Biology subjects

Amores, A.

Publications and source records attributed to Amores, A..

5 recordsLinked to original sources

bioRxiv2025

Complete de novo assembly and re-annotation of the zebrafish genome

The zebrafish (Danio rerio) is widely used in vertebrate research, but its reference genome assembly has contained extensively unresolved regions across both euchromatic and heterochromatic compartments. The previous reference genome assembly, GRCz11, consisted of 19,725 contigs assembled into 1,917 scaffolds. Recent advances in both long-read sequencing technologies and genome assembly algorithms have made "complete" genome assemblies possible for the first time. We used homozygous fish from two lab strains, "Tubingen" and "AB," for de novo genome assemblies. The new assemblies incorporated 7% more genomic sequence than GRCz11 and an additional 130 million bases of previously unassembled sequence. RefSeq annotation incorporating newly generated Iso-Seq cDNA sequences have added notable increases in mRNAs (68%), lncRNAs (47%), and misc_RNAs (1099%). Two assemblies have been elevated to reference genome status (GRCz12tu and GRCz12ab). We generated an additional 40 draft haplotypes to create a zebrafish pangenome resource and demonstrate its utility for variant analysis.

genomics↗

bioRxiv2020

The developmental and genetic architecture of the sexually selected male ornament of swordtails

Sexual selection results in sex-specific characters like the conspicuously pigmented extension of the ventral tip of the caudal fin - the "sword" - in males of several species of Xiphophorus fishes. To uncover the genetic architecture underlying sword formation and to identify genes that are associated with its development, we characterized the sword transcriptional profile and combined it with genetic mapping approaches. Results showed that the male ornament of swordtails develops from a sexually non-dimorphic prepattern of transcription factors in the caudal fin. Among genes that constitute the exclusive sword transcriptome only two are located in the genomic region associated with this trait; the chaperone, fkbp9, and the potassium channel, kcnh8 that in addition to its neural function performs a role known to affect fin growth. This indicates that during evolution of swordtails a brain gene has been recruited for an additional function in establishing a male ornament.

evolutionary biology↗

bioRxiv2020

RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data

The study of sex determination and sex chromosome organisation in non-model species has long been technically challenging, but new sequencing methodologies are now enabling precise and high-throughput identification of sex-specific genomic sequences. In particular, Restriction Site-Associated DNA Sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software designed to specifically search for sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analyzed a published dataset of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyze new RAD-Seq datasets from 15 fish species spanning multiple systematic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in non-model species and outperforms the commonly used RAD-Seq analysis software STACKS. RADSex in speed, resource usage, ease of application, and visualization options. Furthermore, our analysis of new datasets from 15 species provides new insights on sex determination in fish.

bioinformatics↗

bioRxiv2020

Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead such research. Fortunately, integration of additional, independent streams of information, such as a genetic map - particularly a marker-dense map from RADseq, for example - and conserved orthologous gene order from related taxa can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a "chromonome". We demonstrate Chromonomers performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.

genomics↗

bioRxiv2018

Epigenetic factors coordinate intestinal development

Intestinal epithelium development depends on epigenetic modifications, but whether that is also the case for other intestinal tract cell types remains unclear. We found that functional loss of a DNA methylation machinery component, ubiquitin-like protein containing PHD and RING finger domains 1 (uhrf1), leads to reduced enteric neuron number, changes in neuronal morphology, and severe intestinal smooth muscle disruption. Genetic chimeras revealed that Uhrf1 functions both cell-autonomously in enteric neuron progenitors and cell-non-autonomously in surrounding intestinal cells. Uhrf1 recruits the DNA methyltransferase Dnmt1 to unmethylated DNA during replication. Dnmt1 is also expressed in enteric neuron and smooth muscle progenitors. dnmt1 mutants show a strong reduction in enteric neuron number and disrupted intestinal smooth muscle. Because dnmt1;uhrf1 double mutants have a similar phenotype to dnmt1 and uhrf1 single mutants, Dnmt1 and Uhrf1 must function together during enteric neuron and intestinal muscle development. This work shows that genes controlling epigenetic modifications are important in coordinating intestinal tract development, provides the first demonstration that these genes are important in ENS development, and advances uhrf1 and dnmt1 as potential new Hirschsprung disease candidates.\n\nSummaryThis work provides evidence that DNA methylation factors are important in all cell types that contribute to development of a functional intestine.

developmental biology↗