Near-Complete Genome Assembly of Alternaria brassicae-A Necrotrophic Pathogen of Brassica Crops

Karyotype and LTR-RTs analysis provide insights into oak genomic evolution

BACKGROUND

Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests.

RESULTS

Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes.

CONCLUSION

Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.

Fungal effectors versus defense-related genes of B. juncea and the status of resistant transgenics against fungal pathogens

Oilseed brassica has become instrumental in securing global food and nutritional security. B. juncea, colloquially known as Indian mustard, is cultivated across tropics and subtropics including Indian subcontinent. The production of Indian mustard is severely hampered by fungal pathogens which necessitates human interventions. Chemicals are often resorted to as they are quick and effective, but due to their economic and ecological unsustainability, there is a need to explore their alternatives. The B. juncea-fungal pathosystem is quite diverse as it covers broad-host range necrotrophs (Sclerotinia sclerotiorum), narrow-host range necrotrophs (Alternaria brassicae and A. brassicicola) and biotrophic oomycetes (Albugo candida and Hyaloperonospora brassica). Plants ward off fungal pathogens through two-step resistance mechanism; PTI which involves recognition of elicitors and ETI where the resistance gene (R gene) interacts with the fungal effectors. The hormonal signalling is also found to play a vital role in defense as the JA/ET pathway is initiated at the time of necrotroph infection and SA pathway is induced when the biotrophs attack plants. The review discuss the prevalence of fungal pathogens of Indian mustard and the studies conducted on effectoromics. It covers both pathogenicity conferring genes and host-specific toxins (HSTs) that can be used for a variety of purposes such as identifying cognate R genes, understanding pathogenicity and virulence mechanisms, and establishing the phylogeny of fungal pathogens. It further encompasses the studies on identifying resistant sources and characterisation of R genes/quantitative trait loci and defense-related genes identified in Brassicaceae and unrelated species which, upon introgression or overexpression, confer resistance. Finally, the studies conducted on developing resistant transgenics in Brassicaceae have been covered in which chitinase and glucanase genes are mostly used. The knowledge gained from this review can further be used for imparting resistance against major fungal pathogens.

Key Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species

Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.

Transcriptome Analysis of the Necrotrophic Pathogen Alternaria brassicae Reveals Insights into Its Pathogenesis in Brassica juncea

Alternaria blight or leaf spot caused by Alternaria brassicae has an enormous economic impact on the Brassica crops grown worldwide. Although the genome of A. brassicae has been sequenced, little is known about the genes that play a role during the infection of the host species. In this study, the transcriptome expression profile of A. brassicae during growth and infection was determined. Differential expression analysis revealed that 4,430 genes were differentially expressed during infection. Weighted gene coexpression network analysis helped identify 10 modules, which were highly correlated with growth and infection. Subsequent gene ontology (GO) enrichment analysis of the modules highlighted the involvement of biological processes such as toxin metabolism, ribosome biogenesis, polysaccharide catabolism, copper ion transport, and vesicular trafficking during infection. Additionally, 200 carbohydrate-active enzymes (CAZymes) and 80 potential effectors were significantly upregulated during infection. Furthermore, 18 secondary metabolite gene clusters were also differentially expressed during infection. The clusters responsible for the production of destruxin B, brassicicene C, and HC-toxin were significantly upregulated during infection. Collectively, these results provide an overview of the critical pathways underlying the pathogenesis of A. brassicae and highlight the distinct gene networks that are temporally regulated. The study thus provides novel insights into the transcriptional plasticity of a necrotrophic pathogen during infection of its host. Additionally, the in planta expression evidence for many potential effectors provides a theoretical basis for further investigations into the effector biology of necrotrophic pathogens such as A. brassicae. IMPORTANCE Alternaria brassicae is a necrotrophic pathogen that can infect almost all members of the Brassicaceae family. A. brassicae causes extensive yield losses in oilseed mustard and has practically restricted the cultivation of oilseed brassicas in regions with cool and foggy climatic conditions (foothills and mountainous terrains) where the severity of the pathogen is the highest. In this study, I identified the differentially expressed genes associated with the pathogenicity of A. brassicae through transcriptome sequencing. Also, I have been able to delineate pathways that are active during the early and late stages of infection. Consequently, this study has provided crucial insights into the molecular mechanisms underlying the pathogenesis of A. brassicae, an important necrotrophic pathogen.

