Elucidating the evolution of recently diverged and polyploid-rich plant lineages may be challenging even with high-throughput sequencing, both for biological reasons and bioinformatic difficulties. Here, we apply target enrichment with genome skimming (Hyb-Seq) to unravel the evolutionary history of the Alyssum montanum-A. repens species complex. Reconstruction of phylogenetic relationships in diploids supported recent and rapid diversification accompanied by reticulation events. Of the four main clades identified among the diploids, three clades included species from the Alps, Apennine and Balkan peninsulas, indicating close biogeographic links between these regions. We further focused on the clade distributed from the Western Alps to the Iberian Peninsula, which comprises numerous polyploids as opposed to a few diploids. Using a recently developed PhyloSD (phylogenomic subgenome detection) pipeline, we successfully tracked the ancestry of all polyploids. We inferred multiple polyploidization events that involved two closely related diploid progenitors, resulting into several sibling polyploids: two autopolyploids and six allopolyploids. The skewed proportions of major homeolog-types and the occurrence of some minor homeolog-types, both exhibiting geographic patterns, suggest introgression with the progenitors and other related diploids. Our study highlights a unique case of parallel polyploid speciation that was enhanced by ecological and geographic separation and provides an excellent resource for future studies of polyploid evolution.

While the effects of barriers to dispersal such as population declines, habitat fragmentation, and geographic distance have been well-documented in terrestrial wildlife, factors impeding the dispersal of highly vagile taxa such as seabirds are less well understood. The roseate tern (Sterna dougallii) is a globally distributed seabird species, but populations tend to be both fragmented and small, and the species is declining across most of its range. We evaluated structuring of roseate tern populations in the Northwestern Atlantic, the Caribbean, and the Azores using both microsatellite markers and single-nucleotide polymorphisms generated through targeted sequencing of Ultra-conserved Elements. For both marker types, we found significant genetic differentiation among all 3 populations and evidence for moderate contemporary unidirectional gene flow from the Caribbean to the Azores, but not between other populations. Within the Caribbean population, we found high rates of unidirectional migration from the Virgin Islands to Florida, potentially indicative of movement from source population to sink or an artifact of dispersal among other unsampled populations in the Caribbean region. These observations have significance for species persistence in the Atlantic, as our results indicate that loss of genetic diversity within populations is unlikely to be buffered by inflow of new alleles from other breeding populations.

Abstract Certain CRISPR-Cas elements integrate into Tn7-like transposons, forming CRISPR-associated transposon (CAST) systems. How the activity of these systems is controlled in situ has remained largely unknown. Here we characterize the MerR-type transcriptional regulator Alr3614 that is encoded by one of the CAST (AnCAST) system genes in the genome of cyanobacterium Anabaena sp. PCC 7120. We identify a number of Alr3614 homologs across cyanobacteria and suggest naming these regulators CvkR for Cas V-K repressors. Alr3614/CvkR is translated from leaderless mRNA and represses the AnCAST core modules cas12k and tnsB directly, and indirectly the abundance of the tracr-CRISPR RNA. We identify a widely conserved CvkR binding motif 5’-AnnACATnATGTnnT-3’. Crystal structure of CvkR at 1.6 Å resolution reveals that it comprises distinct dimerization and potential effector-binding domains and that it assembles into a homodimer, representing a discrete structural subfamily of MerR regulators. CvkR repressors are at the core of a widely conserved regulatory mechanism that controls type V-K CAST systems.

Early natural historians—Comte de Buffon, von Humboldt, and De Candolle—established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes. , Water availability dictates patterns of global phylogenetic beta diversity in tropical plants.

Since emerging in Brazil in 1985, wheat blast has spread throughout South America and recently appeared in Bangladesh and Zambia. Here we show that two wheat resistance genes, Rwt3 and Rwt4, acting as host-specificity barriers against non-Triticum blast pathotypes encode a nucleotide-binding leucine-rich repeat immune receptor and a tandem kinase, respectively. Molecular isolation of these genes will enable study of the molecular interaction between pathogen effector and host resistance genes.

