The outburst of the changing-look AGN IRAS23226-3843 in 2019

IRAS23226-3843 has previously been classified as a changing-look AGN based on X-ray and optical spectral variations. In 2019, Swift observations revealed a strong rebrightening in X-ray and UV fluxes in comparison to observations in 2017. We took follow-up Swift, XMM-Newton, and NuSTAR observations together with optical spectra (SALT and SAAO 1.9m telescope) from 2019 until 2021. IRAS23226-3843 showed a strong X-ray and optical outburst in 2019. It varied in the X-ray and optical continuum by a factor of 5 and 1.6, respectively, within two months. This corresponds to a factor of 3 in the optical after correction for the host galaxy contribution. The Balmer and FeII emission-line intensities showed comparable variability amplitudes. The Halpha profiles changed from a blue-peaked profile in the years 1997 and 1999 to a broad double-peaked profile in 2017 and 2019. However, there were no major profile variations in the extremely broad double-peaked profiles despite the strong intensity variations in 2019. One year after the outburst, the optical spectral type changed and became a Seyfert type 2 in 2020. Blue outflow components are present in the Balmer lines and in the Fe band in the X-rays. A deep broadband XMM-Newton/NuSTAR spectrum was taken during the maximum state in 2019. This spectrum is qualitatively very similar to a spectrum taken in 2017, but by a factor of 10 higher. The soft X-ray band appears featureless. The soft excess is well modeled with a Comptonization model. A broadband fit with a power-law continuum, Comptonized soft excess, and Galactic absorption gives a good fit to the combined EPIC-pn and NuSTAR spectrum. In addition, we see a complex and broadened Fe K emission-line profile in the X-rays. The changing-look character in IRAS23226-3843 is most probably caused by changes in the accretion rate -- based on the short-term variations on timescales of weeks to months.Comment: 21 pages, 14 figures, Astronomy & Astrophysics in pres

A multi‐omics framework reveals strawberry flavor genes and their regulatory elements

Flavor is essential to consumer preference of foods and is an increasing focus of plant breeding programs. In fruit crops, identifying genes underlying volatile organic compounds has great promise to accelerate flavor improvement, but polyploidy and heterozygosity in many species have slowed progress. Here we use octoploid cultivated strawberry to demonstrate how genomic heterozygosity, transcriptomic intricacy and fruit metabolomic diversity can be treated as strengths and leveraged to uncover fruit flavor genes and their regulatory elements. Multi-omics datasets were generated including an expression quantitative trait loci map with 196 diverse breeding lines, haplotype-phased genomes of a highly-flavored breeding selection, a genome-wide structural variant map using five haplotypes, and volatile genome-wide association study (GWAS) with > 300 individuals. Overlaying regulatory elements, structural variants and GWAS-linked allele-specific expression of numerous genes to variation in volatile compounds important to flavor. In one example, the functional role of anthranilate synthase alpha subunit 1 in methyl anthranilate biosynthesis was supported via fruit transient gene expression assays. These results demonstrate a framework for flavor gene discovery in fruit crops and a pathway to molecular breeding of cultivars with complex and desirable flavor

Blueprint for phasing and assembling the genomes of heterozygous polyploids: Application to the octoploid genome of strawberry

The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its progenitors are outbred octoploids in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the day-neutral octoploid F. × ananassa hybrid 'Royal Royce' from the University of California. Our goal was to produce subgenome- and haplotype-resolved assemblies of all 56 chromosomes, accurately reconstructing the parental haploid chromosome complements. Previous work has demonstrated that partitioning sequences by parental phase supports direct assembly of haplotypes in heterozygous diploid species. We leveraged the accuracy of HiFi sequence data with pedigree-informed sequencing to partition long read sequences by phase, and reduce the downstream risk of subgenomic chimeras during assembly. We were able to utilize an octoploid strawberry recombination breakpoint map containing 3.6 M variants to identify and break chimeric junctions, and perform scaffolding of the phase-1 and phase-2 octoploid assemblies. The N50 contiguity of the phase-1 and phase-2 assemblies prior to scaffolding and gap-filling was 11 Mb. The final haploid assembly represented seven of 28 chromosomes in a single contiguous sequence, and averaged fewer than three gaps per pseudomolecule. Additionally, we re-annotated the octoploid genome to produce a custom F. × ananassa repeat library and improved set of gene models based on IsoSeq transcript data and an expansive RNA-seq expression atlas. Here we present 'FaRR1', a gold-standard reference genome of F. × ananassa cultivar 'Royal Royce' to assist future genomic research and molecular breeding of allo-octoploid strawberry.***WARNING: THIS DATA SUBMISSION CONTAINS FILES ASSOCIATED WITH THREE SEPARATE GENOME ASSEMBLIES: - files with the prefix 'farr1.' are associated with the Royal Royce synthetic haploid genome (for most user applications) - files with the prefix 'farr1_phase1.' are associated with the Royal Royce phase1 (parent haplotype A) genome - files with the prefix 'farr1_phase2.' are associated with the Royal Royce phase2 (parent haplotype B) genom