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Aquatic and terrestrial environmental DNA signals reveal decoupling of blue-green communities along an urbanization gradient

ABSTRACT: This is the COI data from a study which looked at the biodiversity of aquatic and terrestrial invertebrates in the city of Zurich, Switzerland. Using environmental DNA, we characterized biodiversity structure and identified environmental drivers distinct to aquatic and terrestrial communities.

PROVIDER: PRJEB88517 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR14856500_1.fastq.gz	Fastqsanger.gz
	ERR14856500_2.fastq.gz	Fastqsanger.gz
	ERR14856600_1.fastq.gz	Fastqsanger.gz
	ERR14856600_2.fastq.gz	Fastqsanger.gz
	ERR14856700_1.fastq.gz	Fastqsanger.gz

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Project description:Study abstract: Axolotl salamanders (Ambystoma mexicanum) remain aquatic in their natural state, during which biomechanical forces on their diarthrodial limb joints are likely reduced relative to salamanders living on land. However, even as sexually mature adults, these amphibians can be induced to metamorphose into a weight-bearing terrestrial stage by environmental stress or the exogenous administration of thyroxine hormone. In some respects, this aquatic to terrestrial transition of axolotl salamanders through metamorphosis may model developmental and changing biomechanical skeletal forces in mammals during the prenatal to postnatal transition at birth and in the early postnatal period. To assess differences in the appendicular skeleton as a function of metamorphosis, anatomical and gene expression parameters were compared in skeletal tissues between aquatic and terrestrial axolotls that were the same age and genetically full siblings. The length of long bones and area of cuboidal bones in the appendicular skeleton, as well as the cellularity of cartilaginous and interzone tissues of femorotibial joints were generally higher in aquatic axolotls compared to their metamorphosed terrestrial siblings. A comparison of steady state mRNA transcripts encoding aggrecan core protein (ACAN), type II collagen (COL2A1), and growth and differentiation factor 5 (GDF5) in femorotibial cartilaginous and interzone tissues did not reveal any significant differences between aquatic and terrestrial axolotls. RNAseq samples: Total RNA was isolated from whole body tissue samples of Mexican axolotl salamanders (Ambystoma mexicanum) at the following developmental stages: Embryo at the tail bud stage, newly hatched larva, larva at the limb bud stage, juvenile at 8.5 centimeters, and adult using variations of guanidinium-based protocols. RNA quantity, purity, and integrity of both the individual samples and the resulting pool were determined with an Agilent 2100 Bioanalyzer using the Eukaryotic Total RNA nano series II analysis kit. The pooled RNA sample was poly-A selected and used for Illumina random priming directional library prep. Four lanes were sequenced only on one end providing single end reads and 4 lanes were sequenced at both ends giving paired-end reads. The library was sequenced on an Illumina HiSeq 2000 for 75bp reads producing 147,248,512 single end reads and 2 x 153,254,667 paired-end reads.

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Aquatic and terrestrial environmental DNA signals reveal decoupling of blue-green communities along an urbanization gradient

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