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Bamboo resources have garnered significant global attention due to their excellent capacity for regeneration and high yield. Rhombic-spot disease, a substantial threat to fishscale bamboo (Phyllostachys heteroclada), is primarily caused by Neostagonosporella sichuanensis. This study first reported the genome assemblies and characteristics of two N. sichuanensis isolates using PacBio and Illumina sequencing platforms. The genomes of N. sichuanensis strain SICAUCC 16–0001 and strain SICAUCC 23–0140, with sizes of 48.0 Mb and 48.4 Mb, respectively, revealed 10,289 and 10,313 protein-coding genes. Additionally, they contained 34.99 and 34.46% repetitive sequences within AT-rich regions, with notable repeat-induced point mutation activity. Comparative genome analysis identified 1,049 contracted and 45 expanded gene families in the genome of N. sichuanensis , including several related to pathogenicity. Several gene families involved in mycotoxin metabolism, secondary metabolism, sterol biosynthesis and transport, and cell wall degradation were contracted. Compared to most analyzed necrotrophic, hemibiotrophic, and phaeosphaeriacous pathogens, the genomes of two N. sichuanensis isolates exhibited fewer secondary metabolite enzymes, carbohydrate-active enzymes, plant cell wall degrading enzymes, secreted proteins, and effectors. Comparative genomics analysis suggested that N. sichuanensis shares more similar characteristics with hemibiotrophic pathogens. Based on single carbon source tests, N. sichuanensis strains demonstrated a higher potential for xylan decomposition than pectin and cellulose. The proportion of cell wall-degrading enzyme effectors occupied a high proportion of the total effectors of the N. sichuanensis genomes. These findings provide valuable insights into uncovering the pathogenesis of N. sichuanensis toward the efficient management of rhombic-spot disease of fishscale bamboo. [ABSTRACT FROM AUTHOR]

Conventional pre-genomics breeding methodologies have significantly improved crop yields since the mid-twentieth century. Genomics provides breeders with advanced tools for whole-genome study, enabling a direct genotype–phenotype analysis. This shift has led to precise and efficient crop development through genomics-based approaches, including molecular markers, genomic selection, and genome editing. Molecular markers, such as SNPs, are crucial for identifying genomic regions linked to important traits, enhancing breeding accuracy and efficiency. Genomic resources viz. genetic markers, reference genomes, sequence and protein databases, transcriptomes, and gene expression profiles, are vital in plant breeding and aid in the identification of key traits, understanding genetic diversity, assist in genomic mapping, support marker-assisted selection and speeding up breeding programs. Advanced techniques like CRISPR/Cas9 allow precise gene modification, accelerating breeding processes. Key techniques like Genome-Wide Association study (GWAS), Marker-Assisted Selection (MAS), and Genomic Selection (GS) enable precise trait selection and prediction of breeding outcomes, improving crop yield, disease resistance, and stress tolerance. These tools are handy for complex traits influenced by multiple genes and environmental factors. This paper explores new genomic technologies like molecular markers, genomic selection, and genome editing for plant breeding showcasing their impact on developing new plant varieties. [ABSTRACT FROM AUTHOR]

Bamboo resources have garnered significant global attention due to their excellent capacity for regeneration and high yield. Rhombic-spot disease, a substantial threat to fishscale bamboo (Phyllostachys heteroclada), is primarily caused by Neostagonosporella sichuanensis. This study first reported the genome assemblies and characteristics of two N. sichuanensis isolates using PacBio and Illumina sequencing platforms. The genomes of N. sichuanensis strain SICAUCC 16-0001 and strain SICAUCC 23-0140, with sizes of 48.0 Mb and 48.4 Mb, respectively, revealed 10,289 and 10,313 protein-coding genes. Additionally, they contained 34.99 and 34.46% repetitive sequences within ATrich regions, with notable repeat-induced point mutation activity. Comparative genome analysis identified 1,049 contracted and 45 expanded gene families in the genome of N. sichuanensis, including several related to pathogenicity. Several gene families involved in mycotoxin metabolism, secondary metabolism, sterol biosynthesis and transport, and cell wall degradation were contracted. Compared to most analyzed necrotrophic, hemibiotrophic, and phaeosphaeriacous pathogens, the genomes of two N. sichuanensis isolates exhibited fewer secondary metabolite enzymes, carbohydrate-active enzymes, plant cell wall degrading enzymes, secreted proteins, and effectors. Comparative genomics analysis suggested that N. sichuanensis shares more similar characteristics with hemibiotrophic pathogens. Based on single carbon source tests, N. sichuanensis strains demonstrated a higher potential for xylan decomposition than pectin and cellulose. The proportion of cell wall-degrading enzyme effectors occupied a high proportion of the total effectors of the N. sichuanensis genomes. These findings provide valuable insights into uncovering the pathogenesis of N. sichuanensis toward the efficient management of rhombic-spot disease of fishscale bamboo. [ABSTRACT FROM AUTHOR]

