SNP Discovery through
            <i>De Novo</i>
            Deep Sequencing Using the next Generation of DNA Sequencers

Waldbieser, Geoffrey C.

doi:10.1002/9780470958964.ch5

Cited by 1 publication

(3 citation statements)

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“…In these cases, from a sequencing project, individual reads can be assembled into consensus sequences called contigs that may serve as a pseudo-reference genome [146]. There are two…”

Section: Next Generation Sequencing (Ngs) In Molecular Marker Discoverymentioning

confidence: 99%

“…When using NGS technologies, the absence of a reference genome is one of the greatest barriers to discovery of molecular markers in non-model organisms. In these cases, from a sequencing project, individual reads can be assembled into consensus sequences called contigs that may serve as a pseudo-reference genome [146]. There are two alternative techniques for genome reduction to acquire sets of redundant contigs: transcriptome sequencing (RNA-seq) and restriction site-associated DNA (RAD-seq) [144].…”

Section: Next Generation Sequencing (Ngs) In Molecular Marker Discoverymentioning

confidence: 99%

“…Therefore, NGS technologies have become useful for de novo sequencing (sequencing without a reference genome) of eukaryotic genomes [145]. When using NGS technologies, the absence of a reference genome is one of the greatest barriers to discovery of molecular markers in non-model organisms.In these cases, from a sequencing project, individual reads can be assembled into consensus sequences called contigs that may serve as a pseudo-reference genome [146]. There are two…”

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confidence: 99%

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Genetic Applications in the Conservation of Neotropical Freshwater Fish

Mastrochirico-Filho¹,

Freitas²,

Ariede³

et al. 2018

Biological Resources of Water

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Neotropical fish correspond to approximately 30% of all fish species worldwide. The diversity of fish species found in Neotropical basins reflects variations in life-history strategies and exhibition of particular morphological, physiological and ecological attributes. These attributes are mainly related to different forms of feeding, life maintenance and reproduction. Today, fish populations are being threatened by anthropogenic actions that are having a visible impact on the natural state of continental aquatic ecosystems. The main causes are overfishing, non-native species introduction, reservoir-dam systems, mining, pollution and deforestation. The biology and population dynamics of the species are still unclear due to lack of research. Genetic tools can be useful resources for the conservation of Neotropical fish species in several ways. Molecular genetic markers are considered powerful tools to identify cryptic and hybrid fish and also allow the evaluation of the genetic variability and structure of populations of Neotropical ichthyofauna. Several analyses of molecular markers have been performed on Neotropical fish, including allozyme analysis, restriction fragment length polymorphisms in regions of DNA (RFLP), randomly amplified polymorphic DNA (AFLP), randomly amplified polymorphic DNA (RAPD), microsatellites, single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) markers. In order to analyse a high number of markers, next generation sequencing has allowed researchers to generate a large amount of genomic information that can be applied to the conservation of Neotropical fish.Keywords: molecular markers, genetic conservation, Neotropical ichthyofauna, overfishing, dam © 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Rivers of the Neotropical regionThe distribution of freshwater fish around the world was mediated by historical climatic and geological events at different time points. Today, each global region has distinct patterns of distribution due to physical barriers obstructing species dispersion, representing different tolerances to environmental variables [1]. The tropics of the American continent are well known for their high biodiversity. This is due to habitat heterogeneity and a complex geological history. The Neotropical region is a biogeographic region that comprises Central America (including the southern part of Mexico and the peninsula of Baja California), the south of Florida, the Caribbean and South America. The origin and evolution of the Neotropical region arose through a process of synergism between its fauna that experienced local rainfall variations and gradual climate change resulting in a mosaic of habitats controlled by river migrations, sea-level fluctuations, local dryness and local uplifts [2,3].Regional geo...

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“…In these cases, from a sequencing project, individual reads can be assembled into consensus sequences called contigs that may serve as a pseudo-reference genome [146]. There are two…”

Section: Next Generation Sequencing (Ngs) In Molecular Marker Discoverymentioning

confidence: 99%

Section: Next Generation Sequencing (Ngs) In Molecular Marker Discoverymentioning

confidence: 99%

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confidence: 99%

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