De novo SNP calling reveals the candidate genes regulating days to flowering through interspecies GWAS of Amaranthus genus

Amaranths serve as pseudo cereals and also as traditional leafy vegetables worldwide. In addition to high vigor and richness in nutrients, drought and salinity tolerance of amaranth makes it a promising vegetable to acclimatize to the effects of global climate change. The World Vegetable Center genebank conserves about 1,000 amaranth accessions and various agronomic properties of these accessions were recorded during seed regeneration over decades. In this study, we verified the taxonomic annotation of the germplasm based on a 15K SNP set. Besides, in the assumption that the yield components of grain amaranths are different from those of leaf amaranths, we observed that grain amaranths presented larger inflorescences and earlier flowering than leaf amaranths. Dual-purpose amaranth showed larger leaves than leaf amaranths and later flowering than grain amaranths, which seemed reasonable because farmers can harvest more leaves during the prolonged vegetable stage, which also provides recovery time to enrich grain production. Considering frequent interspecies hybridization among grain amaranth complex, we proposed an interspecies GWAS for days to flowering, identifying a AGL20/SOC1 homolog. Meanwhile, another GWAS using only A. tricolor accessions revealed six candidate genes homologous to lba1, bri1, sgs1 and fca. These homologous genes were involved in the regulation of flowering time in Arabidopsis. This study revealed the usefulness of genotypes for species demarcation in the genus Amaranthus and the potential of interspecies GWAS to detect QTLs across different species, opening up the possibility of targeted introduction of specific genetic variants into different Amaranthus species.

Measurement of Chromosomal Arms and FISH Reveal Complex Genome Architecture and Standardized Karyotype of Model Fish, Genus Carassius

The widely distributed ray-finned fish genus Carassius is very well known due to its unique biological characteristics such as polyploidy, clonality, and/or interspecies hybridization. These biological characteristics have enabled Carassius species to be successfully widespread over relatively short period of evolutionary time. Therefore, this fish model deserves to be the center of attention in the research field. Some studies have already described the Carassius karyotype, but results are inconsistent in the number of morphological categories for individual chromosomes. We investigated three focal species: Carassius auratus, C. carassius and C. gibelio with the aim to describe their standardized diploid karyotypes, and to study their evolutionary relationships using cytogenetic tools. We measured length (q+plength) of each chromosome and calculated centromeric index (i value). We found: (i) The relationship between q+plength and i value showed higher similarity of C. auratus and C. carassius. (ii) The variability of i value within each chromosome expressed by means of the first quartile (Q1) up to the third quartile (Q3) showed higher similarity of C. carassius and C. gibelio. (iii) The fluorescent in situ hybridization (FISH) analysis revealed higher similarity of C. auratus and C. gibelio. (iv) Standardized karyotype formula described using median value (Q2) showed differentiation among all investigated species: C. auratus had 24 metacentric (m), 40 submetacentric (sm), 2 subtelocentric (st), 2 acrocentric (a) and 32 telocentric (T) chromosomes (24m+40sm+2st+2a+32T) ; C. carassius: 16m+34sm+8st+42T; and C. gibelio: 16m+22sm+10st+2a+50T. (v) We developed R scripts applicable for the description of standardized karyotype for any other species. The diverse results indicated unprecedented complex genomic and chromosomal architecture in the genus Carassius probably influenced by its unique biological characteristics which make the study of evolutionary relationships more difficult than it has been originally postulated.

GENOMIC DIVERSITY, CHROMOSOMAL REARRANGEMENTS, AND INTERSPECIES HYBRIDIZATION IN THE OGATAEA POLYMORPHA SPECIES COMPLEX

The methylotrophic yeast Ogataea polymorpha has long been a useful system for recombinant protein production, as well as a model system for methanol metabolism, peroxisome biogenesis, thermotolerance, and nitrate assimilation. It has more recently become an important model for the evolution of mating-type switching. Here, we present a population genomics analysis of 47 isolates within the Ogataea polymorpha species complex, including representatives of the species O. polymorpha, O. parapolymorpha, O. haglerorum, and O. angusta. We found low levels of nucleotide sequence diversity within the O. polymorpha species complex and identified chromosomal rearrangements both within and between species. In addition, we found that one isolate is an interspecies hybrid between O. polymorpha and O. parapolymorpha and present evidence for loss of heterozygosity following hybridization.

Paralogous gene modules derived from ancient hybridization drive vesicle traffic evolution in yeast

Modules of interacting proteins regulate vesicle budding and fusion in eukaryotes. Distinct paralogous copies of these modules act at distinct sub-cellular locations. The processes by which such large gene modules are duplicated and retained remain unclear. Here we show that interspecies hybridization is a potent source of paralogous gene modules. We study the dynamics of paralog doublets derived from the 100-million-year-old hybridization event that gave rise to the whole genome duplication clade of budding yeast. We show that paralog doublets encoding vesicle traffic proteins are convergently retained across species. Vesicle coats and adaptors involved in secretory and early-endocytic pathways are retained as doublets, while tethers and other machinery involved in intra-Golgi traffic and later endocytic steps are reduced to singletons. These patterns reveal common selective pressures that have sculpted traffic pathways in diverse yeast species. They suggest that hybridization may have played a pivotal role in the expansion of the endomembrane system.

Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm

Hybridization of closely related plant species is frequently connected to endosperm arrest and seed failure, for reasons that remain to be identified. In this study, we investigated the molecular events accompanying seed failure in hybrids of the closely related species pair Capsella rubella and C. grandiflora. Mapping of QTL for the underlying cause of hybrid incompatibility in Capsella identified three QTL that were close to pericentromeric regions. We investigated whether there are specific changes in heterochromatin associated with interspecific hybridizations and found a strong reduction of chromatin condensation in the endosperm, connected with a strong loss of CHG and CHH methylation and random loss of a single chromosome. Consistent with reduced DNA methylation in the hybrid endosperm, we found a disproportionate deregulation of genes located close to pericentromeric regions, suggesting that reduced DNA methylation allows access of transcription factors to targets located in heterochromatic regions. Since the identified QTL were also associated with pericentromeric regions, we propose that relaxation of heterochromatin in response to interspecies hybridization exposes and activates loci leading to hybrid seed failure.

History and Modern Status of the Black-eared Wheatear, Oenanthe hispanica (L.) (Passeriformes, Muscicapidae), in Ukraine

Th e history of research of the Black-eared Wheatear Oenanthe hispanica (L.) in Ukraine in XIX–XXI centuries is presented. Th e Black-eared Wheatear is now a rare breeding bird in the coastal area of the Crimean peninsula, and a very rare vagrant species on the other territory of Ukraine. Four breeding regions of the Black-eared Wheatear are found in the Crimean peninsula: seacoast between Sudak and Th eodosia cities; neighbourhood of Sevastopol City; Tarkhankut peninsula; Kerch peninsula. Th e fi rst two breeding regions have been known since the middle of XIX century. In the breeding regions, the breeding areas of the Black-eared Wheatear are not constant: the birds almost never nest in a place for a number of years. Oenanthe hispanica breeds in Crimea in the same biotopes as its sibling species, the Pied Wheatear, Oenanthe pleschanka, which is essentially more abundant there. Th e breeding of single Black-eared Wheatears with the numerous Pied Wheatears increases their interspecies hybridization, which is rather common on the Crimean peninsula. Th ree out of fi ve individuals of Oenanthe hispanica collected in Crimea and stored in various museums turned out to be hybrids with Oenanthe pleschanka. Th e Black-eared and Pied Wheatears have hybridized in the Crimean peninsula for a long time: the hybrids have been recorded in XX and in XXI centuries. Th e hybrids do not occur in a specifi c breeding region, and can be found in any of those.

The use of molecular cytogenetic methods in the investigation of distant potato hybrids

This paper reviews the results of studies of interspecies hybridization, polyploidization, as well as phylogenetic relationships of Solanum species and members of closely related taxa by such molecular cytogenetic techniques as genomic (GISH) and fluorescent (FISH) DNA-DNA in situ hybridization. The latter was used to determine the genomic composition and origin of wild species of the Petota section, while the FISH technique was used for detecting intergenomic collinearity. The combination of these two types of research made possible a comparative analysis of karyotypes and genomes, thus allowing a better understanding of the meiotic interchromosomal interactions in hybrids. This review primarily focuses on the studies of wild allopolyploid potato species and artificially created intergeneric and interspecific hybrids of the genus Solanum and their offspring.

Genomic evidence supports the introgression between two sympatric stickleback species inhabiting the White Sea basin

Interspecies hybridization is driven by a complex interplay of factors where introgression plays an important role. In the present study, the transfer of genetic material, between two quite distant fish species from different genera, through spontaneous hybridization was documented with dedicated molecular and bioinformatics tools. We investigate the genomic landscape of putative stickleback-relative introgression by carefully analyzing the tractable transposable elements (TE) on the admixed genome of some individuals of two sympatric stickleback species inhabiting northwestern Russia, namely the three-spined (Gasterosteus aculeatus) and the nine-spined (Pungitius pungitius) sticklebacks. Our data revealed that unique TE amplification types exist, supporting our proposed hypothesis that infers on the interspecific introgression. By running a restriction site-associated DNA sequencing (RAD-Seq) with eight samples of G. aculeatus and P. pungitius and subjecting further the results to a contrasting analysis by variated bioinformatic tools, we identified the related introgression-linked markers. The admixture nature observed in a single sample of the nine-spined stickleback demonstrated the possible traces of remote introgression between these two species. Our work reveals the potential that introgression has on providing particular variants at a high-frequency speed while linking blocks of sequence with multiple functional mutations. However, even though our results are of significant interest, an increased number of samples displaying the introgression are required to further ascertain our conclusions.

Oncogenic allelic interaction inXiphophorushighlights hybrid incompatibility

Mixing genomes of different species by hybridization can disrupt species-specific genetic interactions that were adapted and fixed within each species population. Such disruption can predispose the hybrids to abnormalities and disease that decrease the overall fitness of the hybrids and is therefore named as hybrid incompatibility. Interspecies hybridization between southern platyfish and green swordtails leads to lethal melanocyte tumorigenesis. This occurs in hybrids with tumor incidence following progeny ratio that is consistent with two-locus interaction, suggesting melanoma development is a result of negative epistasis. Such observations makeXiphophorusone of the only two vertebrate hybrid incompatibility examples in which interacting genes have been identified. One of the two interacting loci has been characterized as a mutant epidermal growth factor receptor. However, the other locus has not been identified despite over five decades of active research. Here we report the localization of the melanoma regulatory locus to a single gene,rab3d, which shows all expected features of the long-sought oncogene interacting locus. Our findings provide insights into the role ofegfrregulation in regard to cancer etiology. Finally, they provide a molecular explainable example of hybrid incompatibility.