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Ambystoma macrodactylum

ABSTRACT: Ambystoma macrodactylum krausei (northern long-toed salamander) genomic and transcriptomic data

PROVIDER: PRJNA1001969 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR27920344_subreads.fastq.gz	Fastqsanger.gz
	SRR27920345_subreads.fastq.gz	Fastqsanger.gz
	SRR27920346_subreads.fastq.gz	Fastqsanger.gz
	SRR29059434_subreads.fastq.gz	Fastqsanger.gz
	SRR29059435_subreads.fastq.gz	Fastqsanger.gz

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Project description:Ambystoma macrodactylum krausei (northern long-toed salamander), aAmbMac1

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Comparative Transcriptomics of Limb Regeneration: Identification of Conserved Expression Changes Among Three Species of Ambystoma [microarray]

Project description:Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model – Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. maculatum. Salamanders were administered forelimb amputations and RNA was isolated and analyzed to identify 405 non-redundant genes that were commonly, differentially expressed 24 hours post amputation. Many of the upregulated genes are predicted to function in wound healing and developmental processes, while many of the downregulated genes are typically expressed in muscle. The conserved transcriptional changes identified in this study provide a high-confidence dataset for identifying factors that simultaneous orchestrate wound healing and regeneration processes in response to injury, and more generally for identifying genes that are essential for salamander limb regeneration.

2018-07-04 | GSE116615 | GEO

Comparative Transcriptomics of Limb Regeneration: Identification of Conserved Expression Changes Among Three Species of Ambystoma [RNA-Seq]

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Allele specific expression and gene regulation help explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense)

Project description:Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.

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Project description:Ambystoma mexicanum x (Ambystoma mexicanum x Ambystoma tigrinum) breed:mexicanum/tigrinum hybrid Raw sequence reads