was assembled using long sequence reads. The genome encoded some stress-related genes associated with low-temperature adaptation and biosynthesis of mycosporine-like amino acid (MAA) photoprotective compounds. Empirical experimentation demonstrated constitutive production of the MAA porphyra-334 and total carotenoids without exposure to low temperatures or ultraviolet radiation stress. Phylogenetic analysis provided insights on the taxonomic placement and the evolutionary history of some annotated genes. These data exemplify the importance of ... : Obtaining the genome: Bacteria growing over the surface of H. branconii CENA392 were removed by serial washing following a procedure reported by Delbaje et al. (2021). Total gDNA was extracted from washed cyanobacterial cells using an All-Prep DNA/RNA Mini kit (Qiagen, Hilden, Germany) according to manufacturer’s instructions. DNA stable Plus (Biomatrica, San Diego, USA) was added at a final volume of 25 %(v/v) to preserve integrity of the gDNA during lyophilization. The lyophilized gDNA was sent for whole-genome sequencing to the Joint Genome Institute (Berkley, CA, USA; JGI Project ID: 1338759). A PacBio SMRTbell library was prepared for circular consensus sequencing using a PacBio RS platform. The reads were filtered using BBMap v38.90 (Bushnell et al. 2017) with the icecreamfinder.sh program using default parameters. De novo genome assembly was performed with default parameters using Flye v2.9 (Kolmogorov et al. 2019). The assembled scaffolds were classified with Kaiju v1.7.2 (Menzel et al., 2016) to ... |
format |
Dataset |
author |
Dextro, Rafael B. Delbaje, Endrews Freitas, Paloma N. N. Geraldes, Vanessa Pinto, Ernani Long, Paul F. Fiore, Marli F. |
author_facet |
Dextro, Rafael B. Delbaje, Endrews Freitas, Paloma N. N. Geraldes, Vanessa Pinto, Ernani Long, Paul F. Fiore, Marli F. |
author_sort |
Dextro, Rafael B. |
title |
Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing ... |
title_short |
Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing ... |
title_full |
Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing ... |
title_fullStr |
Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing ... |
title_full_unstemmed |
Metadata for: Environmental adaptations by the intertidal Antarctic cyanobacterium Halotia branconii CENA392 as revealed using long-read genome sequencing ... |
title_sort |
metadata for: environmental adaptations by the intertidal antarctic cyanobacterium halotia branconii cena392 as revealed using long-read genome sequencing ... |
publisher |
Dryad |
publishDate |
2023 |
url |
https://dx.doi.org/10.5061/dryad.k98sf7mb1 https://datadryad.org/stash/dataset/doi:10.5061/dryad.k98sf7mb1 |
long_lat |
ENVELOPE(-150.800,-150.800,-85.600,-85.600) ENVELOPE(-96.083,-96.083,-72.067,-72.067) |
geographic |
Antarctic Bushnell Menzel |
geographic_facet |
Antarctic Bushnell Menzel |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_relation |
https://dx.doi.org/10.1099/ijs.0.070078-0 https://dx.doi.org/10.5281/zenodo.7650767 |
op_rights |
Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode cc0-1.0 |
op_doi |
https://doi.org/10.5061/dryad.k98sf7mb110.1099/ijs.0.070078-010.5281/zenodo.7650767 |
_version_ |
1789966255436857344 |