Conservation and Sustainable Use of Oryza coarctata for Developing "Sea Water Tolerant Rice".

Oryza coarctata is a wild rice species native to saline and coastal environments, making it an important genetic resource for developing salt-tolerant rice varieties. Its unique ability to thrive well on high-saline soil and waterlogged condition that offers valuable traits for breeding programs aimed at addressing the challenges of salinization in agricultural lands. With the rising sea levels as well as increasing salinity of arable land, O.

The Oryza australiensis genome reveals potential as a source of genes for rice improvement.

The wild relatives of cultivated rice (Oryza sativa L.) represent largely untapped sources of novel genetic material for crop improvement. Here, we present a chromosome-level, haplotype-resolved genome for O.

Universal orthologs infer deep phylogenies and improve genome quality assessments.

Background: Universal single-copy orthologs are the most conserved components of genomes. Although they are routinely used for studying evolutionary histories and assessing new assemblies, current methods do not incorporate information from available genomic data.

Results: Here, we first determine the influence of evolutionary history on universal gene content and find that across 11,098 genomes of plants, fungi, and animals comprising 2606 taxonomic groups, 215 groups significantly vary from their respective lineages in terms of BUSCO (Benchmarking Universal Single Copy Orthologs) completeness.

Integrated biotechnological and AI innovations for crop improvement.

Crops provide food, clothing and other important products for the global population. To meet the demands of a growing population, substantial improvements are required in crop yield, quality and production sustainability. However, these goals are constrained by various environmental factors and limited genetic resources.

PacBio genome assembly of Olea europaea L. subsp. europaea cultivars Frantoio and Leccino.

We present two high-quality genome assemblies for Olea europaea L. cultivars 'Frantoio' and 'Leccino,' leveraging PacBio HiFi sequencing to achieve approximately 30 × genome coverage for each cultivar. The assemblies span 1.

Diploidization in a wild rice allopolyploid is both episodic and gradual.

Polyploid organisms evolve from their initial doubled genomic condition through a number of processes collectively termed diploidization, whose tempo and mode remain poorly understood mainly due to the difficulty of discriminating de novo evolution subsequent to polyploidy from variation inherited from progenitors. Here, we generated chromosome-scale genome assemblies for the wild rice allopolyploid and its two diploid progenitors, and , and employed a population genomic approach to investigate the diploidization process in at the sequence and transcriptomic level. We show that this wild rice allopolyploid originated around 0.

Oryza genome evolution through a tetraploid lens.

Oryza is a remarkable genus comprising 27 species and 11 genome types, with ~3.4-fold genome size variation, that possesses a virtually untapped reservoir of genes that can be used for crop improvement and neodomestication. Here we present 11 chromosome-level assemblies (nine tetraploid, two diploid) in the context of ~15 million years of evolution and show that the core Oryza (sub)genome is only ~200 Mb and largely syntenic, whereas the remaining nuclear fractions (~80-600 Mb) are intermingled, plastic and rapidly evolving.

Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in .

Transfer of chloroplast or mitochondrial DNA into the nuclear genome is a common phenomenon in many species. However, little is known about the evolutionary fate and mechanism of transfer of organellar DNA sequences in higher plants. We observe abundant insertions of organelle DNA into the nuclear genomes of 22 genome assemblies across seven species and further categorize nuclear organelle DNA (NORG) into 3406 orthologous groups.

A pan-gene catalogue of Asian cultivated rice.

The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was developed, comprising high-quality assemblies of 16 rice cultivars to represent , , , and varietal groups. The RPRP has been consistently annotated, supported by extensive experimental data and here we report the computational assignment, characterization and dissemination of stably identified pan-genes.

A Chromosome level assembly of pomegranate (Punica granatum L.) variety grown in arid environment.

The pomegranate (Punica granatum L.) is an ancient fruit-bearing tree known for its nutritional and antioxidant properties. They originated from the Middle East in regions having large farms including mountainous regions of Al-Baha in Saudi Arabia.

