Research Articles (Microbiology and Plant Pathology)

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A collection containing some of the full text peer-reviewed/ refereed articles published by researchers from the Department of Microbiology and Plant Pathology

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Chalaropsis pruni sp. nov. (Ceratocystidaceae), a new species from Prunus serrulata var. pubescens in South Korea
(Magnolia Press, 2024-11-12) Cho, Sung-Eun; Seo, Sang-tae; Nam, Youngwoo; Wingfield, Michael J.; Lee, Dong-hyeon
A routine survey in a natural forest located in the Gangwon Province of Korea was undertaken in 2022 to establish an inventory of potentially pathogenic fungi that might affect tree health in the country. An ophiostomatoid fungus was consistently isolated from naturally occurring wounds on Prunus serrulata var. pubescens. Isolates were subjected to morphological and DNA sequence comparisons. The results showed that the fungus resided in a distinct taxonomic lineage, and the novel species is described here as Chalaropsis pruni sp. nov.
Phylodynamic insights into global emergence and diversification of the tomato pathogen Xanthomonas hortorum pv. gardneri
(American Phytopathological Society, 2024) Jibrin, Mustafa O.; Sharma, Anuj; Mavian, Carla N.; Timilsina, Sujan; Kaur, Amandeep; Iruegas-Bocardo, Fernanda; Potnis, Neha; Minsavage, Gerald V.; Coutinho, Teresa A.; Creswell, Tom C.; Egel, Daniel S.; Francis, David M.; Kebede, Misrak; Miller, Sally A.; Montelongo, María J.; Nikolaeva, Ekaterina; Pianzzola, María J.; Pruvost, Olivier; Quezado-Duval, Alice M.; Ruhl, Gail E.; Shutt, Vou M.; Maynard, Elizabeth; Maeso, Diego C.; Siri, María I.; Trueman, Cheryl L.; Salemi, Marco; Vallad, Gary E.; Roberts, Pamela D.; Jones, Jeffrey B.; Goss, Erica M.
The emergence of plant pathogens is often associated with waves of unique evolutionary and epidemiological events. Xanthomonas hortorum pv. gardneri is one of the major pathogens causing bacterial spot disease of tomatoes. After its first report in the 1950s, there were no formal reports on this pathogen until the 1990s, despite active global research on the pathogens that cause tomato and pepper bacterial spot disease. Given the recently documented global distribution of X. hortorum pv. gardneri, our objective was to examine genomic diversification associated with its emergence.We sequenced the genomes of X. hortorum pv. gardneri strains collected in eight countries to examine global population structure and pathways of emergence using phylodynamic analysis.We found that strains isolated post-1990 group by region of collection and show minimal impact of recombination on genetic variation. A period of rapid geographic expansion in X. hortorum pv. gardneri is associated with acquisition of a large plasmid conferring copper tolerance by horizontal transfer and coincides with the burgeoning hybrid tomato seed industry through the 1980s. The ancestry of X. hortorum pv. gardneri is consistent with introduction to hybrid tomato seed production and dissemination during the rapid increase in trade of hybrid seeds.
Polymyxin sensitivity/resistance cosmopolitan status, epidemiology and prevalence among O1/O139 and non-O1/non-O139 Vibrio cholerae : a meta-analysis
(Elsevier, 2023) Igere, Bright E.; Onohuean, Hope; Iwu, Chidozie Declan; Igbinosa, Etinosa O.
