Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species

Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family

Citrus is an important nutritional fruit globally; however, its yield is affected by various stresses. This study presents the draft pangenome of Citrus, developed using 11 species to examine their genetic diversity and identify members of the germin-like proteins (GLPs) gene family involved in disease responsiveness. The developed sequence-based pangenome contains 954 Mb sequence and 74,755 genes. The comparative genomics analysis revealed the presence-absence variations (PAVs) among the Citrus genomes and species-specific protein-coding genes. Gene-based pangenome analysis revealed 4,936 new genes missing in the reference genome and highlighted the core and shell genes with putative functions in stress regulation. The pangenome-wide identification of GLP gene family members indicated the intraspecies diversity among the members across 11 genomes by analyzing their gene structure, motifs, and chromosomal distribution patterns. The synteny and evolutionary constraints analyses of Citrus GLPs provide detailed evidence of their evolutionary conservation and divergence. Further, the interaction, functional enrichment, and promoter analysis revealed their involvement in abiotic-, biotic-stress, signaling, and development-related pathways. The expression patterns of C. sinensis GLPs were studied in Huanglongbing (HLB) and Citrus canker disease. Several genes including CsGLPs1-2 and CsGLPs8-4 showed changes in expression patterns under both disease conditions. The qRT-PCR analysis revealed that these two genes were highly expressed in leaves infected with HLB disease across seven HLB-tolerant and susceptible citrus species. This Citrus pangenome and pangenes family study offers a comprehensive resource and new insights into the structural and functional diversity, identifying candidate genes that are important for future research to understand the stress-responsive mechanisms in Citrus.

A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study

BACKGROUND

The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, and mustards. However, pangenomes for polyploid species are relatively scarce and are available in only few crops including wheat, cotton, rapeseed, and potatoes.

MAIN BODY

In this review, we explore the various methods used in crop pangenome development, discussing the challenges and implications of these techniques based on insights from published pangenome studies. We offer a systematic guide and discuss the tools available for constructing a pangenome and conducting downstream analyses. Alfalfa, a highly heterozygous, cross pollinated and autotetraploid forage crop species, is used as an example to discuss the concerns and challenges offered by polyploid crop species. We conducted a comparative analysis using linear and graph-based methods by constructing an alfalfa graph pangenome using three publicly available genome assemblies. To illustrate the intricacies captured by pangenome graphs for a complex crop genome, we used five different gene sequences and aligned them against the three graph-based pangenomes. The comparison of the three graph pangenome methods reveals notable variations in the genomic variation captured by each pipeline.

CONCLUSION

Pangenome resources are proving invaluable by offering insights into core and dispensable genes, novel gene discovery, and genome-wide patterns of variation. Developing user-friendly online portals for linear pangenome visualization has made these resources accessible to the broader scientific and breeding community. However, challenges remain with graph-based pangenomes including compatibility with other tools, extraction of sequence for regions of interest, and visualization of genetic variation captured in pangenome graphs. These issues necessitate further refinement of tools and pipelines to effectively address the complexities of polyploid, highly heterozygous, and cross-pollinated species.

Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication

Jujube (Ziziphus jujuba Mill.), belonging to the Rhamnaceae family, is gaining increasing prominence as a perennial fruit crop with significant economic and medicinal values. Here, we conduct de novo assembly of four reference-grade genomes, encompassing one wild and three cultivated jujube accessions. We present insights into the population structure, genetic diversity, and genomic variations within a diverse collection of 1059 jujube accessions. Analyzes of the jujube pan-genome, based on our four assemblies and four previously released genomes, reveal extensive genomic variations within domestication-associated regions, potentially leading to the discovery of a candidate gene that regulates flowering and fruit ripening. By leveraging the pan-genome and a large-scale resequencing population, we identify two candidate genes involved in domestication traits, including the seed-setting rate, the bearing-shoot length and the leaf size in jujube. These genomic resources will accelerate evolutionary and functional genomics studies of jujube.

