A robust single-nucleotide polymorphism (SNP) discovery strategy is designed and applied to existing and novel sequence data sets that represent the global diversity in potato production systems and indicates that potato wart was introduced into Canada from a European source.
Abstract
ABSTRACT The chytrid Synchytrium endobioticum causes potato wart disease and is a regulated quarantine pathogen. Due to its obligate association with the potato host, obtaining pure genome sequences has been technically challenging. Previous population studies were limited to microsatellites or mitochondrial genomes, which capture only a small portion of the pathogen’s genetic diversity. To enable the first population genomic analyses of the nuclear genome of S. endobioticum, we designed and applied a robust single-nucleotide polymorphism (SNP) discovery strategy to existing and novel sequence data sets that represent the global diversity in potato production systems. We demonstrate that reliable nuclear genome data can be recovered from contaminated environmental samples, where S. endobioticum constitutes only ~5% of total reads. After stringent filtering, 74 high‑quality data sets for isolates from 10 countries and 12 pathotypes were retained. Phylogenetic analyses of genome-wide SNP alignments, some with up to 188 817 SNPs, identified three well-supported nuclear phylogroups that largely corresponded to mitochondrial haplogroups: (i) a basal Peruvian clade; (ii) a European/Canadian clade containing mostly pathotypes 1(D1), 2(G1), 6(O1), and 8(F1); and (iii) a clade with pathotypes 18(T1) and 38(Nevşehir). Using a subset of 13 327 homozygous SNPs, population structure analysis and phylogenetic networks confirmed three genetic clusters with limited admixture. Our analyses indicate that potato wart was introduced into Canada from a European source. Pathotype designations do not correspond to exclusive monophyletic lineages. Analysis of the AvrSen1 effector revealed that distinct loss-of-function variants can occur in multiple nuclear phylogroups, suggesting independent emergence of some virulence phenotypes. Isolates contain a reservoir of genetic variation, which may allow adaptation to changing host resistance pressures. This nuclear genome approach provides significantly greater resolution than previous molecular markers used for strain tracking. Furthermore, the solid phylogenetic framework developed here will support future effector-based pathotype inference and will aid regulators in surveillance and quarantine decisions for this high-risk pathogen.
Wild perennial plants can be domesticated to make agriculture more diverse and resilient, but many have large genomes that have been recalcitrant to analysis. Here, we report phased genome assemblies for Silphium integrifolium Michx. and S. perfoliatum L., two species native to North America under domestication, and demonstrate the utility of trio-binning for genome assembly using an interspecific hybrid. These genomes have chromosomes reaching 1.8 Gb and a helical structure preserved during interphase with a loop circumference of 43 Mb. A genome-informed low coverage and target sequencing strategy enables the refinement of the genus phylogeny, reveals the spatial distribution and structure of natural populations, and identifies 81 loci associated with environmental and domestication traits. Variants in a MATE transporter, α/β hydrolase, and ortholog of Arabidopsis ACT Domain Repeat (ACR4) protein explain significant variance in floral architecture. These advances in genome assembly and genotyping could expand the range of candidates for de novo crop domestication. Silphium species native to North American prairies show strong drought tolerance. This study presents a haplotype-phased genome of a hybrid between S. integrifolium (oilseed crop) and S. perfoliatum (biomass/fiber crop), identifying loci linked to environmental adaptation and domestication.
Renan Souza, J. Clevenger, Jerry W. Jenkins et al.· Nature Communications· 0 citations
Italian ryegrass (Lolium multiflorum) is a key temperate forage species underpinning livestock production in Europe. Genomic resources remain limited by its large (2.2 Gb), repetitive, and highly heterozygous genome. Here, we present a high-quality chromosome-scale genome assembly of the Swiss L. multiflorum ecotype Tremona, collected in 2008 in Ticino, Switzerland, and subsequently incorporated into recurrent breeding cycles in the Swiss breeding program. To address systematic assembly artefacts caused by unresolved haplotypes in our initial PacBio HiFi assembly, we developed ParaLies, a post-assembly tool that identifies and removes artefactual duplications based on sequence divergence while preserving true paralogous gene copies. ParaLies reduced the duplicated BUSCO rate from 16.91% to 6.72% without loss of bona fide genomic content. The resulting assembly has a contig N50 of 15.69 Mb and captures 94% of the expected 2.2-Gb genome size. We further analyzed whole-genome resequencing data from Tremona, additional Swiss ecotypes, and publicly available North American germplasm. Tremona was genetically homogeneous, with no evidence of pronounced recent bottlenecks or substantial within-population structure, and was genetically distinct from the other Swiss ecotypes analyzed. Together, the Tremona genome and ParaLies provide valuable resources for L. multiflorum genomics and breeding and demonstrate a scalable approach for reducing haplotype-induced redundancy in highly heterozygous genomes.
L. Piat, Gerhard Herren, C. Grieder et al.· bioRxiv· 0 citations
Marine fish trypanosomes are widespread hemoparasites that pose significant threats to wild and farmed teleosts, yet they remain genomically underrepresented compared to their mammalian-infecting counterparts. Here, we present the first chromosome-level, gap-free genome assembly of Trypanosoma larimichthysi, a recently described species causing severe trypanosomiasis outbreaks in the economically important large yellow croaker (Larimichthys crocea) along the Chinese coast. The assembly, generated using PacBio HiFi long-read sequencing combined with Hi-C chromatin conformation capture, spans 51.04 Mb across exactly 35 pseudochromosomes, with a contig N50 of 1.43 Mb and 97.96% of sequences anchored. Exceptional completeness is evidenced by telomere-to-telomere resolution for 25 chromosomes (58 telomeric loci captured in total), a 99.99% HiFi read mapping rate, and > 99% BUSCO completeness. The genome encodes 10,172 protein-coding genes, with repetitive sequences comprising 50.33%, dominated by retrotransposons including LINE and LTR elements. Comparative genomic analyses confirm the phylogenetic placement of T. larimichthysi within Trypanosoma and reveal lineage-specific gene family expansions potentially linked to host adaptation and pathogenicity. This reference-grade genome fills a critical gap in aquatic trypanosomatid genomics and provides a valuable resource for investigating parasite evolution, host-parasite interactions, antigenic variation mechanisms, and disease management strategies in mariculture.
The first complete mitogenome of Eurostus validus is reported and indicates that both mutation pressure and natural selection shape codon usage bias, with natural selection playing a dominant role.
Dongkai Liu, Chao Xue, Yingyin Gao· Journal of the Entomological...· 0 citations