Resistance/sensitivity to polymyxin-B (PB) antibiotic has been employed as one among other epidemiologically relevant biotyping-scheme for Vibrio cholerae into Classical/El Tor biotypes. However, recent studies have re- vealed some pitfalls bordering on PB-sensitivity/resistance (PBR/S) necessitating study. Current study assesses the PBR/S cosmopolitan prevalence, epidemiology/distribution among O1/O139 and nonO1/nonO139 V. cholerae strains. Relevant databases (Web of Science, Scopus and PubMed) were searched to retrieve data from environ- mental and clinical samples employing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Random-effect-model (REM) and common-effect-model (CEM) of meta-analysis was performed to de- termine prevalence of PBR/S V. cholerae strains, describe the cosmopolitan epidemiological potentials and biotype relevance. Heterogeneity was determined by meta-regression and subgroup analyses. The pooled analyzed iso- lates from articles (7290), with sensitive and resistance are 2219 (30.44%) and 5028 (69.56%). Among these PB- sensitive strains, more than 1944 (26.67%) were O1 strains, 132 (1.81%) were nonO1 strains while mis-reported Classical biotype were 2080 (28.53) respectively indicating potential spread of variant/dual biotype. A significant PB-resistance was observed in the models (CEM = 0.66, 95% CI [0.65; 0.68], p -value = 0.001; REM = 0.83 [0.74; 0.90], p = 0.001) as both models had a high level of heterogeneity ( I2 = 98.0%; 2 =33 = 1755 . 09 , = 2 . 4932 ). Egger test ( z = 5.4017, p < 0.0001) reveal publication bias by funnel plot asymmetry. The subgroup analysis for continents (Asia, Africa) and sources (acute diarrhea) revealed (98% CI (0.73; 0.93); 55% CI (0.20; 0.86)), and 92% CI (0.67; 0.98). The Epidemiological prevalence for El tor/variant/dual biotype showed 88% CI (0.78; 0.94) with O1 strains at 88% CI (0.78; 0.94). Such global prevalence, distribution/spread of phenotypes/genotypes ne- cessitates updating the decades-long biotype classification scheme. An antibiotic stewardship in the post antibiotic era is suggestive/recommended. Also, there is need for holistic monitoring/evaluation of clinical/epidemiological relevance of the disseminating strains in endemic localities.
Distribution, causal agents, and infection dynamic of emerging ink disease of sweet chestnut in Southern Switzerland
(Wiley, 2023-11) Prospero, Simone; Heinz, Malve; Augustiny, Eva; Chen, Ying-Yu; Engelbrecht, Juanita; Fonti, Marina; Hoste, Aliona; Ruffner, Beat; Sigrist, Romina; Van den Berg, Noelani; Fonti, Patrick
Emerging diseases caused by both native and exotic pathogens represent a main threat to forest ecosystems worldwide. The two invasive soilborne pathogens Phytophthora cinnamomi and Phytophthora cambivora are the causal agents of ink disease, which has been threatening Castanea sativa in Europe for several centuries and seems to be re-emerging in recent years. Here, we investigated the distribution, causal agents, and infection dynamics of ink disease in southern Switzerland. A total of 25 outbreaks were identified, 19 with only P. cinnamomi, 5 with only P. cambivora, and 1 with both species. Dendrochronological analyses showed that the disease emerged in the last 20–30 years. Infected trees either died rapidly within 5–15 years post-infection or showed a prolonged state of general decline until death. Based on a generalized linear model, the local risk of occurrence of ink disease was increased by an S-SE aspect of the chestnut stand, the presence of a pure chestnut stand, management activities, the proximity of roads and buildings, and increasing annual mean temperature and precipitation. The genetic structure of the local P. cinnamomi population suggests independent introductions and local spread of the pathogen.
Genetic diversity and origin of captive lion (Panthera leo) in South Africa : an assessment and comparison to wild populations
(Springer, 2023-05-29) Miller, Susan M.; Kotze, Antoinette; Harper, Cindy Kim; Bishop, Jacqueline M.; Williams, Vivienne L.; Rossouw, Charne; Schoeman, Johanita; De Bruyn, Marli; Lee Dalton, Desire; Selier, S.A. Jeanetta
South Africa has a large captive lion (Panthera leo) sector, but detailed knowledge on the origin of individuals and any potential genetic value to conservation targets is lacking. In 2021, the South African government committed to closing the sector and have since appointed a Ministerial Lion Task Team (2022) to initiate this process. Some have suggested that captive lions could be integrated into wild populations as part of the process but information on the genetic origins and diversity of captive lions is critical if this is to be explored further. Both the Biodiversity Management Plan for lions in South Africa (2015) and a High-Level Ministerial report for the South African government (2021) have called for more information on the genetic composition of captive lions. To determine the probable origin of captive lions in South Africa we summarised existing survey responses from captive facilities (collected 2017–2018) and CITES permit data (issued 1991–2019). Survey data suggest that most lions were sourced from within the South African captive sector. However, many CITES permits were also issued for the import of lions from across Africa and beyond, indicating possible mixed origins within the sector. To evaluate genetic relationships between captive and wild lions in South Africa we standardised existing microsatellite marker data from three laboratories and analysed genotypes of captive lions from 31 properties. A comparison of captive and wild lion genotypes revealed that the genetic composition of captive lions is currently comparable to existing wild South African lions. Captive lions cluster with similar probabilities to three of four regional reference populations of wild lions included in the study and no major signatures of inbreeding were identified. However, captive lions are highly genetically interconnected across properties and represent a smaller effective population size compared to Kruger National Park, the largest population of wild lions in South Africa, suggesting some risk of future inbreeding. There were also signatures of genetic drift which should be investigated further as it will likely compromise any potential conservation genetic value of captive lions in the future. The findings of this study should be considered when planning the fate of individuals within South Africa’s captive lion sector and within the broader context of African lion conservation.