Genetic markers are powerful tools for understanding genetic diversity and the molecular basis of traits, ushering in a new era of molecular breeding in crops. Over the past 50 years, DNA markers have rapidly changed, moving from hybridization-based and second-generation-based to sequence-based markers. Simple sequence repeats (SSRs) are the ideal markers in plant breeding, and they have numerous desirable properties, including their repeatability, codominance, multi-allelic nature, and locus specificity. They can be generated from any species, which requires prior sequence knowledge. SSRs may serve as evolutionary tuning knobs, allowing for rapid identification and adaptation to new circumstances. The evaluations published thus far have mostly ignored SSR polymorphism and gene evolution due to a lack of data regarding the precise placements of SSRs on chromosomes. However, NGS technologies have made it possible to produce high-throughput SSRs for any species using massive volumes of genomic sequence data that can be generated fast and at a minimal cost. Though SNP markers are gradually replacing the erstwhile DNA marker systems, SSRs remain the markers of choice in orphan crops due to the lack of genomic resources at the reference level and their adaptability to resource-limited labor. Several bioinformatic approaches and tools have evolved to handle genomic sequences to identify SSRs and generate primers for genotyping applications in plant breeding projects. This paper includes the currently available methodologies for producing SSR markers, genomic resource databases, and computational tools/pipelines for SSR data mining and primer generation. This review aims to provide a 'one-stop shop' of information to help each new user carefully select tools for identifying and utilizing SSRs in genetic research and breeding programs. [ABSTRACT FROM AUTHOR]

Main conclusion: This article explores possible future initiatives, such as the development of targeted breeding and integrated omics approach to boost little millet production, nutritional value, and environmental adaptation. Little millet (P. sumatrense) is a staple grain in many parts of Asia and Africa owing to its abundance in vitamins and minerals and its ability to withstand harsh agro-ecological conditions. Enhancing little millet using natural resources and novel crop improvement strategy is an effective way of boosting nutritional and food security. To understand the genetic makeup of the crop and figure out important characteristics linked to nutritional value, biotic and abiotic resistance, and production, researchers in this field are currently resorting on genomic technology. These realizations have expedited the crop's response to shifting environmental conditions by enabling the production of superior cultivars through targeted breeding. Going forward, further improvements in breeding techniques and genetics may boost the resilience, nutritional content, and production of little millet, which would benefit growers and consumers alike. The research and development on little millet improvement using novel omics platform and the integration of genetic resources are summarized in this review paper. Improved cultivars of little millet that satisfy changing farmer and consumer demands have already been developed through the use of these novel breeding strategies. This article also explores possible future initiatives, such as the development of targeted breeding, genomics, and sustainable agriculture methods. The potential for these measures to boost little millet's overall production, nutritional value, and climate adaptation will be extremely helpful in addressing nutritional security. Integrated omics for little millet improvement [ABSTRACT FROM AUTHOR]

Abstract Conventional pre-genomics breeding methodologies have significantly improved crop yields since the mid-twentieth century. Genomics provides breeders with advanced tools for whole-genome study, enabling a direct genotype–phenotype analysis. This shift has led to precise and efficient crop development through genomics-based approaches, including molecular markers, genomic selection, and genome editing. Molecular markers, such as SNPs, are crucial for identifying genomic regions linked to important traits, enhancing breeding accuracy and efficiency. Genomic resources viz. genetic markers, reference genomes, sequence and protein databases, transcriptomes, and gene expression profiles, are vital in plant breeding and aid in the identification of key traits, understanding genetic diversity, assist in genomic mapping, support marker-assisted selection and speeding up breeding programs. Advanced techniques like CRISPR/Cas9 allow precise gene modification, accelerating breeding processes. Key techniques like Genome-Wide Association study (GWAS), Marker-Assisted Selection (MAS), and Genomic Selection (GS) enable precise trait selection and prediction of breeding outcomes, improving crop yield, disease resistance, and stress tolerance. These tools are handy for complex traits influenced by multiple genes and environmental factors. This paper explores new genomic technologies like molecular markers, genomic selection, and genome editing for plant breeding showcasing their impact on developing new plant varieties.

Background: The oceanic whitetip shark Carcharhinus longimanus (family Carcharhinidae) is one of the largest sharks inhabiting all tropical and subtropical oceanic regions. Due to their life history traits and mortality attributed to pelagic longline fishing practices, this species is experiencing substantial population decline. Currently, C. longimanus is considered by the IUCN Red List of Threatened Species as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. This study sequences and describes the complete mitochondrial genome of C. longimanus in detail. Methods and results: The mitochondrial genome of C. longimanus was assembled through next-generation sequencing and then analyzed using specialized bioinformatics tools. The circular, double-stranded AT-rich mitogenome of C. longimanus is 16,704 bp long and contains 22 tRNA genes, 2 rRNA genes, 13 protein coding genes and a 1,065 bp long control region (CR). Out of the 22 tRNA genes, only one (tRNA-Ser1) lacked a typical 'cloverleaf' secondary structure. The prevalence of TTA (Leu), ATT (Ile) and CTA (Leu) codons in the PCGs likely contributes to the AT-rich nature of this mitogenome. In the CR, ten microsatellites were detected but no tandem repeats were found. Stem-and-loop secondary structures were common along the entire length of the CR. Ka/Ks values estimated for all PCGs were < 1, indicating that all the PCGs experience purifying selection. A phylomitogenomic analysis based on translated PCGs confirms the sister relationship between C. longimanus and C. obscurus. The analysis did not support the monophyly of the genus Carcharhinus. Conclusions: The assembled mitochondrial genome of this pelagic shark can provide insight into the phylogenetic relationships in the genus Carcharhinus and aid conservation and management efforts in the Central Pacific Ocean. [ABSTRACT FROM AUTHOR]

