scholarly journals Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin

Gigabyte ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Alexandre Wagner Silva Hilsdorf ◽  
Marcela Uliano-Silva ◽  
Luiz Lehmann Coutinho ◽  
Horácio Montenegro ◽  
Vera Maria Fonseca Almeida-Val ◽  
...  
2021 ◽  
Author(s):  
Alexandre Wagner Silva Hilsdorf ◽  
Marcela Uliano-Silva ◽  
Luiz Lehmann Coutinho ◽  
Horácio Montenegro ◽  
Vera Maria Fonseca Almeida-Val ◽  
...  

ABSTRACTColossoma macropomum known as “tambaqui” is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and great adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39X coverage of long reads and polished to a QV=36 with 130X coverage of short reads. The genome was assembled into 1,269 scaffolds to a total of 1,221,847,006 bases, with a scaffold N50 size of 40 Mb where 93% of all assembled bases were placed in the largest 54 scaffolds that corresponds to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced which benefits any groups interested in exploring unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for novel insights about ecological and evolutionary facets and is a helpful resource for aquaculture purposes.


2021 ◽  
Author(s):  
Suyog Chaudhari ◽  
Erik Brown ◽  
Raul Quispe-Abad ◽  
Emilio Moran ◽  
Norbert Mueller ◽  
...  

<p>Given the ongoing and planned hydropower development projects in the Amazon River basin, appalling losses in biodiversity, river ecology and river connectivity are inevitable. These hydropower projects are proposed to be built in exceptionally endemic sites, setting records in environmental losses by impeding fish movement, altering flood pulse, causing large-scale deforestation, and increasing greenhouse gas emissions. With the burgeoning energy demand combined with the aforementioned negative impacts of conventional hydropower technology, there is an imminent need to re-think the design of hydropower to avoid the potentially catastrophic consequences of large dams. It is certain that the Amazon will undergo some major hydrological changes in the near future because of the compounded effects of climate change and proposed dams, if built with the conventional hydropower technology. In this study, we present a transformative hydropower outlook that integrates low-head hydropower technology (e.g., in-stream turbines) and multiple environmental aspects, such as river ecology and protected areas. We employ a high resolution (~2km) continental scale hydrological model called LEAF-Hydro-Flood (LHF) to assess the in-stream hydropower potential in the Amazon River basin. We particularly focus on quantifying the potential and feasibility of employing instream turbines in the Amazon instead of building large dams. We show that a significant portion of the total energy planned to be generated from conventional hydropower in the Brazilian Amazon could be harnessed using in-stream turbines that utilize kinetic energy of water without requiring storage. Further, we also find that implementing in-stream turbines as an alternative to large storage-based dams could prove economically feasible, since most of the environmental and social costs associated with dams are eliminated. Our results open multiple pathways to achieve sustainable hydropower development in the Amazon to meet the ever-increasing energy demands while minimizing hydrological, social, and ecological impacts. It also provides important insight for sustainable hydropower development in other global regions. The results presented are based on a manuscript under revision for Nature Sustainability.</p>


2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Victor Hugo da Motta Paca ◽  
Gonzalo E. Espinoza-Dávalos ◽  
Tim M. Hessels ◽  
Daniel Medeiros Moreira ◽  
Georges F. Comair ◽  
...  

Zootaxa ◽  
2020 ◽  
Vol 4820 (2) ◽  
pp. 323-336
Author(s):  
DARIO R. FAUSTINO-FUSTER ◽  
HERNÁN ORTEGA

Mastiglanis is a genus of heptapterid catfish represented by two valid species. These freshwater species are widely distributed along the Amazon, Orinoco, and Maroni River basins. However, a taxonomic review of specimens collected in the Putumayo and Nanay rivers, Amazon River basin in Peru revealed a new species of Mastiglanis. A morphological analysis was completed for morphometric (36 measurements) and meristic (20 counts) data. Osteological counts and descriptions were made from clear and stained specimens and x-rays images. The new species of Mastiglanis differs from M. asopos and M. durantoni by having a long pelvic fin, short snout, eight branched anal-fin rays, and a higher number of vertebrae and gill rakers. The distribution of the new species is restricted to the upper Amazon River basin.


2015 ◽  
Vol 13 (1) ◽  
pp. 1-46 ◽  
Author(s):  
Stephen J. Walsh ◽  
Frank Raynner Vasconcelos Ribeiro ◽  
Lúcia Helena Rapp Py-Daniel

The Neotropical catfish genus Tympanopleura, previously synonymized within Ageneiosus, is revalidated and included species are reviewed. Six species are recognized, two of which are described as new. Tympanopleura is distinguished from Ageneiosus by having an enlarged gas bladder not strongly encapsulated in bone; a prominent pseudotympanum consisting of an area on the side of the body devoid of epaxial musculature where the gas bladder contacts the internal coelomic wall; short, blunt head without greatly elongated jaws; and smaller adult body size. Species of Tympanopleura are distinguished from each other on the basis of unique meristic, morphometric, and pigmentation differences. Ageneiosus melanopogon and Tympanopleura nigricollis are junior synonyms of Tympanopleura atronasus. Tympanopleura alta is a junior synonym of Tympanopleura brevis. A lectotype is designated for T. brevis. Ageneiosus madeirensis is a junior synonym of Tympanopleura rondoni. Tympanopleura atronasus, T. brevis, T. longipinna, and T. rondoni are relatively widespread in the middle and upper Amazon River basin. Tympanopleura cryptica is described from relatively few specimens collected in the upper portion of the Amazon River basin in Peru and the middle portion of that basin in Brazil. Tympanopleura piperata is distributed in the upper and middle Amazon River basin, as well as in the Essequibo River drainage of Guyana.


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