Cultivated hawthorn (Crataegus pinnatifida var. major) genome sheds light on the evolution of Maleae (apple tribe)
(Wiley, 2022-08) Zhang, Ticao; Qiao, Qin; Du, Xiao; Zhang, Xiao; Hou, Yali; Wei, Xin; Sun, Chao; Zhang, Rengang; Yun, Quanzheng; Crabbe, M. James C.; Van de Peer, Yves; Dong, Wenxuan
Cultivated hawthorn (Crataegus pinnatifida var. major) is an important medicinal and edible plant with a long history of use for health protection in China. Herein, we provide a de novo chromosomelevel genome sequence of the hawthorn cultivar “Qiu Jinxing.” We assembled an 823.41Mb genome encoding 40 571 genes and further anchored the 779.24Mb sequence into 17 pseudo‐chromosomes, which account for 94.64% of the assembled genome. Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae (apple tribe) at approximately 35.4 Mya. Notably, genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome. In addition, our results indicated that the Maleae share a unique ancient tetraploidization event; however, no recent independent whole‐genome duplication event was specifically detected in hawthorn. The amplification of non‐specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome. Furthermore, we identified two paleo‐sub‐genomes in extant species of Maleae and found that these two sub‐genomes showed different rearrangement mechanisms. We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleopolyploid origin patterns (autopolyploidization or allopolyploidization) of Maleae. Overall, our study provides an improved context for understanding the evolution of Maleae species, and this new highquality reference genome provides a useful resource for the horticultural improvement of hawthorn.
The neighborhood of the spike gene Is a hotspot for modular intertypic homologous and nonhomologous recombination in coronavirus genomes
(Oxford University Press, 2022-01) Nikolaidis, Marios; Markoulatos, Panayotis; Van de Peer, Yves; Oliver, Stephen G.; Amoutzias, Grigorios D.
Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and nonhomologous recombination, because such events may affect the emergence of novel CoV strains, alter their host range, infection rate, tissue tropism pathogenicity, and their ability to escape vaccination programs. Intratypic recombination among closely related CoVs of the same subgenus has often been reported; however, the patterns and limits of genomic exchange between more distantly related CoV lineages (intertypic recombination) need further investigation. Here, we report computational/evolutionary analyses that clearly demonstrate a substantial ability for CoVs of different subgenera to recombine. Furthermore, we show that CoVs can obtain—through nonhomologous recombination—accessory ORFs from core ORFs, exchange accessory ORFs with different CoV genera, with other viruses (i.e., toroviruses, influenza C/D, reoviruses, rotaviruses, astroviruses) and even with hosts. Intriguingly, most of these radical events result from double crossovers surrounding the Spike ORF, thus highlighting both the instability and mobile nature of this genomic region. Although many such events have often occurred during the evolution of various CoVs, the genomic architecture of the relatively young SARS-CoV/SARS-CoV-2 lineage so far appears to be stable.
Evolution of isoform-level gene expression patterns across tissues during lotus species divergence
(Wiley, 2022-11) Zhang, Yue; Yang, Xingyu; Van de Peer, Yves; Chen, Jinming; Marchal, Kathleen; Shi, Tao
Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea and Nelumbo nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms of local, small-scale duplicates, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contributed to the diversity of gene function during the evolution of lotus.
In vitro dual activity of Aloe marlothii roots and its chemical constituents against Plasmodium falciparum asexual and sexual stage parasites
(Elsevier, 2022-10) Mianda, S.M.; Invernizzi, Luke; Van der Watt, Mariette Elizabeth; Reader, Janette; Moyo, Phanankosi; Birkholtz, Lyn-Marie; Maharaj, Vinesh J.; lbirkholtz@up.ac.za
Please abstract in the article.