Penicillium spp. occupy many diverse biological niches that include plant pathogens, opportunistic human pathogens, saprophytes, indoor air contaminants, and those selected specifically for industrial applications to produce secondary metabolites and lifesaving antibiotics. Recent phylogenetic studies have established Penicillium fuscoglaucum as a synonym for Penicillium commune, which is an indoor air contaminant and toxin producer and can infect apple fruit during storage. During routine culturing on selective media in the lab, we obtained an isolate of P. fuscoglaucum Pf_T2 and sequenced its genome. The Pf_T2 genome is far superior to available genomic resources for the species. Our assembly exhibits a length of 35.1 Mb, a BUSCO score of 97.9% complete, and consists of five scaffolds/contigs representing the four expected chromosomes. It was determined that the Pf_T2 genome was colinear with a type specimen P. fuscoglaucum and contained a lineage-specific, intact cyclopiazonic acid (CPA) gene cluster. For comparison, a highly virulent postharvest apple pathogen, P. expansum strain TDL 12.1, was included and showed a similar growth pattern in culture to our Pf_T2 isolate but was far more aggressive in apple fruit than P. fuscoglaucum. The genome of Pf_T2 serves as a major improvement over existing resources, has superior annotation, and can inform forthcoming omics-based work and functional genetic studies to probe secondary metabolite production and disparities in aggressiveness during apple fruit decay. [ABSTRACT FROM AUTHOR]

Finger millet (Eleusine coracana) is an essential staple crop in many regions of Africa and Asia, valued for its nutritional content and resilience in challenging agro-ecological conditions. The enhancement of finger millet through genomic resources and breeding methods represents a promising avenue for addressing food and nutritional security. Current efforts in this field have harnessed genomic technologies to decipher the crop's genetic diversity and identify key traits related to yield, disease resistance, and nutritional content. These insights have facilitated the development of improved varieties through selective breeding, accelerating the crop's adaptation to changing environmental conditions. In the future, continued advancements in genomics and breeding methodologies hold the potential to further enhance finger millet's resilience, nutritional value, and productivity, ultimately benefiting both farmers and consumers. This review article synthesizes the current state of research and development in finger millet enhancement through the integration of genomic resources and innovative breeding methods. The utilization of these insights in selective breeding has already yielded promising results in developing improved finger millet varieties that meet the evolving needs of farmers and consumers. Moreover, this article discusses potential future interventions, including the continued advancement of genomics, precision breeding, and sustainable agricultural practices. These interventions hold the promise of further enhancing finger millet's adaptability to changing climates, its nutritional quality, and its overall productivity, thereby contributing to food security and improved livelihoods in finger millet-dependent regions. [ABSTRACT FROM AUTHOR]

To preserve biodiversity and maintain ecosystem services provided by trees in the course of climate change, it is essential to consider challenging tree species, which are less studied primarily due to a lack of investment compared to commercial species. Species of the genus Quercus present an interesting case because of their economic and ecological importance, and their syngameon biology. As a model for exploring ecological diversification, and with recent advances in forest genomics, knowledge, data, and genomic resources for oak have accumulated and are summarized in this review to foster oaks as potential candidate species for future reforestation programs in Canadian natural, peri-urban, and urban ecosystems. We summarize the state of current genomic research in oak and the accompanying opportunities genomics can provide to achieve the potential of oak silviculture in Canada. Further, we highlight the socio-economic benefits of planting oaks and genomic tools for the development of a traceability system along the value chain. Finally, we discuss some of the remaining challenges to successfully integrate oaks into different forest management programs. In light of their increased drought resistance, oak species exhibit a strong potential as viable choices for future forests, resilient agricultural landscapes, and urban areas. By leveraging the progress made in oak genomics and the new applications that have been developed for commercial species, we can foster the successful management of oak genetic resources for the production of suitable seedlings, thereby aiding Canada in its ambitious pursuit of planting two billion trees to combat climate change. [ABSTRACT FROM AUTHOR]

High species diversity, hybridization potential, broad geographical dispersal range and ornamental characteristics (i.e., attractive size, shape, structure, flowers, and evergreen) have fetched a good international market for Rhododendron. However, most species are restricted to specific geographic areas due to their habitat specificity in acidic soil and cold climates, resulting many species being classified under threat categories of the IUCN. In this review, advances in research on Rhododendron for improvement to floral display quality and stress resistance have been described. The low genetic barrier among species has created opportunities for extensive hybridization and ploidy alteration for introducing quality and adaptive traits during the development of new varieties. Recent technological advances have supported investigations into the mechanism of flower development, as well as cold tolerance and pathogen resistance mechanisms in the Rhododendron. However, most of the species have limited adaptability to drought, line-tolerance, pathogen resistance, and high-temperature conditions and this resistance ability present in few species largely remains unexplored. Additionally, the available genetic diversity and genomic information on species, and possibilities for their application in molecular breeding have been summarized. Overall, genomic resource data are scarce in the majority of the members of this genus. Finally, various research gaps such as genetic mapping of quality traits, understanding the molecular mechanism of quality-related traits and genomic assortment in Rhododendron members have been discussed in the future perspective section. [ABSTRACT FROM AUTHOR]