Exploring the genetic makeup of Xanthomonas species causing bacterial spot in Taiwan: evidence of population shift and local adaptation

The introduction of plant pathogens can quickly reshape disease dynamics in island agro-ecologies, representing a continuous challenge for local crop management strategies. Xanthomonas pathogens causing tomato bacterial spot were probably introduced in Taiwan several decades ago, creating a unique opportunity to study the genetic makeup and adaptive response of this alien population. We examined the phenotypic and genotypic identity of 669 pathogen entries collected across different regions of Taiwan in the last three decades. The analysis detected a major population shift, where X. euvesicatoria and X. vesicatoria races T1 and T2 were replaced by new races of X. perforans. After its introduction, race T4 quickly became dominant in all tomato-growing areas of the island. The genomic analysis of 317 global genomes indicates that the Xanthomonas population in Taiwan has a narrow genetic background, most likely resulting from a small number of colonization events. However, despite the apparent genetic uniformity, X. perforans race T4 shows multiple phenotypic responses in tomato lines. Additionally, an in-depth analysis of effector composition suggests diversification in response to local adaptation. These include unique mutations on avrXv3 which might allow the pathogen to overcome Xv3/Rx4 resistance gene. The findings underscore the dynamic evolution of a pathogen when introduced in a semi-isolated environment and provide insights into the potential management strategies for this important disease of tomato.

Technological Development and Advances for Constructing and Analyzing Plant Pangenomes

A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly, and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatic tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations.

A comprehensive evaluation of the potential of three next-generation short-read-based plant pan-genome construction strategies for the identification of novel non-reference sequence

Pan-genome studies are important for understanding plant evolution and guiding the breeding of crops by containing all genomic diversity of a certain species. Three short-read-based strategies for plant pan-genome construction include iterative individual, iteration pooling, and map-to-pan. Their performance is very different under various conditions, while comprehensive evaluations have yet to be conducted nowadays. Here, we evaluate the performance of these three pan-genome construction strategies for plants under different sequencing depths and sample sizes. Also, we indicate the influence of length and repeat content percentage of novel sequences on three pan-genome construction strategies. Besides, we compare the computational resource consumption among the three strategies. Our findings indicate that map-to-pan has the greatest recall but the lowest precision. In contrast, both two iterative strategies have superior precision but lower recall. Factors of sample numbers, novel sequence length, and the percentage of novel sequences' repeat content adversely affect the performance of all three strategies. Increased sequencing depth improves map-to-pan's performance, while not affecting the other two iterative strategies. For computational resource consumption, map-to-pan demands considerably more than the other two iterative strategies. Overall, the iterative strategy, especially the iterative pooling strategy, is optimal when the sequencing depth is less than 20X. Map-to-pan is preferable when the sequencing depth exceeds 20X despite its higher computational resource consumption.

A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)

Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.

Methods for Pangenomic Core Detection

Computational pangenomics deals with the joint analysis of all genomic sequences of a species. It has already been successfully applied to various tasks in many research areas. Further advances in DNA sequencing technologies constantly let more and more genomic sequences become available for many species, leading to an increasing attractiveness of pangenomic studies. At the same time, larger datasets also pose new challenges for data structures and algorithms that are needed to handle the data. Efficient methods oftentimes make use of the concept of k-mers.Core detection is a common way of analyzing a pangenome. The pangenome's core is defined as the subset of genomic information shared among all individual members. Classically, it is not only determined on the abstract level of genes but can also be described on the sequence level.In this chapter, we provide an overview of k-mer-based methods in the context of pangenomics studies. We first revisit existing software solutions for k-mer counting and k-mer set representation. Afterward, we describe the usage of two k-mer-based approaches, Pangrowth and Corer, for pangenomic core detection.

Evaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis

Cyclospora cayetanensis is an enteric coccidian parasite responsible for gastrointestinal disease transmitted through contaminated food and water. It has been documented in several countries, mostly with low-socioeconomic levels, although major outbreaks have hit developed countries. Detection methods based on oocyst morphology, staining, and molecular testing have been developed. However, the current MLST panel offers an opportunity for enhancement, as amplification of all molecular markers remains unfeasible in the majority of samples. This study aims to address this challenge by evaluating two approaches for analyzing the genetic diversity of C. cayetanensis and identifying reliable markers for subtyping: core homologous genes and mitochondrial genome analysis. A pangenome was constructed using 36 complete genomes of C. cayetanensis, and a haplotype network and phylogenetic analysis were conducted using 33 mitochondrial genomes. Through the analysis of the pangenome, 47 potential markers were identified, emphasizing the need for more sequence data to achieve comprehensive characterization. Additionally, the analysis of mitochondrial genomes revealed 19 single-nucleotide variations that can serve as characteristic markers for subtyping this parasite. These findings not only contribute to the selection of molecular markers for C. cayetanensis subtyping, but they also drive the knowledge toward the potential development of a comprehensive genotyping method for this parasite.