New transmission-selective antimalarial agents through hit-to-lead optimization of 2-([1,1 '-Biphenyl]-4-carboxamido)benzoic acid derivatives
(Wiley, 2022-11) Reader, Janette; Opperman, Daniel; Van der Watt, Mariette Elizabeth; Theron, Anjo; Leshabane, Meta Kgaogelo; Da Rocha, Michelle; Turner, Jonathan; Garrabrant, Kathleen; Pina, Ivett; Mills, Catherine; Woster, Patrick M.; Birkholtz, Lyn-Marie; lbirkholtz@up.ac.za
Malaria elimination requires multipronged approaches, including the application of antimalarial drugs able to block humanto- mosquito transmission of malaria parasites. The transmissible gametocytes of Plasmodium falciparum seem to be highly sensitive towards epidrugs, particularly those targeting demethylation of histone post-translational marks. Here, we report exploration of compounds from a chemical library generated during hit-to-lead optimization of inhibitors of the human histone lysine demethylase, KDM4B. Derivatives of 2-([1,1’- biphenyl]-4-carboxamido) benzoic acid, around either the amide or a sulfonamide linker backbone (2-(arylcarboxamido) benzoic acid, 2-carboxamide (arylsulfonamido)benzoic acid and N-(2-(1H-tetrazol-5-yl)phenyl)-arylcarboxamide), showed potent activity towards late-stage gametocytes (stage IV/V) of P. falciparum, with the most potent compound reaching single digit nanomolar activity. Structure-activity relationship trends were evident and frontrunner compounds also displayed microsomal stability and favourable solubility profiles. Simplified synthetic routes support further derivatization of these compounds for further development of these series as malaria transmission-blocking agents.
syntenet : an R/Bioconductor package for the inference and analysis of synteny networks
(Oxford University Press, 2023-01) Almeida-Silva, Fabricio; Zhao, Tao; Ullrich, Kristian K.; Schranz, M. Eric; Van de Peer, Yves
Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet, an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate.
By blood or by choice? On relational autonomy and the familial ties that bind us
(Stellenbosch University, Faculty of Theology, 2022) Van Wyk, Tanya; tanya.vanwyk@up.ac.za
This article explores the range of the construct “family” in light of the author’s experience of how the death of a congregation-member exposed the strength, persistence and immovability of the construct, “family”. Despite different attempts and approaches to deconstruct and broaden the notion of what family refers to that originated in the 1970s, a traditional notion of what kinship (family) entails remains focused on ties that bind people by blood or by marriage. The article provides a brief overview and evaluation of different attempts at a postmodern understanding of family, but ultimately it is illustrated that there has been little change to the construct of family. The notion of “relational autonomy” from a Trinitarian theological perspective is presented as a more thorough foundation for familial ties that are characterised by a creative tension of both distance and belonging. This theological foundation provides a point of departure for a dynamic understanding of the range of choices related to what constitutes, “family”, which does not cast someone in the stone of the construct of a “family”, even beyond their own death.
Novel 3-trifluoromethyl-1,2,4-oxadiazole analogues of astemizole with multi-stage antiplasmodium activity and in vivo efficacy in a Plasmodium berghei mouse malaria infection model
(American Chemical Society, 2022-12) Mambwe, Dickson; Korkor, Constance M.; Mabhula, Amanda; Ngqumba, Zama; Cloete, Cleavon; Kumar, Malkeet; Barros, Paula Ladeia; Leshabane, Meta Kgaogelo; Coertzen, Dina; Taylor, Dale; Gibhard, Liezl; Njoroge, Mathew; Lawrence, Nina; Reader, Janette; Moreira, Diogo Rodrigo; Birkholtz, Lyn-Marie; Wittlin, Sergio; Egan, Timothy J.; Chibale, Kelly
Please read abstract in the article.