Uncontrolled crossbreeding is a major challenge to the conservation of landrace horses in East Asia. Understanding the factors driving this trend is crucial for effective conservation efforts. Here, we investigate the genomic makeup of 40 Mongolian Naadam racehorses and 21 Asian landrace horse breeds through analyzing whole‐genome resequencing and Y chromosome data. Our results show that crossbreeding practices are linked to horse‐racing traditions. Regions characterized by strong horse‐racing traditions and a lack of crossbreeding regulations exhibit significant levels of exotic genetic introgression, as observed in populations from Inner Mongolia and Central Asia. However, in Mongolia, despite having strong horse‐racing traditions, the implementation of policies aimed at preserving traditional horse‐racing culture effectively reduces exotic introgression. These results suggest that horse‐racing traditions are the main driver of crossbreeding practices. Our research highlights that the preservation of traditional values in landrace horses, achieved through carefully managed horse‐racing activities, can lead to successful conservation outcomes. [ABSTRACT FROM AUTHOR]

Wild pomegranate is a high-value crop for pharmaceutical industries. The lack of genetic and genomic resources in this medicinally important plant requires the development of simple sequence repeat (SSR) markers necessary for breeding programmes. In the present study, genomic sequences obtained using the Illumina platform revealed the presence of 8,000 sequences having genomic simple sequence repeats (gSSRs), with dinucleotide repeats being the most abundant (50.96%). A total of 103 marker pairs were randomly designed for the validation of 45 wild pomegranate accessions for diversity analysis. The amplicon size of developed gSSRs ranged between 141 and 297 base pairs. From a total of 57 polymorphic primers, 21 SSR pairs revealed 100% polymorphism. The existence of high genetic diversity (average Na-0.506, He-0.395, Ho-0.246) indicated the presence of heterozygotes in the wild pomegranate population. The polymorphism information content value ranged from 0.01 to 0.53, with the Shannon index values being between 0.09 and 1.60. Further, the genetic dissimilarity value ranged from 0.05 to 0.45, which grouped the wild pomegranate accessions into three clusters with two out-groups through a neighbour-joining analysis. The analysis of molecular variance indicated 25 and 75% of the total variation between and within the accessions, and population genetic structure research grouped the wild pomegranate accessions into four populations, which were partly bolstered by a principal component analysis and a neighbour-joining tree. Cross-species amplification demonstrated that out of 57 SSRs, 26 SSR loci had the transferability rate in cultivated pomegranate cultivars Ganesh and Dholka and 18 in Kandhari and Bedana, whereas the transferability rate was between 13.46 and 26.92% for plants from other families. Unique alleles were observed for both cultivated pomegranates and three cross-species tested in the present investigation. This is the first report where developed genomic SSRs would contribute to the genomic resources that will provide the basis for breeding-aided programmes for wild pomegranates. [ABSTRACT FROM AUTHOR]

The Ranunculales are a hyperdiverse lineage in many aspects of their phenotype, including growth habit, floral and leaf morphology, reproductive mode, and specialized metabolism. Many Ranunculales species, such as opium poppy and goldenseal, have a high medicinal value. In addition, the order includes a large number of commercially important ornamental plants, such as columbines and larkspurs. The phylogenetic position of the order with respect to monocots and core eudicots and the diversity within this lineage make the Ranunculales an excellent group for studying evolutionary processes by comparative studies. Lately, the phylogeny of Ranunculales was revised, and genetic and genomic resources were developed for many species, allowing comparative analyses at the molecular scale. Here, we review the literature on the resources for genetic manipulation and genome sequencing, the recent phylogeny reconstruction of this order, and its fossil record. Further, we explain their habitat range and delve into the diversity in their floral morphology, focusing on perianth organ identity, floral symmetry, occurrences of spurs and nectaries, sexual and pollination systems, and fruit and dehiscence types. The Ranunculales order offers a wealth of opportunities for scientific exploration across various disciplines and scales, to gain novel insights into plant biology for researchers and plant enthusiasts alike. [ABSTRACT FROM AUTHOR]

This article discusses the increasing availability of reference mitochondrial genomes for imperiled fishes in western North America for environmental DNA (eDNA) assay design and species monitoring. The authors highlight the limitations of traditional monitoring methods and the benefits of eDNA sampling. The study focuses on the design of eDNA assays using mitochondrial genes and provides complete mitochondrial genomes for several endangered fish species. The article emphasizes the importance of access to sequence data for effective eDNA monitoring. Another document provides information on the sequencing of mitochondrial genomes for various species of threatened and endangered freshwater fishes in New Mexico. The researchers successfully sequenced 63 complete mitogenomes, including those of 22 species protected under the Endangered Species Act. The findings highlight the importance of community-level mitogenome sampling for eDNA monitoring and provide valuable data for conservation and management. Another article discusses the use of eDNA methods for monitoring species distribution and biodiversity in aquatic ecosystems. The authors highlight the importance of considering geographic representation and phylogeographic variation when designing eDNA assays. They also discuss the challenges of using eDNA methods in highly biodiverse ecosystems and the need for comprehensive reference databases. The authors suggest that federal agencies should provide genomic resources to support conservation actions. The article emphasizes the importance of minimizing impacts on populations and habitats while conducting eDNA research. A compilation of various scientific articles related to eDNA and its applications in biodiversity monitoring and conservation is also available. The articles cover topics such as assessing fish communities, detecting endangered species, and studying microbial communities. They [Extracted from the article]

