The white-blotched river stingray(Potamotrygon leopoldi)is a cartilaginous fish native to the Xingu River,a tributary of the Amazon River system.As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae...The white-blotched river stingray(Potamotrygon leopoldi)is a cartilaginous fish native to the Xingu River,a tributary of the Amazon River system.As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available,P.leopoldi provides the evolutionary details in fish phylogeny,niche adaptation,and skeleton formation.In this study,we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds,with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size.Our analysis shows that P.leopoldi is a slow-evolving fish that diverged from elephant sharks about 96 million years ago.Moreover,two gene families related to the immune system(immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes)exhibit expansion in P.leopoldi only.We also identified the Hox gene clusters in P.leopoldi and discovered that seven Hox genes shared by five representative fish species are missing in P.leopoldi.The RNA sequencing data from P.leopoldi and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to mammals.Our functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes(both P.leopoldi and Callorhinchus milii)could partly explain the absence of hard bone in their endoskeleton.Overall,this genome resource provides new insights into the niche adaptation,body plan,and skeleton formation of P.leopoldi,as well as the genome evolution in cartilaginous fishes.展开更多
Many invasive species exploit anthropogenically disturbed habitats, but most of those taxa evolved long before humans. Presumably, then, an ability to use natural （non-anthropogenic） disturbances pre-adapted invader...Many invasive species exploit anthropogenically disturbed habitats, but most of those taxa evolved long before humans. Presumably, then, an ability to use natural （non-anthropogenic） disturbances pre-adapted invaders to a world later degraded by people. Studies on invasive species in naturally disturbed habitats thus can clarify the ancestral niche of invaders. In the Australian tropics, metallic starlings Aplonis metallica nest communally in emergent rainforest trees during the wet-season, and invasive cane toads Rhinella marina join other predators （mammals, birds, reptiles, and other anurans） to exploit the food resources beneath those trees. Compared to conspecifics found along nearby roads through the forest, cane toads beneath bird-nesting trees occur at higher densities, and are smaller in body size. The sex ratio is female-biased, and recapture records suggest that fe- males may be philopatric at these sites （whereas recaptures were rare for both sexes found along the roads）. Some toads were found under the same trees in successive wet-seasons. Spooling showed that distances moved per night were similar along the road versus under the trees, but toads under trees showed lower net displacements. Diets also differed （based upon scat analysis）, with tree toads feeding more on beetles and less on ants. These nutrient-rich hotspots are ex- ploited primarily by adult females and juvenile toads, whereas adult males congregate at breeding sites. By magnifying pre-existing intraspecific divergences in habitat use, bird rookeries may en- hance population viability of cane toads by enabling critical age and sex classes to exploit food- rich patches that are rarely used by adult males.展开更多
基金financially supported by the National Natural Science Foundation of China(Grant No.31801049)the Major Science and Technology Innovation Program of Shanghai Municipal Education Commission,China(Grant No.2019-01-07-00-01-E00059)the Shanghai Nanmulin Biotechnology Company Limited.
文摘The white-blotched river stingray(Potamotrygon leopoldi)is a cartilaginous fish native to the Xingu River,a tributary of the Amazon River system.As a rare freshwater-dwelling cartilaginous fish in the Potamotrygonidae family in which no member has the genome sequencing information available,P.leopoldi provides the evolutionary details in fish phylogeny,niche adaptation,and skeleton formation.In this study,we present its draft genome of 4.11 Gb comprising 16,227 contigs and 13,238 scaffolds,with contig N50 of 3937 kb and scaffold N50 of 5675 kb in size.Our analysis shows that P.leopoldi is a slow-evolving fish that diverged from elephant sharks about 96 million years ago.Moreover,two gene families related to the immune system(immunoglobulin heavy constant delta genes and T-cell receptor alpha/delta variable genes)exhibit expansion in P.leopoldi only.We also identified the Hox gene clusters in P.leopoldi and discovered that seven Hox genes shared by five representative fish species are missing in P.leopoldi.The RNA sequencing data from P.leopoldi and other three fish species demonstrate that fishes have a more diversified tissue expression spectrum when compared to mammals.Our functional studies suggest that lack of the gc gene encoding vitamin D-binding protein in cartilaginous fishes(both P.leopoldi and Callorhinchus milii)could partly explain the absence of hard bone in their endoskeleton.Overall,this genome resource provides new insights into the niche adaptation,body plan,and skeleton formation of P.leopoldi,as well as the genome evolution in cartilaginous fishes.
文摘Many invasive species exploit anthropogenically disturbed habitats, but most of those taxa evolved long before humans. Presumably, then, an ability to use natural （non-anthropogenic） disturbances pre-adapted invaders to a world later degraded by people. Studies on invasive species in naturally disturbed habitats thus can clarify the ancestral niche of invaders. In the Australian tropics, metallic starlings Aplonis metallica nest communally in emergent rainforest trees during the wet-season, and invasive cane toads Rhinella marina join other predators （mammals, birds, reptiles, and other anurans） to exploit the food resources beneath those trees. Compared to conspecifics found along nearby roads through the forest, cane toads beneath bird-nesting trees occur at higher densities, and are smaller in body size. The sex ratio is female-biased, and recapture records suggest that fe- males may be philopatric at these sites （whereas recaptures were rare for both sexes found along the roads）. Some toads were found under the same trees in successive wet-seasons. Spooling showed that distances moved per night were similar along the road versus under the trees, but toads under trees showed lower net displacements. Diets also differed （based upon scat analysis）, with tree toads feeding more on beetles and less on ants. These nutrient-rich hotspots are ex- ploited primarily by adult females and juvenile toads, whereas adult males congregate at breeding sites. By magnifying pre-existing intraspecific divergences in habitat use, bird rookeries may en- hance population viability of cane toads by enabling critical age and sex classes to exploit food- rich patches that are rarely used by adult males.