Genome-scale data have significantly increased the number of informative characters for phylogenetic analyses and recent studies have also revealed widespread phylogenomic discordance in many plant lineages. Aralia sect. Aralia is a small plant lineage (14 spp.) of the ginseng family Araliaceae with a disjunct distribution between eastern Asia (11 spp.) and North America (3 spp.). We herein employ sequences of hundreds of nuclear loci and the complete plastomes using targeted sequence capture and genome skimming to reconstruct the phylogenetic and biogeographic history of this section. We detected substantial conflicts among nuclear genes, yet different analytical strategies generated largely congruent topologies from the nuclear data. Significant cytonuclear discordance was detected, especially concerning the positions of the three North American species. The phylogenomic results support two intercontinental disjunctions: (1) Aralia californica of western North America is sister to the eastern Asian clade consisting of A. cordata and A. continentalis in the nuclear tree, and (2) the eastern North American A. racemosa forms a clade with A. bicrenata from southwestern North America, and the North American A. racemosa – A. bicrenata clade is then sister to the eastern Asian clade consisting of A. glabra (Japan), A. fargesii (C China), and A. apioides and A. atropurpurea (the Hengduan Mountains). Aralia cordata is supported to be disjunctly distributed in Japan, Taiwan, the Ulleung island of Korea, and in Central, Southwest and South China, and Aralia continentalis is redefined with a narrower distribution in Northeast China, eastern Russia and peninsular Korea.

‘Staggering disease’ is a neurological disease entity considered a threat to European domestic cats (Felis catus) for almost five decades. However, its aetiology has remained obscure. Rustrela virus (RusV), a relative of rubella virus, has recently been shown to be associated with encephalitis in a broad range of mammalian hosts. Here, we report the detection of RusV RNA and antigen by metagenomic sequencing, RT-qPCR, in situ hybridization and immunohistochemistry in brain tissues of 27 out of 29 cats with non-suppurative meningoencephalomyelitis and clinical signs compatible with’staggering disease’ from Sweden, Austria, and Germany, but not in non-affected control cats. Screening of possible reservoir hosts in Sweden revealed RusV infection in wood mice (Apodemus sylvaticus). Our work indicates that RusV is the long-sought cause of feline ‘staggering disease’. Given its reported broad host spectrum and considerable geographic range, RusV may be the aetiological agent of neuropathologies in further mammals, possibly even including humans.

Centromeres in the legume genera Pisum and Lathyrus exhibit unique morphological characteristics, including extended primary constrictions and multiple separate domains of centromeric chromatin. These so-called metapolycentromeres resemble an intermediate form between monocentric and holocentric types, and therefore provide a great opportunity for studying the transitions between different types of centromere organizations. However, because of the exceedingly large and highly repetitive nature of metapolycentromeres, highly contiguous assemblies needed for these studies are lacking. Here, we report on the assembly and analysis of a 177.6 Mb region of pea ( Pisum sativum ) chromosome 6, including the 81.6 Mb centromere region (CEN6) and adjacent chromosome arms. Genes, DNA methylation profiles, and most of the repeats were uniformly distributed within the centromere, and their densities in CEN6 and chromosome arms were similar. The exception was an accumulation of satellite DNA in CEN6, where it formed multiple arrays up to 2 Mb in length. Centromeric chromatin, characterized by the presence of the CENH3 protein, was predominantly associated with arrays of three different satellite repeats; however, five other satellites present in CEN6 lacked CENH3. The presence of CENH3 chromatin was found to determine the spatial distribution of the respective satellites during the cell cycle. Finally, oligo-FISH painting experiments, performed using probes specifically designed to label the genomic regions corresponding to CEN6 in Pisum , Lathyrus , and Vicia species, revealed that metapolycentromeres evolved via the expansion of centromeric chromatin into neighboring chromosomal regions and the accumulation of novel satellite repeats. However, in some of these species, centromere evolution also involved chromosomal translocations and centromere repositioning.

Seoul orthohantavirus (SEOV) is a rat-associated zoonotic pathogen with an almost worldwide distribution. In 2019, the first autochthonous human case of SEOV-induced hemorrhagic fever with renal syndrome was reported in Germany, and a pet rat was identified as the source of the zoonotic infection. To further investigate the SEOV reservoir, additional rats from the patient and another owner, all of which were purchased from the same vendor, were tested. SEOV RNA and anti-SEOV antibodies were found in both of the patient’s rats and in two of the three rats belonging to the other owner. The complete coding sequences of the small (S), medium (M), and large (L) segments obtained from one rat per owner exhibited a high sequence similarity to SEOV strains of breeder rat or human origin from the Netherlands, France, the USA, and Great Britain. Serological screening of 490 rats from breeding facilities and 563 wild rats from Germany (2007–2020) as well as 594 wild rats from the Netherlands (2013–2021) revealed 1 and 6 seropositive individuals, respectively. However, SEOV RNA was not detected in any of these animals. Increased surveillance of pet, breeder, and wild rats is needed to identify the origin of the SEOV strain in Europe and to develop measures to prevent transmission to the human population.