Barnyard millet is a vital yet underutilized cereal crop due to limited genetic research and improvement efforts. This review explores promising avenues like QTL mapping and Marker-Assisted Selection for targeted breeding, along with the exciting possibilities of genomic selection and speed breeding for faster variety development in barnyard millet. Even gene editing with CRISPR-Cas holds promise, but challenges like incomplete genome knowledge need to be addressed. Additionally, bioinformatics and systems biology approaches offer powerful tools to understand the complex interaction of genes and traits in barnyard millet. While limitations exist, actively pursuing these advancements can unlock barnyard millet's full potential, significantly impacting global food security and sustainable agriculture.

Genetic markers are powerful tools for understanding genetic diversity and the molecular basis of traits, ushering in a new era of molecular breeding in crops. Over the past 50 years, DNA markers have rapidly changed, moving from hybridization-based and second-generation-based to sequence-based markers. Simple sequence repeats (SSRs) are the ideal markers in plant breeding, and they have numerous desirable properties, including their repeatability, codominance, multi-allelic nature, and locus specificity. They can be generated from any species, which requires prior sequence knowledge. SSRs may serve as evolutionary tuning knobs, allowing for rapid identification and adaptation to new circumstances. The evaluations published thus far have mostly ignored SSR polymorphism and gene evolution due to a lack of data regarding the precise placements of SSRs on chromosomes. However, NGS technologies have made it possible to produce high-throughput SSRs for any species using massive volumes of genomic sequence data that can be generated fast and at a minimal cost. Though SNP markers are gradually replacing the erstwhile DNA marker systems, SSRs remain the markers of choice in orphan crops due to the lack of genomic resources at the reference level and their adaptability to resource-limited labor. Several bioinformatic approaches and tools have evolved to handle genomic sequences to identify SSRs and generate primers for genotyping applications in plant breeding projects. This paper includes the currently available methodologies for producing SSR markers, genomic resource databases, and computational tools/pipelines for SSR data mining and primer generation. This review aims to provide a ‘one-stop shop’ of information to help each new user carefully select tools for identifying and utilizing SSRs in genetic research and breeding programs.

This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops. [ABSTRACT FROM AUTHOR]

Introduction: Momordica balsamina is the closest wild species that can be crossed with an important fruit vegetable crop, Momordica charantia, has immense medicinal value, and placed under II subclass of primary gene pool of bitter gourd. M. balsamina is tolerant to major biotic and abiotic stresses. Genome characterization of Momordica balsamina as a wild relative of bitter gourd will contribute to the knowledge of the gene pool available for improvement in bitter gourd. There is potential to transfer gene/s related to biotic resistance and medicinal importance from M. balsamina to M. charantia to produce high-quality, better yielding and stress tolerant bitter gourd genotypes. Methods: The present study provides the first and high-quality chromosomelevel genome assembly of M. balsamina with size 384.90 Mb and N50 30.96 Mb using sequence data from 10x Genomics, Nanopore, and Hi-C platforms. Results: A total of 6,32,098 transposons elements; 2,15,379 simple sequence repeats; 5,67,483 transcription factor binding sites; 3,376 noncoding RNA genes; and 41,652 protein-coding genes were identified, and 4,347 disease resistance, 67 heat stress-related, 05 carotenoid-related, 15 salt stress-related, 229 cucurbitacin-related, 19 terpenes-related, 37 antioxidant activity, and 06 sex determination-related genes were characterized. Conclusion: Genome sequencing of M. balsamina will facilitate interspecific introgression of desirable traits. This information is cataloged in the form of webgenomic resource available at http://webtom.cabgrid.res.in/mbger/. Our finding of comparative genome analysis will be useful to get insights into the patterns and processes associated with genome evolution and to uncover functional regions of cucurbit genomes. [ABSTRACT FROM AUTHOR]

The Mediterranean purple sea urchin Paracentrotus lividus (Lamarck 1816) is a remarkable model system for molecular, evolutionary and cell biology studies, particularly in the field of developmental biology. We sequenced the genome, performed a de novo assembly, and analysed the assembly content. The genome of P. lividus was sequenced using Illumina NextSeq 500 System (Illumina) in a 2 × 150 paired-end format. More than 30,000 open reading frames (ORFs), (more than 8000 are unique), were identified and analysed to provide molecular tools accessible for the scientific community. In particular, several genes involved in complex innate immune responses, oxidative metabolism, signal transduction, and kinome, as well as genes regulating the membrane receptors, were identified in the P. lividus genome. In this way, the employment of the Mediterranean sea urchin for investigations and comparative analyses was empowered, leading to the explanation of cis-regulatory networks and their evolution in a key developmental model occupying an important evolutionary position with respect to vertebrates and humans. [ABSTRACT FROM AUTHOR]

