Project description:The clapper rail (Rallus crepitans), of the family Rallidae, is a secretive marsh bird species that is adapted for high salinity habitats. They are very similar in appearance to the closely related king rail (R. elegans), but while king rails are limited primarily to freshwater marshes, clapper rails are highly adapted to tolerate salt marshes. Both species can be found in brackish marshes where they freely hybridize, but the distribution of their respective habitats precludes the formation of a continuous hybrid zone and secondary contact can occur repeatedly. This system, thus, provides unique opportunities to investigate the underlying mechanisms driving their differential salinity tolerance as well as the maintenance of the species boundary between the 2 species. To facilitate these studies, we assembled a de novo reference genome assembly for a female clapper rail. Chicago and HiC libraries were prepared as input for the Dovetail HiRise pipeline to scaffold the genome. The pipeline, however, did not recover the Z chromosome so a custom script was used to assemble the Z chromosome. We generated a near chromosome level assembly with a total length of 994.8 Mb comprising 13,226 scaffolds. The assembly had a scaffold N50 was 82.7 Mb, L50 of four, and had a BUSCO completeness score of 92%. This assembly is among the most contiguous genomes among the species in the family Rallidae. It will serve as an important tool in future studies on avian salinity tolerance, interspecific hybridization, and speciation.

| S-EPMC10484055 | biostudies-literature

icBraCrep

Project description:Brachinus crepitans, genomic and transcriptomic data

| PRJEB59134 | ENA

Project description:Genome sequencing of Linum usitatissimum convar. crepitans

| PRJNA1006423 | ENA

Genome of Linum usitatissimum convar. crepitans expands the view on the section Linum.

Project description:Sequencing whole plant genomes provides a solid foundation for applied and basic studies. Genome sequences of agricultural plants attract special attention, as they reveal information on the regulation of beneficial plant traits. Flax is a valuable crop cultivated for oil and fiber. Genome sequences of its representatives are rich sources of genetic information for the improvement of cultivated forms of the plant. In our work, we sequenced the first genome of flax with the dehiscence of capsules-Linum usitatissimum convar. сrepitans (Boenn.) Dumort-on the Oxford Nanopore Technologies (ONT) and Illumina platforms. We obtained 23 Gb of raw ONT data and 89 M of 150 + 150 paired-end Illumina reads and tested different tools for genome assembly and polishing. The genome assembly produced according to the Canu-Racon ×2-medaka-POLCA scheme had optimal contiguity and completeness: assembly length-412.6 Mb, N50-5.2 Mb, L50-28, and complete BUSCO-94.6% (64.0% duplicated, eudicots_odb10). The obtained high-quality genome assembly of L. usitatissimum convar. crepitans provides opportunities for further studies of evolution, domestication, and genome regulation in the section Linum.

| S-EPMC10702972 | biostudies-literature

Tbx6b ChIP-chip on Ciona intestinalis embryo (early gastrula)

Project description:A genomic overview of in vivo binding of a transcription factor Tbx6b in the ascidian early gastrula embryo.

2010-03-09 | GSE17694 | GEO