Chromosome-scale pearl millet genomes reveal CLAMT1b as key determinant of strigolactone pattern and Striga susceptibility.

The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released hormones, called strigolactones (SLs), for seed germination. Herein, we identify four SLs present in the Striga-susceptible line SOSAT-C88-P10 (P10) but absent in the resistant 29Aw (Aw). We generate chromosome-scale genome assemblies, including four gapless chromosomes for each line.

An NLR paralog Pit2 generated from tandem duplication of Pit1 fine-tunes Pit1 localization and function.

NLR family proteins act as intracellular receptors. Gene duplication amplifies the number of NLR genes, and subsequent mutations occasionally provide modifications to the second gene that benefits immunity. However, evolutionary processes after gene duplication and functional relationships between duplicated NLRs remain largely unclear.

Multitrait engineering of Hassawi red rice for sustainable cultivation.

Sustainable agriculture requires locally adapted varieties that produce nutritious food with limited agricultural inputs. Genome engineering represents a viable approach to develop cultivars that fulfill these criteria. For example, the red Hassawi rice, a native landrace of Saudi Arabia, tolerates local drought and high-salinity conditions and produces grain with diverse health-promoting phytochemicals.

A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset.

Background: Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable.

High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup.

High-quality genome assemblies across a range of nontraditional model organisms can accelerate the discovery of novel aspects of genome evolution. The Drosophila virilis group has several attributes that distinguish it from more highly studied species in the Drosophila genus, such as an unusual abundance of repetitive elements and extensive karyotype evolution, in addition to being an attractive model for speciation genetics. Here, we used long-read sequencing to assemble five genomes of three virilis group species and characterized sequence and structural divergence and repetitive DNA evolution.

Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice.

Developing drought-resistant rice (Oryza sativa, L.) is essential for improving field productivity, especially in rain-fed areas affected by climate change. Wild relatives of rice are potential sources for drought-resistant traits.

High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in the sub-group.

High-quality genome assemblies across a range of non-traditional model organisms can accelerate the discovery of novel aspects of genome evolution. The group has several attributes that distinguish it from more highly studied species in the genus, such as an unusual abundance of repetitive elements and extensive karyotype evolution, in addition to being an attractive model for speciation genetics. Here we used long-read sequencing to assemble five genomes of three virilis group species and characterized sequence and structural divergence and repetitive DNA evolution.

Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud.

African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses.

Multi-omics resources for targeted agronomic improvement of pigmented rice.

Pigmented rice (Oryza sativa L.) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties.

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.

Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogon and O.

Prediction of crossover recombination using parental genomes.

Meiotic recombination is a crucial cellular process, being one of the major drivers of evolution and adaptation of species. In plant breeding, crossing is used to introduce genetic variation among individuals and populations. While different approaches to predict recombination rates for different species have been developed, they fail to estimate the outcome of crossings between two specific accessions.

The gyrfalcon (Falco rusticolus) genome.

High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and population genomics. To provide this valuable resource for conservation projects and comparative genomics studies on gyrfalcon (Falco rusticolus), we sequenced and assembled the genome of this species using third-generation sequencing strategies and optical maps. Here, we describe a highly contiguous and complete genome assembly comprising 20 scaffolds and 13 contigs with a total size of 1.

The International Oryza Map Alignment Project (IOMAP): the Americas-past achievements and future directions.

The wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (OMAP) initiated in 2003 has provided comprehensive genomic resources for comparative, evolutionary, and functional characterization of the wild relatives of rice, facilitating the cloning of >600 rice genes, including those for grain width (GW5) and submergence tolerance (SUB1A). Following in the footsteps of the original project, the goal of 'IOMAP: the Americas' is to investigate the present and historic genetic diversity of wild Oryza species endemic to the Americas through the sequencing of herbaria and in situ specimens.