Interplay between transcriptional regulators and VapBC toxin-antitoxin loci during thermal stress response in extremely thermoacidophilic archaea

Thermoacidophilic archaea lack sigma factors and the large inventory of heat shock proteins (HSPs) widespread in bacterial genomes, suggesting other strategies for handling thermal stress are involved. Heat shock transcriptomes for the thermoacidophilic archaeon Saccharolobus (f. Sulfolobus) solfataricus 98/2 revealed genes that were highly responsive to thermal stress, including transcriptional regulators YtrASs (Ssol_2420) and FadRSs (Ssol_0314), as well as type II toxin-antitoxin (TA) loci VapBC6 (Ssol_2337, Ssol_2338) and VapBC22 (Ssol_0819, Ssol_0818). The role, if any, of type II TA loci during stress response in microorganisms, such as Escherichia coli, is controversial. But, when genes encoding YtrASs , FadRSs , VapC22, VapB6, and VapC6 were systematically mutated in Sa. solfataricus 98/2, significant up-regulation of the other genes within this set was observed, implicating an interconnected regulatory network during thermal stress response. VapBC6 and VapBC22 have close homologues in other Sulfolobales, as well as in other archaea (e.g. Pyrococcus furiosus and Archaeoglobus fulgidus), and their corresponding genes were also heat shock responsive. The interplay between VapBC TA loci and heat shock regulators in Sa solfataricus 98/2 not only indicates a cellular mechanism for heat shock response that differs from bacteria but one that could have common features within the thermophilic archaea.

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

The presence of mobile genetic elements in Salmonella isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three Salmonella isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was Salmonella Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand, Salmonella Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of Salmonella Heidelberg isolates carrying the IncI1-Iα plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.

Citrus genomic resources unravel putative genetic determinants of Huanglongbing pathogenicity

Citrus HLB caused by Candidatus Liberibacter asiaticus is a pathogen-triggered immune disease. Here, we identified putative genetic determinants of HLB pathogenicity by integrating citrus genomic resources to characterize the pan-genome of accessions that differ in their response to HLB. Genome-wide association mapping and analysis of allele-specific expression between susceptible, tolerant, and resistant accessions further refined candidates underlying the response to HLB. We first developed a phased diploid assembly of Citrus sinensis 'Newhall' genome and produced resequencing data for 91 citrus accessions that differ in their response to HLB. These data were combined with previous resequencing data from 356 accessions for genome-wide association mapping of the HLB response. Genes determinants for HLB pathogenicity were associated with host immune response, ROS production, and antioxidants. Overall, this study has provided a significant resource of citrus genomic data and identified candidate genes to be further explored to understand the genetic determinants of HLB pathogenicity.

Long non-coding RNAs reveal new regulatory mechanisms controlling gene expression

A plethora of non-coding RNAs have been found in eukaryotes, notably with the advent of modern sequencing technologies to analyze the transcriptome. Apart from the well-known housekeeping RNA genes (such as the ribosomal RNA or the transfer RNA), many thousands of transcripts detected are not evidently linked to a protein-coding gene. These, so called non-coding RNAs, may code for crucial regulators of gene expression, the small si/miRNAs, for small peptides (translated under specific conditions) or may act as long RNA molecules (antisense, intronic or intergenic long non-coding RNAs or lncRNAs). The lncRNAs interact with members of multiple machineries involved in gene regulation. In this review, we discussed about how plant lncRNAs permitted to discover new regulatory mechanisms acting in epigenetic control, chromatin 3D structure and alternative splicing. These novel regulations diversified the expression patterns and protein variants of target protein-coding genes and are an important element of the response of plants to environmental stresses and their adaptation to changing conditions.

Resequencing of durian genomes reveals large genetic variations among different cultivars

Durian (Durio zibethinus), which yields the fruit known as the "King of Fruits," is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.

Graph-based pan-genomes: increased opportunities in plant genomics

Due to the development of sequencing technology and the great reduction in sequencing costs, an increasing number of plant genomes have been assembled, and numerous genomes have revealed large amounts of variations. However, a single reference genome does not allow the exploration of species diversity, and therefore the concept of pan-genome was developed. A pan-genome is a collection of all sequences available for a species, including a large number of consensus sequences, large structural variations, and small variations including single nucleotide polymorphisms and insertions/deletions. A simple linear pan-genome does not allow these structural variations to be intuitively characterized, so graph-based pan-genomes have been developed. These pan-genomes store sequence and structural variation information in the form of nodes and paths to store and display species variation information in a more intuitive manner. The key role of graph-based pan-genomes is to expand the coordinate system of the linear reference genome to accommodate more regions of genetic diversity. Here, we review the origin and development of graph-based pan-genomes, explore their application in plant research, and further highlight the application of graph-based pan-genomes for future plant breeding.

Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable "occupancy" in the pan-genome - genes which are either present in all studied genotypes or missing in some genotypes - show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.

Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber

Structural variants (SVs) represent a major source of genetic diversity and are related to numerous agronomic traits and evolutionary events; however, their comprehensive identification and characterization in cucumber (Cucumis sativus L.) have been hindered by the lack of a high-quality pan-genome. Here, we report a graph-based cucumber pan-genome by analyzing twelve chromosome-scale genome assemblies. Genotyping of seven large chromosomal rearrangements based on the pan-genome provides useful information for use of wild accessions in breeding and genetic studies. A total of ~4.3 million genetic variants including 56,214 SVs are identified leveraging the chromosome-level assemblies. The pan-genome graph integrating both variant information and reference genome sequences aids the identification of SVs associated with agronomic traits, including warty fruits, flowering times and root growth, and enhances the understanding of cucumber trait evolution. The graph-based cucumber pan-genome and the identified genetic variants provide rich resources for future biological research and genomics-assisted breeding.

Increasing studies have suggested that single reference genome is insufficient to capture all variations in the genome. Here, the authors report a graph-based cucumber pan-genome by analyzing 12 chromosome-scale assemblies and reveal variations associated with agronomic traits and domestication.

Pangenome Analysis of Plant Transcripts and Coding Sequences

The pangenome of a species is the sum of the genomes of its individuals. As coding sequences often represent only a small fraction of each genome, analyzing the pangene set can be a cost-effective strategy for plants with large genomes or highly heterozygous species. Here, we describe a step-by-step protocol to analyze plant pangene sets with the software GET_HOMOLOGUES-EST . After a short introduction, where the main concepts are illustrated, the remaining sections cover the installation and typical operations required to analyze and annotate pantranscriptomes and gene sets of plants. The recipes include instructions on how to call core and accessory genes, how to compute a presence-absence pangenome matrix, and how to identify and analyze private genes, present only in some genotypes. Downstream phylogenetic analyses are also discussed.

Searching for Homologous Genes Using Daisychain

Genome assemblies have become a standard tool of genomics research and are relatively inexpensive to produce due to falling sequencing costs. For many species, there are now several reference-grade genome assemblies. However, comparing different assemblies or the same or related individuals is not an easy task, especially with different levels of quality of assembly and annotation. Tools are needed to visualise related genes with different IDs across genome assemblies. Here, we present a workflow to search and visualise related genes using Daisychain, a web-based tool aimed at researchers who wish to compare genes between assemblies.

Making a Pangenome Using the Iterative Mapping Approach

Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.

Pangenome of white lupin provides insights into the diversity of the species

White lupin is an old crop with renewed interest due to its seed high protein content and high nutritional value. Despite a long domestication history in the Mediterranean basin, modern breeding efforts have been fairly scarce. Recent sequencing of its genome has provided tools for further description of genetic resources but detailed characterization of genomic diversity is still missing. Here, we report the genome sequencing of 39 accessions that were used to establish a white lupin pangenome. We defined 32 068 core genes that are present in all individuals and 14 822 that are absent in some and may represent a gene pool for breeding for improved productivity, grain quality, and stress adaptation. We used this new pangenome resource to identify candidate genes for alkaloid synthesis, a key grain quality trait. The white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability within this crop. Thus, this pangenome resource is an important step towards the effective and efficient genetic improvement of white lupin to help meet the rapidly growing demand for plant protein sources for human and animal consumption.

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes

The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts.

Genomic analysis and characterization of Scenedesmus glucoliberatum PABB004: An unconventional sugar-secreting green alga

AIMS

In this report, we present Scenedesmus glucoliberatum PABB004, a microalga that was isolated from an association with Paramecium bursaria with the potential for application in fermentative processes and co-culture schemes due to its advantageous high sugar secretion phenotype.

