Suchergebnisse

In microorganisms, Ion Torrent sequencing technology has been proved to be useful in whole-genome sequencing of bacterial genomes (5 Mbp). In our study, for the first time we used this technology to perform a resequencing approach in a whole fungal genome (36 Mbp), a non-ochratoxin A producing strain of Aspergillus carbonarius. Ochratoxin A (OTA) is a potent nephrotoxin which is found mainly in cereals and their products, but it also occurs in a variety of common foods and beverages. Due to the fact that this strain does not produce OTA, we focused some of the bioinformatics analyses in genes involved in OTA biosynthesis, using a reference genome of an OTA producing strain of the same species. This study revealed that in the atoxigenic strain there is a high accumulation of nonsense and missense mutations in several genes. Importantly, a two fold increase in gene mutation ratio was observed in PKS and NRPS encoding genes which are suggested to be involved in OTA biosynthesis. ; We thank P. Battilani (Università Cattolica del Sacro Cuore, Italy) for kindly providing us the strain W-201 ( = A-1796 = ITEM 5010) used in this study. The sequence Aspergillus carbonarius ITEM 5010 v3 data used in this publication were generated by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility and is supported under Contract No. DE-AC02-05CH11231 (Principal Investigator: Scott E. Baker). This research was supported by the Ministerio de Ciencia e Innovación of the Spanish Government (AGL2010-22182-C04-02). ; Peer reviewed

This upload contains the article as originally published in Astro et al. Front Cell Dev Biol. 2022 Feb 3;9:801597. doi:10.3389/fcell.2021.801597 (https://www.frontiersin.org/articles/10.3389/fcell.2021.801597/full) In addition to the funding listed in the original publication, Alfonso Saera-Vila received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 712949 (TECNIOspring PLUS)" and the Government of Catalonia's Agency for Business Competitiveness (ACCIÓ).

We report an improved assembly (v3.6.1) of the melon (Cucumis melo L.) genome and a new genome annotation (v4.0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. A new comprehensive annotation was also built in order to update the previous annotation v3.5.1, released more than six years ago. Using an integrative annotation pipeline, based on exhaustive RNA-Seq collections and ad-hoc transposable element annotation, we identified 29,980 protein-coding loci. Compared to the previous version, the v4.0 annotation improved gene models in terms of completeness of gene structure, UTR regions definition, intron-exon junctions and reduction of fragmented genes. More than 8,000 new genes were identified, one third of them being well supported by RNA-Seq data. To make all the new resources easily exploitable and completely available for the scientific community, a redesigned Melonomics genomic platform was released at http://melonomics.net. The resources produced in this work considerably increase the reliability of the melon genome assembly and resolution of the gene models paving the way for further studies in melon and related species. ; This work was supported by the Spanish Ministry of Economy and Competitiveness grant AGL2015–64625-C2-1-R, Severo Ochoa Programme for Centres of Excellence in R&D 2016–2010 (SEV-2015–0533) and the CERCA Programme/Generalitat de Catalunya to JGM. VR was supported by the European Union's Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement No 665919. ; Peer reviewed

Mammalian gametogenesis involves dramatic and tightly regulated chromatin remodeling, whose regulatory pathways remain largely unexplored. Here, we generate a comprehensive high-resolution structural and functional atlas of mouse spermatogenesis by combining in situ chromosome conformation capture sequencing (Hi-C), RNA sequencing (RNA-seq), and chromatin immunoprecipitation sequencing (ChIP-seq) of CCCTC-binding factor (CTCF) and meiotic cohesins, coupled with confocal and super-resolution microscopy. Spermatogonia presents well-defined compartment patterns and topological domains. However, chromosome occupancy and compartmentalization are highly re-arranged during prophase I, with cohesins bound to active promoters in DNA loops out of the chromosomal axes. Compartment patterns re-emerge in round spermatids, where cohesin occupancy correlates with transcriptional activity of key developmental genes. The compact sperm genome contains compartments with actively transcribed genes but no fine-scale topological domains, concomitant with the presence of protamines. Overall, we demonstrate how genome-wide cohesin occupancy and transcriptional activity is associated with three-dimensional (3D) remodeling during spermatogenesis, ultimately reprogramming the genome for the next generation. ; This work was supported by the Ministry of Economy and Competitiveness (BFU2017-89408-R to A.M.P.; BFU2013-47736-P and BFU2017-85926-P to M.A.M.-R.; and CGL2014-54317-P and CGL2017-83802-P to A.R.-H.) and the Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) (DI2015 to A.R.-H. and R.A.C., as well as SGR468 to M.A.M-R.). Work at CRG, BIST, and UPF was in part funded by the Spanish Ministry of Economy and Competitiveness, 'Centro de Excelencia Severo Ochoa 2013-2017' (SEV-2012-0208), and 'Centro de Excelencia María de Maeztu 2016-2019.' CIC-IBMCC is supported by the Programa de Apoyo a Planes Estratégicos de Investigación de Estructuras de Investigación de Excelencia, co-funded by Junta de Castilla y León (CSI239P18) and the European Regional Development Fund (CLC–2017–01). C.V. is supported by a FPI predoctoral fellowship from the Ministry of Economy and Competitiveness (BES-2015-072924). A.P.-G. is supported by a 'Doctorats Industrials' predoctoral fellowship (AGAUR). H.H. is a Miguel Servet (CP14/00229) researcher funded by the Spanish Institute of Health Carlos III (ISCIII), the Agencia Estatal de Investigación (AEI), and FEDER (SAF2017-89109-P). C.M. is an Asociación Española Contra el Cáncer (AECC) postdoctoral fellow. M.A.M.-R. acknowledges support by the European Research Council under the 7th Framework Program FP7/2007-2013 (ERC grant agreement 609989) and the European Union's Horizon 2020 Research and Innovation Programme (grant agreement 676556). A.M.P. and A.R.-H. also acknowledge support from MeioNet (BFU2015-71786-REDT).