Population genetics of a lethally managed medium-sized predator
(Wiley, 2022-09) Slater, K.; De Jager, Deon; Van Wyk, A.M.; Dalton, Desire Lee; Kropff, Anna S.; Du Preez, Ilse
Globally, levels of human–wildlife conflict are increasing as a direct consequence of the expansion of people into natural areas resulting in competition with wildlife for food and other resources. By being forced into increasingly smaller pockets of suitable habitat, many animal species are at risk of becoming susceptible to loss of genetic diversity, inbreeding depression and the associated inability to adapt to environmental changes. Predators are often lethally controlled due to their threat to livestock. Predators such as jackals (black backed, golden and side striped; Canis mesomelas, C. aureus and C. adustus, respectively), red foxes (Vulpes vulpes) and coyotes (C. latrans) are highly adaptable and may respond to ongoing persecution through compensatory reproduction such as reproducing at a younger age, producing larger litters and/or compensatory immigration including dispersal into vacant territories. Despite decades of lethal management, jackals are problematic predators of livestock in South Africa and, although considered a temporary measure, culling of jackals is still common. Culling may affect social groups, kinship structure, reproductive strategies and sex-biased dispersal in this species. Here, we investigated genetic structure, variation and relatedness of 178 culled jackals on private small-livestock farms in the central Karoo of South Africa using 13 microsatellites. Genetic variation was moderate to high and was similar per year and per farm. An absence of genetic differentiation was observed based on STRUCTURE, principal component analysis and AMOVA. Relatedness was significantly higher within farms (r = 0.189) than between farms (r = 0.077), a result corroborated by spatial autocorrelation analysis. We documented 18 occurrences of dispersal events where full siblings were detected on different farms (range: 0.78–42.93 km). Distance between identified parent–offspring varied from 0 to 36.49 km. No evidence for sex-biased dispersal was found. Our results suggest that in response to ongoing lethal management, this population is most likely able to maintain genetic diversity through physiological and behavioural compensation mechanisms.
The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences
(Nature Research, 2022-09) Fang, Yuhan; Qin, Xing; Liao, Qinggang; Du, Ran; Luo, Xizhi; Zhou, Qian; Li, Zhen; Chen, Hengchi; Jin, Wanting; Yuan, Yaning; Sun, Pengbo; Zhang, Rui; Zhang, Jiao; Wang, Li; Cheng, Shifeng; Yang, Xueyong; Yan, Yuehong; Zhang, Xingtan; Zhang, Zhonghua; Bai, Shunong; Van de Peer, Yves; Lucas, William John; Huang, Sanwen; Yan, Jianbin
Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.
Genome-informed design of a LAMP assay for the specific detection of the strain of 'Candidatus Phytoplasma asteris' phytoplasma occurring in grapevines in South Africa
(American Phytopathological Society, 2022-11) Alic, Spela; Dermastia, Marina; Burger, Johan; Dickinson, Matthew; Pietersen, Gerhard; Pietersen, Gert; Dreo, Tanja
Grapevine yellows is one of the most damaging phytoplasma-associated diseases worldwide. It is linked to several phytoplasma species, which can vary regionally due to phytoplasma and insect-vector diversity. Specific, rapid, and reliable detection of the grapevine yellows pathogen has an important role in phytoplasma control. The purpose of this study was to develop and validate a specific loop-mediated isothermal amplification (LAMP) assay for detection of a distinct strain of grapevine ‘Candidatus Phytoplasma asteris’ that is present in South Africa, through implementation of a genome-informed test design approach. Several freely available, user-friendly, web-based tools were coupled to design the specific LAMP assays. The criteria for selection of the assays were set for each step of the process, which resulted in four experimentally operative LAMP assays that targeted the ftsH/hflB gene region, specific to the aster yellows phytoplasma strain from South Africa. A real-time PCR was developed, targeting the same genetic region, to provide extensive validation of the LAMP assay. The validated molecular assays are highly specific to the targeted aster yellows phytoplasma strain from South Africa, with good sensitivity and reproducibility. We show a genome-informed molecular test design and an efficient validation approach for molecular tests if reference and sample materials are sparse and hard to obtain.
Chromosome-scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication
(Wiley Open Access, 2022-09) Chang, Jiyang; Marczuk-Rojas, Juan Pablo; Waterman, Carrie; Garcia-Llanos, Armando; Chen, Shiyu; Ma, Xiao; Hulse-Kemp, Amanda; Van Deynze, Allen; Van de Peer, Yves; Carretero-Paulet, Lorenzo
The African Orphan Crops Consortium (AOCC) selected the highly nutritious, fast growing and drought tolerant tree crop moringa (Moringa oleifera Lam.) as one of the first of 101 plant species to have its genome sequenced and a first draft assembly was published in 2019. Given the extensive uses and culture of moringa, often referred to as the multipurpose tree, we generated a significantly improved new version of the genome based on long-read sequencing into 14 pseudochromosomes equivalent to n = 14 haploid chromosomes. We leveraged this nearly complete version of the moringa genome to investigate main drivers of gene family and genome evolution that may be at the origin of relevant biological innovations including agronomical favorable traits. Our results reveal that moringa has not undergone any additional whole-genome duplication (WGD) or polyploidy event beyond the gamma WGD shared by all core eudicots. Moringa duplicates retained following that ancient gamma events are also enriched for functions commonly considered as dosage balance sensitive. Furthermore, tandem duplications seem to have played a prominent role in the evolution of specific secondary metabolism pathways including those involved in the biosynthesis of bioactive glucosinolate, flavonoid, and alkaloid compounds as well as of defense response pathways and might, at least partially, explain the outstanding phenotypic plasticity attributed to this species. This study provides a genetic roadmap to guide future breeding programs in moringa, especially those aimed at improving secondary metabolism related traits.
Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)
(National Academy of Sciences, 2021-10) Qiao, Qin; Edger, Patrick P.; Xue, Li; Qiong, La; Lu, Jie; Zhang, Yichen; Cao, Qiang; Yocca, Alan E.; Platts, Adrian E.; Knapp, Steven J.; Van Montagu, Marc; Van de Peer, Yves; Lei, Jiajun; Zhang, Ticao
Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species’ genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (Fragaria emeiensis Jia J. Lei). Finally, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These reference genomes and datasets, combined with our phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.
Endemic persistence of a highly contagious pathogen : foot-and-mouth disease in its wildlife host
(American Association for the Advancement of Science, 2021-09) Jolles, Anna; Gorsich, Erin; Gubbins, Simon; Beechler, Brianna; Buss, Peter Erik; Juleff, Nick; De Klerk-Lorist, Lin-Mari; Maree, Francois Frederick; Perez-Martin, Eva; Van Schalkwyk, Ockert Louis; Scott, Katherine; Zhang, Fuquan; Medlock, Jan; Charleston, Bryan
Extremely contagious pathogens are a global biosecurity threat because of their high burden of morbidity and mortality, as well as their capacity for fast-moving epidemics that are difficult to quell. Understanding the mechanisms enabling persistence of highly transmissible pathogens in host populations is thus a central problem in disease ecology. Through a combination of experimental and theoretical approaches, we investigated how highly contagious foot-and-mouth disease viruses persist in the African buffalo, which serves as their wildlife reservoir. We found that viral persistence through transmission among acutely infected hosts alone is unlikely. However, the inclusion of occasional transmission from persistently infected carriers reliably rescues the most infectious viral strain from fade-out. Additional mechanisms such as antigenic shift, loss of immunity, or spillover among host populations may be required for persistence of less transmissible strains.
The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat
(Oxford University Press, 2022-03-23) Wang, Zhiquan; Xue, Jia-Yu; Hu, Shuai-Ya; Zhang, Fengjiao; Yu, Ranran; Chen, Dijun; Van de Peer, Yves; Jiang, Jiafu; Song, Aiping; Ni, Longjie; Hua, Jianfeng; Lu, Zhiguo; Yu, Chaoguang; Yin, Yunlong; Gu, Chunsun
Hibiscus hamabo is a semi-mangrove species with strong tolerance to salt and waterlogging stress. However, the molecular basis and mechanisms that underlie this strong adaptability to harsh environments remain poorly understood. Here, we assembled a high-quality, chromosome-level genome of this semi-mangrove plant and analyzed its transcriptome under different stress treatments to reveal regulatory responses and mechanisms. Our analyses suggested that H. hamabo has undergone two recent successive polyploidy events, a whole-genome duplication followed by a whole-genome triplication, resulting in an unusually large gene number (107 309 genes). Comparison of the H. hamabo genome with that of its close relative Hibiscus cannabinus, which has not experienced a recent WGT, indicated that genes associated with high stress resistance have been preferentially preserved in the H. hamabo genome, suggesting an underlying association between polyploidy and stronger stress resistance. Transcriptomic data indicated that genes in the roots and leaves responded differently to stress. In roots, genes that regulate ion channels involved in biosynthetic and metabolic processes responded quickly to adjust the ion concentration and provide metabolic products to protect root cells, whereas no such rapid response was observed from genes in leaves. Using co-expression networks, potential stress resistance genes were identified for use in future functional investigations. The genome sequence, along with several transcriptome datasets, provide insights into genome evolution and the mechanism of salt and waterlogging tolerance in H. hamabo, suggesting the importance of polyploidization for environmental adaptation.

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