METHODS AND RESULTS

We sequenced, assembled and annotated the draft genome and transcriptome for this newly reported strain. The nuclear genome has an exceptionally high GC content of 78%. Our results revealed significant sugar accumulation over a range from 6.2 to 7.8 pH units. The predicted proteome was compared with other green algae that show different sugar secretion phenotypes aiming to help uncover their common features for simple sugar secretion and those unique to S. glucoliberatum PABB004.

CONCLUSIONS

The evolutionary history of this organism, inferred from its genomic traits, expands our current understanding of algal mutualistic relationships involving photosynthate exchanges. S. glucoliberatum PABB004 secreted ready-to-use fermentable sugars (glucose and maltose) directly to the extracellular media achieving concentrations greater than 2.7 g/L of free glucose and 1.2 g/L of maltose in batch cultures.

SIGNIFICANCE AND IMPACT OF THE STUDY

A draft genome is provided for a new member of an important class of green algae. Scenedesmus glucoliberatum PABB004 secretes high levels of simple sugars over a broad pH range.

The pan-genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content

Studies on structural variation in plants have revealed the inadequacy of a single reference genome for an entire species and suggest that it is necessary to build a species-representative genome called a pan-genome to better capture the extent of both structural and nucleotide variation. Here, we present a pan-genome of cultivated soybean (Glycine max), termed PanSoy, constructed using the de novo genome assembly of 204 phylogenetically and geographically representative improved accessions selected from the larger GmHapMap collection. PanSoy uncovers 108 Mb (˜11%) of novel nonreference sequences encompassing 3621 protein-coding genes (including 1659 novel genes) absent from the soybean 'Williams 82' reference genome. Nonetheless, the core genome represents an exceptionally large proportion of the genome, with >90.6% of genes being shared by >99% of the accessions. A majority of PAVs encompassing genes could be confirmed with long-read sequencing on a subset of accessions. The PanSoy is a major step towards capturing the extent of genetic variation in cultivated soybean and provides a resource for soybean genomics research and breeding.

Next-Generation Breeding Strategies for Climate-Ready Crops

Climate change is a threat to global food security due to the reduction of crop productivity around the globe. Food security is a matter of concern for stakeholders and policymakers as the global population is predicted to bypass 10 billion in the coming years. Crop improvement via modern breeding techniques along with efficient agronomic practices innovations in microbiome applications, and exploiting the natural variations in underutilized crops is an excellent way forward to fulfill future food requirements. In this review, we describe the next-generation breeding tools that can be used to increase crop production by developing climate-resilient superior genotypes to cope with the future challenges of global food security. Recent innovations in genomic-assisted breeding (GAB) strategies allow the construction of highly annotated crop pan-genomes to give a snapshot of the full landscape of genetic diversity (GD) and recapture the lost gene repertoire of a species. Pan-genomes provide new platforms to exploit these unique genes or genetic variation for optimizing breeding programs. The advent of next-generation clustered regularly interspaced short palindromic repeat/CRISPR-associated (CRISPR/Cas) systems, such as prime editing, base editing, and de nova domestication, has institutionalized the idea that genome editing is revamped for crop improvement. Also, the availability of versatile Cas orthologs, including Cas9, Cas12, Cas13, and Cas14, improved the editing efficiency. Now, the CRISPR/Cas systems have numerous applications in crop research and successfully edit the major crop to develop resistance against abiotic and biotic stress. By adopting high-throughput phenotyping approaches and big data analytics tools like artificial intelligence (AI) and machine learning (ML), agriculture is heading toward automation or digitalization. The integration of speed breeding with genomic and phenomic tools can allow rapid gene identifications and ultimately accelerate crop improvement programs. In addition, the integration of next-generation multidisciplinary breeding platforms can open exciting avenues to develop climate-ready crops toward global food security.

Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding

Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant '67/3' reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.

Genome-wide association study and its applications in the non-model crop Sesamum indicum

BACKGROUND

Sesame is a rare example of non-model and minor crop for which numerous genetic loci and candidate genes underlying features of interest have been disclosed at relatively high resolution. These progresses have been achieved thanks to the applications of the genome-wide association study (GWAS) approach. GWAS has benefited from the availability of high-quality genomes, re-sequencing data from thousands of genotypes, extensive transcriptome sequencing, development of haplotype map and web-based functional databases in sesame.

RESULTS

In this paper, we reviewed the GWAS methods, the underlying statistical models and the applications for genetic discovery of important traits in sesame. A novel online database SiGeDiD ( http://sigedid.ucad.sn/ ) has been developed to provide access to all genetic and genomic discoveries through GWAS in sesame. We also tested for the first time, applications of various new GWAS multi-locus models in sesame.

