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Open accessJournal ArticleDOI: 10.1038/S41467-021-21733-Z

A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution

04 Mar 2021-Nature Communications (Nature Publishing Group)-Vol. 12, Iss: 1, pp 1447-1447
Abstract: Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. Cave-dwelling Astyanax mexicanus populations are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability across cavefish populations to gain insight into this potential source of cave adaptation. The surface fish genome reference now provides a more complete resource for comparative, functional and genetic studies of drastic trait differences within a species.

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Topics: Cavefish (57%), Quantitative trait locus (55%), Candidate gene (54%) ... read more

7 results found

Open accessJournal ArticleDOI: 10.3389/FNBEH.2021.659615
Abstract: Aggressive behavior is thought to have evolved as a strategy for gaining access to resources such as territory, food, and potential mates. Across species, secondary sexual characteristics such as competitive aggression and territoriality are considered male-specific behaviors. However, although female-female aggression is often a behavior that is displayed almost exclusively to protect the offspring, multiple examples of female-female competitive aggression have been reported in both invertebrate and vertebrate species. Moreover, cases of intersexual aggression have been observed in a variety of species. Genetically tractable model systems such as mice, zebrafish, and fruit flies have proven extremely valuable for studying the underlying neuronal circuitry and the genetic architecture of aggressive behavior under laboratory conditions. However, most studies lack ethological or ecological perspectives and the behavioral patterns available are limited. The goal of this review is to discuss each of these forms of aggression, male intrasexual aggression, intersexual aggression and female intrasexual aggression in the context of the most common genetic animal models and discuss examples of these behaviors in other species.

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Topics: Aggression (63%)

3 Citations

Open accessPosted ContentDOI: 10.1101/2021.05.05.442716
05 May 2021-bioRxiv
Abstract: The vertebrate retinas originate from a specific anlage in the anterior neural plate called the eyefield. The eyefield shares its anterior border with the prospective telencephalon and is in contact ventrally and posteriorly with hypothalamic and diencephalic precursors. Eyefield identity is conferred by a set of "eye transcription factors", whose combinatorial expression has not been precisely characterized. Here, we use the dimorphic teleost species Astyanax mexicanus, which develops proper eyes in the wild type and smaller colobomatous eyes in the blind cavefish embryo, to unravel the molecular anatomy of the eyefield and its micro-evolutionary variations in the two Astyanax morphs. Using a series of markers (Rx3, Pax6, CxCr4b, Zic1, Lhx2, Emx3, Nkx2.1), we draw a comparative 3D expression map at the end of gastrulation/onset of neurulation, which highlights hyper-regionalization of the eyefield into sub-territories of distinct sizes, shapes, cell identities and putative fates along the three body axes. We also discover sub-domains within the prospective telencephalon, and we characterize cell identities at the frontiers of the eyefield. Analyses at the tissue scale and single cell level show variations in volumes and shapes of eyefield subdivisions as well as cellular gene expression levels and identity changes in cavefish. The ventro-medial border and the anterior border of the eyefield contain cells co-expressing hypothalamic and telencephalic marker, respectively, in cavefish embryos. Altogether, we provide a new model of eyefield patterning in 3D and suggest a developmental origin for the emergence of the coloboma phenotype in the natural mutant cavefish embryo.

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Topics: Cavefish (65%), Neural plate (51%), Neurulation (50%)

1 Citations

Open accessPosted ContentDOI: 10.1101/2021.09.08.459456
09 Sep 2021-bioRxiv
Abstract: Colossoma 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.

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Topics: Reference genome (56%), Tambaqui (54%)

Open accessJournal ArticleDOI: 10.1016/J.CONB.2021.08.004
Abstract: All animals carefully studied sleep, suggesting that sleep as a behavioral state exists in all animal life. Such evolutionary maintenance of an otherwise vulnerable period of environmental detachment suggests that sleep must be integral in fundamental biological needs. Despite over a century of research, the knowledge of what sleep does at the tissue, cellular or molecular levels remain cursory. Currently, sleep is defined based on behavioral criteria and physiological measures rather than at the cellular or molecular level. Physiologically, sleep has been described as two main states, non-rapid eye moment (NREM) and REM/paradoxical sleep (PS), which are defined in the neocortex by synchronous oscillations and paradoxical wake-like activity, respectively. For decades, these two sleep states were believed to be defining characteristics of only mammalian and avian sleep. Recent work has revealed slow oscillation, silencing, and paradoxical/REM-like activities in reptiles, fish, flies, worms, and cephalopods suggesting that these sleep dynamics and associated physiological states may have emerged early in animal evolution. Here, we discuss these recent developments supporting the conservation of neural dynamics (silencing, oscillation, paradoxical activity) of sleep states across phylogeny.

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Journal ArticleDOI: 10.1007/S11160-021-09691-7
Abstract: The living fishes span a unique and interesting set of animals because of their vast diversity, morphology, ecology, genetics and genomics, and higher importance to biology, economy and culture. During the past decade, the remarkable increase in fish genome sequencing has revolutionized comparative and evolutionary genomics, with the outcome of stimulating insights into vertebrate genome biology. Fish genomics has been transformed rapidly, with the availability of high-quality chromosome level genome assemblies and large collections of sequencing datasets, which are roadmaps for striking discoveries. Landmark achievements are being made; such as the accomplishment of fully assembled lungfish genome which is biggest genome ever sequenced. Here, we highlight current developments in vertebrate’s comparative genomics and discuss how fish genomes could be considered as vital resources for genomic studies. We present a recent overview of genomics data, address different approaches applicable to comparative genomics analyses, and illustrate these comparisons to better understand the complex mechanisms under the vertebrate genomes. We also summarize the applications in chromosomes research and cytogenomics.

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Topics: Comparative genomics (64%), Genomics (62%), Vertebrate Biology (60%) ... read more


86 results found

Journal ArticleDOI: 10.1016/0263-7855(96)00018-5
Abstract: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.

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Topics: Rendering (computer graphics) (52%), Molecular graphics (52%), Visualization (51%) ... read more

36,939 Citations

Open accessJournal ArticleDOI: 10.1093/BIOINFORMATICS/BTP352
Heng Li1, Bob Handsaker2, Alec Wysoker2, T. J. Fennell2  +5 moreInstitutions (4)
01 Aug 2009-Bioinformatics
Abstract: Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: Contact: [email protected]

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Topics: Variant Call Format (62%), Stockholm format (61%), FASTQ format (56%) ... read more

35,747 Citations

Open accessJournal ArticleDOI: 10.1038/NMETH.2019
01 Jul 2012-Nature Methods
Abstract: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

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Topics: Software design (51%), Software (50%)

30,888 Citations

Open accessJournal ArticleDOI: 10.1038/NMETH.1923
01 Apr 2012-Nature Methods
Abstract: As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

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27,973 Citations

Open accessJournal ArticleDOI: 10.1093/BIOINFORMATICS/BTQ033
Aaron R. Quinlan1, Ira M. Hall1Institutions (1)
15 Mar 2010-Bioinformatics
Abstract: Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing webbased methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at

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Topics: Software suite (52%), Source code (50%)

14,088 Citations

No. of citations received by the Paper in previous years