The Fabeae tribe comprises five legume genera, which include some of the most ancient and important crops, like peas, lentils, and faba beans. Biotic and environmental stresses are major threats to the stable and high productivity of Fabeae crops. The use of omics resources can provide breeders with the tools needed to develop new crop varieties in a more efficient and sustainable way. However, the genomic efforts on Fabeae crops have lagged behind compared to other legume species, mainly due to their large genome size and repeat content. The first annotated chromosome-level reference genome assembly in Fabeae was published for pea (Pisum sativum cv. Caméor) in 2019. Since then, many efforts have been made to sequence the genome of other species from this tribe. Currently, 17 genomes of Fabeae species are available for the scientific community; five of them are at the chromosome level. Fundamental knowledge and molecular tools for breeding have been boosted on the legume resistance/tolerance against biotic and abiotic stresses by the availability of some of these recent reference genomes, especially the pea cv. Caméor genome. This review provides a comparison of the Fabeae tribe genomes available and an overview of recent accomplishments in their application in abiotic and biotic stress research. [ABSTRACT FROM AUTHOR]

The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, markerassisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes. [ABSTRACT FROM AUTHOR]

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Forest trees are beleaguered by the ever-increasing onslaught of invasive pests and pathogens, with some species in danger of functional extinction. Recent successes in developing resistant populations using traditional tree breeding assures that some of the affected species will persist in future forests. However, the sheer number of threatened species requires increases in breeding efficiency. The time is right to consider how the use of genomic resources might aid breeding efforts in the next 20 years. Any operational benefit of genomic resources will be minimal without closer collaboration between tree breeders, forest managers, and genomic researchers. We reflect here on what attributes were responsible for the success of traditional resistance breeding programs and whether advances in genomics can realistically accelerate breeding. We conclude that the use of genomics to directly advance resistance breeding efforts in the next 20 years will be limited. Major obstacles will include factors such as the undomesticated nature of most tree species, the quantitative genetic nature of resistance in many species, and the lack of adequate funding to accelerate and more fully develop genomic resources. Despite these limitations, genomic tools have potential to help increase our understanding of the nature of resistance, and the genetic variability in the host, which can aid in the deployment of resistant populations and may assist in marker-assisted selection, particularly for major gene resistance. [ABSTRACT FROM AUTHOR]

Abstract Uncontrolled crossbreeding is a major challenge to the conservation of landrace horses in East Asia. Understanding the factors driving this trend is crucial for effective conservation efforts. Here, we investigate the genomic makeup of 40 Mongolian Naadam racehorses and 21 Asian landrace horse breeds through analyzing whole‐genome resequencing and Y chromosome data. Our results show that crossbreeding practices are linked to horse‐racing traditions. Regions characterized by strong horse‐racing traditions and a lack of crossbreeding regulations exhibit significant levels of exotic genetic introgression, as observed in populations from Inner Mongolia and Central Asia. However, in Mongolia, despite having strong horse‐racing traditions, the implementation of policies aimed at preserving traditional horse‐racing culture effectively reduces exotic introgression. These results suggest that horse‐racing traditions are the main driver of crossbreeding practices. Our research highlights that the preservation of traditional values in landrace horses, achieved through carefully managed horse‐racing activities, can lead to successful conservation outcomes.

Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.

Penicillium spp. occupy many diverse biological niches that include plant pathogens, opportunistic human pathogens, saprophytes, indoor air contaminants, and those selected specifically for industrial applications to produce secondary metabolites and lifesaving antibiotics. Recent phylogenetic studies have established Penicillium fuscoglaucum as a synonym for Penicillium commune, which is an indoor air contaminant and toxin producer and can infect apple fruit during storage. During routine culturing on selective media in the lab, we obtained an isolate of P. fuscoglaucum Pf_T2 and sequenced its genome. The Pf_T2 genome is far superior to available genomic resources for the species. Our assembly exhibits a length of 35.1 Mb, a BUSCO score of 97.9% complete, and consists of five scaffolds/contigs representing the four expected chromosomes. It was determined that the Pf_T2 genome was colinear with a type specimen P. fuscoglaucum and contained a lineage-specific, intact cyclopiazonic acid (CPA) gene cluster. For comparison, a highly virulent postharvest apple pathogen, P. expansum strain TDL 12.1, was included and showed a similar growth pattern in culture to our Pf_T2 isolate but was far more aggressive in apple fruit than P. fuscoglaucum. The genome of Pf_T2 serves as a major improvement over existing resources, has superior annotation, and can inform forthcoming omics-based work and functional genetic studies to probe secondary metabolite production and disparities in aggressiveness during apple fruit decay.

This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.