CONCLUSIONS

Collectively, this work portrays steps and provides guidelines for efficient GWAS implementation in sesame, a non-model crop.

Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper

BACKGROUND

Peppers (Capsicum annuum L.) containing distinct capsaicinoids are the most widely cultivated spices in the world. However, extreme genomic diversity among species represents an obstacle to breeding pepper.

RESULTS

Here, we report de novo genome assemblies of Capsicum annuum 'Early Calwonder (non-pungent, ECW)' and 'Small Fruit (pungent, SF)' along with their annotations. In total, we assembled 2.9 Gb of ECW and SF genome sequences, representing over 91% of the estimated genome sizes. Structural and functional annotation of the two pepper genomes generated about 35,000 protein-coding genes each, of which 93% were assigned putative functions. Comparison between newly and publicly available pepper gene annotations revealed both shared and specific gene content. In addition, a comprehensive analysis of nucleotide-binding and leucine-rich repeat (NLR) genes through whole-genome alignment identified five significant regions of NLR copy number variation (CNV). Detailed comparisons of those regions revealed that these CNVs were generated by intra-specific genomic variations that accelerated diversification of NLRs among peppers.

CONCLUSIONS

Our analyses unveil an evolutionary mechanism responsible for generating CNVs of NLRs among pepper accessions, and provide novel genomic resources for functional genomics and molecular breeding of disease resistance in Capsicum species.

Plant NLR diversity: the known unknowns of pan-NLRomes

Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same species. While this diversity has long been appreciated, its true extent has remained unknown. With pan-genome and pan-NLRome studies becoming more and more comprehensive, our knowledge of NLR sequence diversity is growing rapidly, and pan-NLRomes provide powerful platforms for assigning function to NLRs. These efforts are an important step toward the goal of comprehensively predicting from sequence alone whether an NLR provides disease resistance, and if so, to which pathogens.

The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago

Caffeine is the most consumed alkaloid stimulant in the world. It is synthesized through the activity of three known N-methyltransferase proteins. Here we are reporting on the 422-Mb chromosome-level assembly of the Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from the Comoro archipelago. We predicted 32,874 genes and anchored 88.7% of the sequence onto the 11 chromosomes. Comparative analyses with the African Robusta coffee genome (C. canephora) revealed an extensive genome conservation, despite an estimated 11 million years of divergence and a broad diversity of genome sizes within the Coffea genus. In this genome, the absence of caffeine is likely due to the absence of the caffeine synthase gene which converts theobromine into caffeine through an illegitimate recombination mechanism. These findings pave the way for further characterization of caffeine-free species in the Coffea genus and will guide research towards naturally-decaffeinated coffee drinks for consumers.

Design of a diagnostic system based on molecular markers derived from the ascomycetes pan-genome analysis: The case of Fusarium dieback disease

A key factor to take actions against phytosanitary problems is the accurate and rapid detection of the causal agent. Here, we develop a molecular diagnostics system based on comparative genomics to easily identify fusariosis and specific pathogenic species as the Fusarium kuroshium, the symbiont of the ambrosia beetle Euwallaceae kuroshio Gomez and Hulcr which is responsible for Fusarium dieback disease in San Diego CA, USA. We performed a pan-genome analysis using sixty-three ascomycetes fungi species including phytopathogens and fungi associated with the ambrosia beetles. Pan-genome analysis revealed that 2,631 orthologue genes are only shared by Fusarium spp., and on average 3,941 (SD ± 1,418.6) are species-specific genes. These genes were used for PCR primer design and tested on DNA isolated from i) different strains of ascomycete species, ii) artificially infected avocado stems and iii) plant tissue of field-collected samples presumably infected. Our results let us propose a useful set of primers to either identify any species from Fusarium genus or, in a specific manner, species such as F. kuroshium, F. oxysporum, and F. graminearum. The results suggest that the molecular strategy employed in this study can be expanded to design primers against different types of pathogens responsible for provoking critical plant diseases.

GreenPhylDB v5: a comparative pangenomic database for plant genomes

Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.

Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain

Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.

Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication

Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.

Phased diploid genomes of the cultivated apple Malus domestica cv. Gala and its two major wild progenitors M. sieversii and M. sylvestris, as well as pan-genome analyses, provide insights into the genetic history of apple domestication.

