Malaclemys terrapin centrata
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA992388 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| Other | ||||
| SRR25299035_1.fastq.gz | Fastqsanger.gz | |||
| SRR25299037_1.fastq.gz | Fastqsanger.gz | |||
| SRR25299037_2.fastq.gz | Fastqsanger.gz |
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Project description:The initial discovery in May 2009 of eelgrass (Zostera marina) seeds in fecal samples of wild-caught northern diamondback terrapins (Malaclemys terrapin terrapin) was the first field evidence of eelgrass seed ingestion in this species. This finding suggested the potential of terrapins as seed dispersers in eelgrass beds, which we sampled for two additional years (2010 and 2011). Seeds were only found in feces of terrapins captured prior to June 8 in all three years, coinciding with eelgrass seed maturation and release. Numbers of seeds in terrapin feces varied annually and decreased greatly in 2011 after an eelgrass die off in late 2010. The condition of seeds in terrapin feces was viable-mature, germinated, damaged, or immature. Of terrapins captured during time of seed release, 97% were males and juvenile females, both of which had head widths <30 mm. The fraction of individuals with ingested seeds was 33% for males, 35% for small females, and only 6% for large (mature) females. Probability of seed ingestion decreased exponentially with increasing terrapin head width; only males and small females (head width <30 mm) were likely to be vectors of seed dispersal. The characteristic that diamondback terrapins have well-defined home ranges allowed us to estimate the number of terrapins potentially dispersing eelgrass seeds annually. In seagrass beds of the Goodwin Islands region (lower York River, Virginia), there were 559 to 799 terrapins, which could disperse between 1,341 and 1,677 eelgrass seeds annually. These would represent a small proportion of total seed production within a single seagrass bed. However, based on probable home range distances, terrapins can easily traverse eelgrass meadow boundaries, thereby dispersing seeds beyond the bed of origin. Given the relatively short dispersion distance of eelgrass seeds, the diamondback terrapin may be a major source of inter-bed seed dispersal and genetic diversity.
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Project description:This study focused on an estuarine wildlife species exhibiting high site fidelity and ubiquitous distribution in coastal environments along the Atlantic and Gulf coasts of the United States to monitor per- and polyfluoroalkyl substances (PFAS). A total of 75 diamondback terrapin (Malaclemys terrapin) plasma samples were collected from five creeks associated with Kiawah (Oyster Creek, Fiddler Creek, Sandy Creek, Gnat Creek) and Edisto (Townsend Creek) islands in Charleston County, South Carolina and investigated for 15 legacy PFAS. Of those, PFHxS was the only PFAS found in all terrapin plasma samples. Four additional PFAS were routinely detected (greater than 90% of the samples) and were included in statistical analyses: PFOS, PFNA, PFDA, and PFUnA. Sex-differences were observed for two creeks with male plasma containing higher PFAS than female plasma (PFHxS at Townsend Creek, PFOS at Oyster Creek). Sex-specific site differences in PFAS concentrations were observed primarily for males, suggesting male terrapins may be more sensitive indicators of localized contaminant profiles than females. Three PFAS were observed to have negative correlations with body mass: PFOS in males (p = 0.045, tau = -0.220), PFNA in males (p = 0.016, tau = -0.269), and PFHxS in both males (p = 0.007, tau = -0.302) and females (p = 0.001, tau = -0.379). No relationships for body mass and PFDA and PFUnA were observed.
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Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
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