Current Status of the Disease-Resistant Gene(s)/QTLs, and Strategies for Improvement in Brassica juncea

Brassica juncea is a major oilseed crop in tropical and subtropical countries, especially in south-east Asia like India, China, Bangladesh, and Pakistan. The widespread cultivation of genetically similar varieties tends to attract fungal pathogens which cause heavy yield losses in the absence of resistant sources. The conventional disease management techniques are often expensive, have limited efficacy, and cause additional harm to the environment. A substantial approach is to identify and use of resistance sources within the Brassica hosts and other non-hosts to ensure sustainable oilseed crop production. In the present review, we discuss six major fungal pathogens of B. juncea: Sclerotinia stem rot (Sclerotinia sclerotiorum), Alternaria blight (Alternaria brassicae), White rust (Albugo candida), Downy mildew (Hyaloperonospora parasitica), Powdery mildew (Erysiphe cruciferarum), and Blackleg (Leptoshaeria maculans). From discussing studies on pathogen prevalence in B. juncea, the review then focuses on highlighting the resistance sources and quantitative trait loci/gene identified so far from Brassicaceae and non-filial sources against these fungal pathogens. The problems in the identification of resistance sources for B. juncea concerning genome complexity in host subpopulation and pathotypes were addressed. Emphasis has been laid on more elaborate and coordinated research to identify and deploy R genes, robust techniques, and research materials. Examples of fully characterized genes conferring resistance have been discussed that can be transformed into B. juncea using advanced genomics tools. Lastly, effective strategies for B. juncea improvement through introgression of novel R genes, development of pre-breeding resistant lines, characterization of pathotypes, and defense-related secondary metabolites have been provided suggesting the plan for the development of resistant B. juncea.

Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era

Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.

Emerging Advanced Technologies to Mitigate the Impact of Climate Change in Africa

Agriculture remains critical to Africa's socioeconomic development, employing 65% of the work force and contributing 32% of GDP (Gross Domestic Product). Low productivity, which characterises food production in many Africa countries, remains a major concern. Compounded by the effects of climate change and lack of technical expertise, recent reports suggest that the impacts of climate change on agriculture and food systems in African countries may have further-reaching consequences than previously anticipated. Thus, it has become imperative that African scientists and farmers adopt new technologies which facilitate their research and provide smart agricultural solutions to mitigating current and future climate change-related challenges. Advanced technologies have been developed across the globe to facilitate adaptation to climate change in the agriculture sector. Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), synthetic biology, and genomic selection, among others, constitute examples of some of these technologies. In this work, emerging advanced technologies with the potential to effectively mitigate climate change in Africa are reviewed. The authors show how these technologies can be utilised to enhance knowledge discovery for increased production in a climate change-impacted environment. We conclude that the application of these technologies could empower African scientists to explore agricultural strategies more resilient to the effects of climate change. Additionally, we conclude that support for African scientists from the international community in various forms is necessary to help Africans avoid the full undesirable effects of climate change.

Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae - a pathogen of the Brassicaceae family

BACKGROUND

Alternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and A. alternata are known to cause secondary infections in the A. brassicae-infected Brassicas. The genome architecture, pathogenicity factors, and determinants of host-specificity of A. brassicae are unknown. In this study, we annotated and characterised the recently announced genome assembly of A. brassicae and compared it with other Alternaria spp. to gain insights into its pathogenic lifestyle.

RESULTS

We also sequenced the genomes of two A. alternata isolates that were co-infecting B. juncea using Nanopore MinION sequencing for additional comparative analyses within the Alternaria genus. Genome alignments within the Alternaria spp. revealed high levels of synteny between most chromosomes with some intrachromosomal rearrangements. We show for the first time that the genome of A. brassicae, a large-spored Alternaria species, contains a dispensable chromosome. We identified 460 A. brassicae-specific genes, which included many secreted proteins and effectors. Furthermore, we have identified the gene clusters responsible for the production of Destruxin-B, a known pathogenicity factor of A. brassicae.

CONCLUSION

The study provides a perspective into the unique and shared repertoire of genes within the Alternaria genus and identifies genes that could be contributing to the pathogenic lifestyle of A. brassicae.