Project description:The Ganges River dolphin (Platanista gangetica gangetica) (GRD) is classified as one of the most endangered of all cetaceans in the world and the second scarcest freshwater cetacean. The population is estimated to be less than 2,000 individuals. In Nepal's Narayani, Sapta Koshi, and Karnali river systems, survival of GRD continues to be threatened by various anthropogenic activities, such as dam construction and interactions with artisanal fisheries. A basic description of the geographic scope, economics, and types of gear used in these fisheries would help managers understand the fishery-dolphin interaction conflict and assist with developing potential solutions. The main goal was to provide new information on the artisanal fishing communities in Nepal. The specific objectives were to identify, compile, and investigate the demographics, economics, fishing characteristics, and perception of fishermen about GRD conservation in the Narayani, Sapta Koshi, and Karnali rivers so conservation managers can develop and implement a potential solution to the GRD-fishery interaction problem in Nepal. Based on 169 interviews, 79% of Nepalese fishermen indicated fishing was their primary form of income. Fishermen reported fishing effort was greater in summer than winter; greatest in the afternoon (14:30 hrs ± 0:27) and during low water level conditions; and gear was set 4.8 ± 0.2 days/week. Fishermen reported using eight different types of monofilament nets (gillnets and cast nets). Sixty percent used gillnets less than 10 m long, and nearly 30% preferred gillnets between 10 and 100 m long; a few used gillnets longer than 100 m. Most fishermen reported they believed education, awareness, and changing occupations were important for GRD conservation, but they indicated that alternative occupational options were currently limited in Nepal. Nepalese fishermen acknowledged that fisheries posed a risk to GRD, but they believed water pollution, and dam/irrigation developments were the greatest threats.

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.

			Action	DRS
	SRR28748673_1.fastq.gz	Fastqsanger.gz
	SRR28748673_2.fastq.gz	Fastqsanger.gz

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Asystasia gangetica

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