IntroductionMomordica balsamina is the closest wild species that can be crossed with an important fruit vegetable crop, Momordica charantia, has immense medicinal value, and placed under II subclass of primary gene pool of bitter gourd. M. balsamina is tolerant to major biotic and abiotic stresses. Genome characterization of Momordica balsamina as a wild relative of bitter gourd will contribute to the knowledge of the gene pool available for improvement in bitter gourd. There is potential to transfer gene/s related to biotic resistance and medicinal importance from M. balsamina to M. charantia to produce high-quality, better yielding and stress tolerant bitter gourd genotypes.MethodsThe present study provides the first and high-quality chromosome-level genome assembly of M. balsamina with size 384.90 Mb and N50 30.96 Mb using sequence data from 10x Genomics, Nanopore, and Hi-C platforms.ResultsA total of 6,32,098 transposons elements; 2,15,379 simple sequence repeats; 5,67,483 transcription factor binding sites; 3,376 noncoding RNA genes; and 41,652 protein-coding genes were identified, and 4,347 disease resistance, 67 heat stress–related, 05 carotenoid-related, 15 salt stress–related, 229 cucurbitacin-related, 19 terpenes-related, 37 antioxidant activity, and 06 sex determination–related genes were characterized.ConclusionGenome sequencing of M. balsamina will facilitate interspecific introgression of desirable traits. This information is cataloged in the form of webgenomic resource available at http://webtom.cabgrid.res.in/mbger/. Our finding of comparative genome analysis will be useful to get insights into the patterns and processes associated with genome evolution and to uncover functional regions of cucurbit genomes.

The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, marker-assisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes.

Eurasian perch Perca fluviatilis has been a popular model species for decades in the fields of aquatic ecology, community dynamics, behaviour, physiology and ecotoxicology. Yet, despite extensive research, the progress of integrating genomic perspective into existing ecological knowledge in perch has been relatively modest. Meanwhile, the emergence of high‐throughput sequencing technologies has completely changed the methods for genetic variation assessment and conducting biodiversity and evolutionary research. During the last 5 years, three genome assemblies of P. fluviatilis have been generated, allowing substantial advancement of our understanding of the interactions between ecological and evolutionary processes at the whole‐genome level. We review the past progress, current status and potential future impact of the genomic resources and tools for ecological research in Eurasian perch focusing on the utility of recent whole‐genome assemblies. Furthermore, we demonstrate the power of genome‐wide approaches and newly developed tools and outline recent cases where genomics have contributed to new ecological and evolutionary knowledge. We explore how the availability of reference assembly enables the efficient application of various statistical tools, and how genomic approaches can provide novel insights into resource polymorphism, host–parasite interactions and to genetic and phenotypic changes associated with climate change and harvesting‐induced evolution. In summary, we call for increased integration of genomic tools into ecological research for perch, as well as for other fish species, which is likely to yield novel insights into processes linking the adaptation and plasticity to ecosystem functioning and environmental change. [ABSTRACT FROM AUTHOR]

SUMMARY: Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. The availability of whole genome assemblies and annotations of olive tree cultivars and oleaster (O. europaea subsp. europaea var. sylvestris) has contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources for olive tree populations that span the entire Mediterranean region. In the present study we developed the most complete genomic variation map and the most comprehensive catalog/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Additionally, the monumental ancient tree 'Throuba Naxos' was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by a selective sweep scan to be under selection pressure on all olive tree chromosomes. To further exploit the genomic and phenotypic resources obtained from the current work, genome‐wide association analyses were performed for 23 morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of olive tree biology. Significance Statement: The most comprehensive genomic variation map to date has been developed for olive trees (Olea europaea L. subsp. europaea var. europaea) originating from the entire Mediterranean basin, providing insights into the complex olive tree domestication and biology, and through a selective sweep scan and genome‐wide association approaches candidate genes controlling important agronomic traits in olive tree have been identified. [ABSTRACT FROM AUTHOR]

Advances in genomics resources have facilitated the evolution of cereal crops with enhanced yield, improved nutritional values, and heightened resistance to various biotic and abiotic stresses. Genomic approaches present a promising avenue for the development of high-yielding varieties, thereby ensuring food and nutritional security. Significant improvements have been made within the omics domain, specifically in genomics, transcriptomics, and proteomics. The advent of Next-Generation Sequencing (NGS) techniques has yielded an immense volume of data, accompanied by substantial progress in bioinformatic tools for proficient analysis. The synergy between genomics and computational tools has been acknowledged as pivotal for unravelling the intricate mechanisms governing genome-wide gene regulation. Within this review, the essential genomic resources are delineated, and their harmonization in the enhancement of cereal crop varieties is expounded upon, with a paramount focus on fulfilling the nutritional requisites of humankind. Furthermore, an encompassing compendium of the available genomic resources for cereal crops is presented, accompanied by an elucidation of their judicious utilization in the advancement of crop attributes. [ABSTRACT FROM AUTHOR]

The potential yield of maize (Zea mays L.) and other major crops is curtailed by several biotic, abiotic, and socio-economic constraints. Parasitic weeds, Striga spp., are major constraints to cereal and legume crop production in sub-Saharan Africa (SSA). Yield losses reaching 100% are reported in maize under severe Striga infestation. Breeding for Striga resistance has been shown to be the most economical, feasible, and sustainable approach for resource-poor farmers and for being environmentally friendly. Knowledge of the genetic and genomic resources and components of Striga resistance is vital to guide genetic analysis and precision breeding of maize varieties with desirable product profiles under Striga infestation. This review aims to present the genetic and genomic resources, research progress, and opportunities in the genetic analysis of Striga resistance and yield components in maize for breeding. The paper outlines the vital genetic resources of maize for Striga resistance, including landraces, wild relatives, mutants, and synthetic varieties, followed by breeding technologies and genomic resources. Integrating conventional breeding, mutation breeding, and genomic-assisted breeding [i.e., marker-assisted selection, quantitative trait loci (QTL) analysis, next-generation sequencing, and genome editing] will enhance genetic gains in Striga resistance breeding programs. This review may guide new variety designs for Striga-resistance and desirable product profiles in maize. [ABSTRACT FROM AUTHOR]

