Biology subjects

Ens, J.

Publications and source records attributed to Ens, J..

5 recordsLinked to original sources

bioRxiv2026

Evolutionary dynamics of Aegilops revealed through comparative genome assembly of all 25 species

Aegilops species are the closest wild relatives of wheat and an important reservoir of genetic diversity for its improvement. Despite their potential, many Aegilops genomes remain poorly characterized. Here we present high-quality assemblies of 18 diploid, tetraploid, and hexaploid Aegilops genomes, which, along with the previously published genomes, complete the production of reference assemblies for all 25 genomes in this genus. Assembly sizes ranged from 5.24 Gb in diploids to 12.65 Gb in hexaploids, with scaffold N50 values up to 749.2 Mb. Gene annotation identified 53,035-156,779 protein-coding genes, of which 21,865-60,490 were classified as high-confidence. Orthogroup-based pangenome analysis across the 25 Aegilops genomes identified 80,521 orthogroups, including 15,809 core, 61,735 dispensable, and 2,977 species-specific orthogroups, highlighting substantial gene content variation among genomes. Phylogenetic analysis of 63 Triticum and Aegilops genomes/subgenomes based on near single-copy orthologs defines the phylogenetic relationships within the Triticum/Aegilops complex and confirms diploid progenitors of polyploid lineages. Ae. mutica (T) and Ae. speltoides (S) belong to the B lineage while the remaining Sitopsis grouped within the D lineage. Structural variation analyses using diploid progenitors as references revealed extensive large-scale rearrangements following polyploidization, emphasizing the dynamics of their evolution. Transposable element (TE) annotation further highlighted subgenome-specific TE expansions and contractions, providing insights into the mechanisms shaping genome structure after polyploidization. Collectively, these genomic resources provide a comprehensive framework for exploring Aegilops diversity, understanding polyploid evolution, and accelerating wheat improvement.

genomics↗

bioRxiv2024

Coordinated function of paired NLRs confers Yr84 -mediated stripe rust resistance in wheat

Cloning of resistance genes expands our understanding of their function and facilitates their deployment in breeding. Here, we report the cloning of two genes from wild emmer wheat (Triticum turgidum ssp. dicoccoides) underlying Yr84-mediated stripe rust resistance using a combination of fine mapping, long read-sequencing and mutation-induced functional validation. In contrast to all previously cloned stripe rust genes, the incompletely dominant Yr84 phenotype is conferred through the coordinated function of paired nucleotide-binding leucine-rich repeats (NLR) genes CNL and NL. We hypothesize that based on their genomic organization, annotation, expression profiles and predicted protein structure, CNL functions as a sensor NLR (sNLR) responsible for effector recognition, and NL acts as a helper NLR (hNLR) initiating downstream resistance cascades. The CNL and NL lack an integrated domain(s) previously implicated in effector recognition by paired NLRs, therefore these findings contribute new insights into plant paired NLRs structure and molecular mechanisms of function.

genetics↗

bioRxiv2022

Long-read genome sequencing accelerated the cloning of Pm69 by resolving the complexity of a rapidly evolving resistance gene cluster in wheat

Gene cloning in repeat-rich polyploid genomes remains challenging. Here we describe a strategy for overcoming major bottlenecks in the cloning of the powdery mildew (Pm) resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat (WEW). A conventional positional cloning approach encountered suppressed recombination due to structural variations, while chromosome sorting yielded an insufficient purity level. A Pm69 physical map, constructed by assembling ONT long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster. A single candidate NLR was identified within this cluster by anchoring RNASeq reads of susceptible mutants to ONT contigs and was validated by the virus-induced gene silencing (VIGS) approach. Pm69, comprising Rx_N with RanGAP interaction sites, NB-ARC, and LRR domains, is probably a newly evolved NLR discovered only in one location across the WEW distribution range in the Fertile Crescent. Pm69 was successfully introgressed into durum and bread wheat, and a diagnostic molecular marker could be used to accelerate its deployment and pyramiding with other resistance genes.

genetics↗

bioRxiv2021

Genome sequences of Aegilops species of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Ae. longissima and Ae. speltoides. Whole-genome comparative analysis, along with the recently sequenced Ae. sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly similar and most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides is the closest ancestor of the wheat B subgenome and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding site leucine-rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement. TeaserGenome sequences of Aegilops species provides a key for efficient exploitation of this rich genetic resource in wheat improvement.

plant biology↗

bioRxiv2019

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We have developed TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluated the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and constructed an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.

genomics↗