Pan-genome: A promising resource for noncoding RNA discovery in plants

Plant genomes contain both protein-coding and noncoding sequences including transposable elements (TEs) and noncoding RNAs (ncRNAs). The ncRNAs are recognized as important elements that play fundamental roles in the structural organization and function of plant genomes. Despite various hypotheses, TEs are believed to be a major precursor of ncRNAs. Transposable elements are also prime factors that cause genomic variation among members of a species. Hence, TEs pose a major challenge in the discovery and analysis of ncRNAs. With the increase in the number of sequenced plant genomes, it is now accepted that a single reference genome is insufficient to represent the complete genomic diversity and contents of a species, and exploring the pan-genome of a species is critical. In this review, we summarize the recent progress in the field of plant pan-genomes. We also discuss TEs and their roles in ncRNA biogenesis and present our perspectives on the application of pan-genomes for the discovery of ncRNAs to fully explore and exploit their biological roles in plants.

Plant pan-genomes are the new reference

Recent years have seen a surge in plant genome sequencing projects and the comparison of multiple related individuals. The high degree of genomic variation observed led to the realization that single reference genomes do not represent the diversity within a species, and led to the expansion of the pan-genome concept. Pan-genomes represent the genomic diversity of a species and includes core genes, found in all individuals, as well as variable genes, which are absent in some individuals. Variable gene annotations often show similarities across plant species, with genes for biotic and abiotic stress commonly enriched within variable gene groups. Here we review the growth of pan-genomics in plants, explore the origins of gene presence and absence variation, and show how pan-genomes can support plant breeding and evolution studies.

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.

Global Role of Crop Genomics in the Face of Climate Change

The development of climate change resilient crops is necessary if we are to meet the challenge of feeding the growing world's population. We must be able to increase food production despite the projected decrease in arable land and unpredictable environmental conditions. This review summarizes the technological and conceptual advances that have the potential to transform plant breeding, help overcome the challenges of climate change, and initiate the next plant breeding revolution. Recent developments in genomics in combination with high-throughput and precision phenotyping facilitate the identification of genes controlling critical agronomic traits. The discovery of these genes can now be paired with genome editing techniques to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value. Utilizing the genetic potential of crop wild relatives (CWRs) enables the domestication of new species and the generation of synthetic polyploids. The high-quality crop plant genome assemblies and annotations provide new, exciting research targets, including long non-coding RNAs (lncRNAs) and cis-regulatory regions. Metagenomic studies give insights into plant-microbiome interactions and guide selection of optimal soils for plant cultivation. Together, all these advances will allow breeders to produce improved, resilient crops in relatively short timeframes meeting the demands of the growing population and changing climate.

Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation

Root architecture varies widely between species; it even varies between ecotypes of the same species, despite strong conservation of the coding portion of their genomes. By contrast, noncoding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long noncoding RNAs (lncRNAs) are known to quantitatively regulate gene expression. Roots from ecotypes Columbia and Landsberg erecta of Arabidopsis (Arabidopsis thaliana) respond differently to phosphate starvation. Here, we compared transcriptomes (mRNAs, lncRNAs, and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of lncRNAs that were largely conserved at the DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independent of phosphate availability. We further characterized these ecotype-related lncRNAs and studied their link with small interfering RNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes, including antisense RNAs targeting key regulators of root-growth responses. Misregulation of several lincRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in ecotype Columbia. RNA-sequencing analysis following deregulation of lncRNA NPC48 revealed a potential link with root growth and transport functions. This exploration of the noncoding transcriptome identified ecotype-specific lncRNA-mediated regulation in root apexes. The noncoding genome may harbor further mechanisms involved in ecotype adaptation of roots to different soil environments.

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

The pangenome provides genomic variations in the cultivated gene pool for a given species. However, as the crop's gene pool comprises many species, especially wild relatives with diverse genetic stock, here we suggest using accessions from all available species of a given genus for the development of a more comprehensive and complete pangenome, which we refer to as a super-pangenome. The super-pangenome provides a complete genomic variation repertoire of a genus and offers unprecedented opportunities for crop improvement. This opinion article focuses on recent developments in crop pangenomics, the need for a super-pangenome that should include wild species, and its application for crop improvement.

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities.

ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline

Summary

Since the idea of pan-genomics emerged several tools and pipelines have been introduced for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been reported which could overcome multiple challenges associated with eukaryotic pan-genomics. To aid the eukaryotic pan-genomic studies, here we present ppsPCP pipeline which is designed for eukaryotes especially for plants. It is capable of scanning presence/absence variants (PAVs) and constructing a fully annotated pan-genome. We believe with these unique features of PAV scanning and building a pan-genome together with its annotation, ppsPCP will be useful for plant pan-genomic studies and aid researchers to study genetic/phenotypic variations and genomic diversity.

Availability and implementation

The ppsPCP is freely available at github DOI: https://doi.org/10.5281/zenodo.2567390 and webpage http://cbi.hzau.edu.cn/ppsPCP/.

Supplementary information

Supplementary data are available at Bioinformatics online.

Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes

Mutualistic symbiosis and eusociality have developed through gradual evolutionary processes at different times in specific lineages. Like some species of termites and ants, ambrosia beetles have independently evolved a mutualistic nutritional symbiosis with fungi, which has been associated with the evolution of complex social behaviors in some members of this group. We sequenced the transcriptomes of two ambrosia complexes (Euwallacea sp. near fornicatus⁻Fusarium euwallaceae and Xyleborus glabratus⁻Raffaelea lauricola) to find evolutionary signatures associated with mutualism and behavior evolution. We identified signatures of positive selection in genes related to nutrient homeostasis; regulation of gene expression; development and function of the nervous system, which may be involved in diet specialization; behavioral changes; and social evolution in this lineage. Finally, we found convergent changes in evolutionary rates of proteins across lineages with phylogenetically independent origins of sociality and mutualism, suggesting a constrained evolution of conserved genes in social species, and an evolutionary rate acceleration related to changes in selective pressures in mutualistic lineages.

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.

The role of differential gene content in the evolution and function of eukaryotic genomes remains poorly explored. Here the authors assemble and annotate the Brachypodium distachyon pan-genome consisting of 54 diverse lines and reveal the differential present genes as a major driver of phenotypic variation.

Sequencing and De Novo Assembly of the Toxicodendron radicans (Poison Ivy) Transcriptome

Contact with poison ivy plants is widely dreaded because they produce a natural product called urushiol that is responsible for allergenic contact delayed-dermatitis symptoms lasting for weeks. For this reason, the catchphrase most associated with poison ivy is "leaves of three, let it be", which serves the purpose of both identification and an appeal for avoidance. Ironically, despite this notoriety, there is a dearth of specific knowledge about nearly all other aspects of poison ivy physiology and ecology. As a means of gaining a more molecular-oriented understanding of poison ivy physiology and ecology, Next Generation DNA sequencing technology was used to develop poison ivy root and leaf RNA-seq transcriptome resources. De novo assembled transcriptomes were analyzed to generate a core set of high quality expressed transcripts present in poison ivy tissue. The predicted protein sequences were evaluated for similarity to SwissProt homologs and InterProScan domains, as well as assigned both GO terms and KEGG annotations. Over 23,000 simple sequence repeats were identified in the transcriptome, and corresponding oligo nucleotide primer pairs were designed. A pan-transcriptome analysis of existing Anacardiaceae transcriptomes revealed conserved and unique transcripts among these species.

Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace

Drought causes important losses in crop production every season. Improvement for drought tolerance could take advantage of the diversity held in germplasm collections, much of which has not been incorporated yet into modern breeding. Spanish landraces constitute a promising resource for barley breeding, as they were widely grown until last century and still show good yielding ability under stress. Here, we study the transcriptome expression landscape in two genotypes, an outstanding Spanish landrace-derived inbred line (SBCC073) and a modern cultivar (Scarlett). Gene expression of adult plants after prolonged stresses, either drought or drought combined with heat, was monitored. Transcriptome of mature leaves presented little changes under severe drought, whereas abundant gene expression changes were observed under combined mild drought and heat. Developing inflorescences of SBCC073 exhibited mostly unaltered gene expression, whereas numerous changes were found in the same tissues for Scarlett. Genotypic differences in physiological traits and gene expression patterns confirmed the different behavior of landrace SBCC073 and cultivar Scarlett under abiotic stress, suggesting that they responded to stress following different strategies. A comparison with related studies in barley, addressing gene expression responses to drought, revealed common biological processes, but moderate agreement regarding individual differentially expressed transcripts. Special emphasis was put in the search of co-expressed genes and underlying common regulatory motifs. Overall, 11 transcription factors were identified, and one of them matched cis-regulatory motifs discovered upstream of co-expressed genes involved in those responses.