Millets are known for their resilience and nutritional benefits and hence believed to have a promising role in ensuring food and nutritional security under changing climatic conditions. Research on millets has intensified in recent years, especially in dissecting the genetic components of yield, stress tolerance and nutritional quality traits. Recent advances in next‐generation sequencing, bioinformatics and associated statistical procedures for genome‐wide association studies (GWAS) have provided wide opportunities to resolve the genetic complexity of polygenic traits by measuring historical and evolutionary recombination events in the natural population(s). During the past decade, GWAS has been successfully employed to identify key genes controlling growth, development, stress tolerance, nutrient use efficiency and nutritional quality traits in sorghum, pearl millet, foxtail millet and finger millet. However, progress in other minor millets is still in its infancy. Genetic dissection of these complex traits in millets may pave the way for genetic alteration of climate resilience, photosynthesis and nutrient accumulation in rice and wheat. In this review, progress in GWAS analysis in detecting QTLs underlying complex traits in sorghum and other millets is highlighted. [ABSTRACT FROM AUTHOR]

Drought is becoming a major threat to rice farming across the globe owing to the depletion of water tables in rice‐growing belts. Drought affects rice plants at multiple stages, causing damage at morphological and physio‐biochemical levels, leading to severe losses that exceed losses from all other stresses. The amalgamation of conventional breeding methods with modern molecular biology tools and biometrical methods could help accelerate the genetic gain for drought tolerance in rice. Many drought‐tolerance traits with genetic determinants have been identified and exploited for tolerance rice variety breeding. The integration of genome‐wide association study and genomic selection tools with speed breeding shortened the breeding cycle and aided in rapid improvement of genetic gain. In this review, we emphasized the progress made through classical breeding as well as the limitations and usefulness of current genomic methods in improving drought tolerance. We briefly addressed methods for identifying genetic determinants for drought tolerance and deploying them through genomics‐assisted breeding programmes to develop high‐yielding drought‐tolerant rice cultivars. [ABSTRACT FROM AUTHOR]

In this study, we evaluated the occurrence, relative abundance (RA), and density (RD) of simple sequence repeats (SSRs) in the complete genome and transcriptomic sequences of the plant pathogenic species of Pythium to acquire a better knowledge of their genome structure and evolution. Among the species, P. ultimum had the highest RA and RD of SSRs in the genomic sequences, whereas P. vexans had the highest RA and RD in the transcriptomic sequences. The genomic and transcriptomic sequences of P. aphanidermatum showed the lowest RA and RD of SSRs. Trinucleotide SSRs were the most prevalent class in both genomic and transcriptomic sequences, while dinucleotide SSRs were the least prevalent. The G + C content of the transcriptomic sequences was found to be positively correlated with the number (r = 0.601) and RA (r = 0.710) of SSRs. A motif conservation study revealed the highest number of unique motifs in P. vexans (9.9%). Overall, a low conservation of motifs was observed among the species (25.9%). A gene enrichment study revealed P. vexans and P. ultimum carry SSRs in their genes that are directly connected to virulence, whereas the remaining two species, P. aphanidermatum and P. arrhenomanes, harbour SSRs in genes involved in transcription, translation, and ATP binding. In an effort to enhance the genomic resources, a total of 11,002 primers from the transcribed regions were designed for the pathogenic Pythium species. Furthermore, the unique motifs identified in this work could be employed as molecular probes for species identification. [ABSTRACT FROM AUTHOR]

The volcano rabbit Romerolagus diazi is an endemic neotropical species restricted to the central part of the Trans-Mexican Volcanic Belt and considered 'endangered' by the International Union for Conservation of Nature Red List of Threatened Species. This study formally tested whether complete mitochondrial genomes of R. diazi can be assembled from non-enriched metagenomic libraries generated from eDNA (field droppings) using Illumina 300 bp pair-end reads. Using a direct assembly strategy, the mitogenome of R. diazi was assembled and circularised using the pipeline GetOrganelle with a coverage of 18.5× from one eDNA sample. A second strategy in which reads were first mapped to a reference mitochondrial genome and then assembled using the software SPAdes retrieved a second nearly complete mitogenome (2.7×) of R. diazi from a second eDNA sample. Complete or nearly complete mitochondrial genomes were not retrieved from two other eDNA samples. The organisation of the complete or nearly complete mitochondrial genomes recovered from eDNA samples is identical to that already described for the studied species. A phylomitogenomic analysis based on all protein coding genes (PCGs) demonstrated that the mitochondrial genomes assembled from eDNA can and do reliably identify the sequenced samples as belonging to R. diazi and distinguished the same samples from closely and distantly related cofamilial species. This study demonstrates the feasibility of retrieving fully accurate whole and nearly complete mitochondrial chromosomes of host species from eDNA without enrichment strategies and using straightforward bioinformatics pipelines. This new genomic resource developed for R. diazi represents a new tool to boost conservation strategies (bioprospecting and/or biomonitoring) and improve our understanding of the evolutionary history of this endemic and endangered species. [ABSTRACT FROM AUTHOR]