The Genome Sequence of Five Highly Pathogenic Isolates of Fusarium oxysporum f. sp. lini

Fusarium wilt is the most destructive fungal disease in flax, limiting flax cultivation in all the main flax and linseed growing countries. The causative agent is seedborne and soilborne fungus F. oxysporum f. sp. lini. Here, we report, for the first time, genome assemblies of five highly pathogenic isolates of Fusarium oxysporum f. sp. lini, namely monoisolate 39 and strains F329, F324, F282, F287. In addition, syntenic analysis provided a powerful approach to distinguish between core and lineage-specific parts of the genome. These results lay a solid foundation for comparative genomics studies of plant fungal pathogens, evolution of pathogenicity, and virulence factors underlying the dynamics of host-pathogen interactions, thus eventually offering solutions to Fusarium disease control.

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Two-speed genome expansion drives the evolution of pathogenicity in animal fungal pathogens

10.1101/2021.11.03.467166 ◽

2021 ◽

Author(s):

Theresa Wacker ◽

Nicolas Helmstetter ◽

Duncan Wilson ◽

Matthew C Fisher ◽

David John Studholme ◽

...

Keyword(s):

Virulence Factors ◽

Fungal Pathogens ◽

Batrachochytrium Dendrobatidis ◽

Gene Copy Number ◽

Copy Number Variations ◽

Gene Copy ◽

Batrachochytrium Salamandrivorans ◽

Conserved Genes ◽

Genome Assemblies ◽

High Quality Genome

The origins of virulence in amphibian-infecting chytrids Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are largely unknown. Here, we use deep nanopore sequencing of Bsal and comparative genomics against 21 high quality genome assemblies that span the fungal Chytridiomycota. Bsal has the most repeat-rich genome, comprising 40.9% repetitive elements, which has expanded to more than 3X the length of its conspecific Bd. M36 metalloprotease virulence factors are highly expanded in Bsal and 53% of the 177 unique genes are flanked by transposable elements, suggesting a repeat-driven expansion. Genes of the largest M36 sub-family of are mostly (84%) flanked upstream by a novel LINE element, a repeat superfamily implicated with gene copy number variations. We find that Bsal has a highly compartmentalized genome architecture, with these virulence factors enriched in gene-sparse/repeat-rich genome compartments, while core conserved genes occur in gene-rich/repeat-poor compartments; this is a hallmark of two-speed genome evolution. Furthermore, genes with signatures of positive selection in Bd are enriched in repeat-rich regions, suggesting they are a cradle for the evolution of chytrid pathogenicity, and also has a two-speed genome. This is the first evidence of two-speed genomes in any animal pathogen, and sheds new light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.

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Whole Genome Sequencing and Comparative Genomics of Two Nematicidal Bacillus Strains Reveals a Wide Range of Possible Virulence Factors

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400716 ◽

2020 ◽

Vol 10 (3) ◽

pp. 881-890 ◽

Cited By ~ 1

Author(s):

Nik Susič ◽

Sandra Janežič ◽

Maja Rupnik ◽

Barbara Gerič Stare

Keyword(s):

Comparative Genomics ◽

Virulence Factors ◽

Control Plant ◽

Whole Genome ◽

Virulence Determinants ◽

Bacterial Strains ◽

Small Peptides ◽

Wide Range ◽

Nematode Virulence ◽

Genome Assemblies

Bacillus firmus nematicidal bacterial strains are used to control plant parasitic nematode infestation of crops in agricultural production. Proteases are presumed to be the primary nematode virulence factors in nematicidal B. firmus degrading the nematode cuticle and other organs. We determined and compared the whole genome sequences of two nematicidal strains. Comparative genomics with a particular focus on possible virulence determinants revealed a wider range of possible virulence factors in a B. firmus isolate from a commercial bionematicide and a wild type Bacillus sp. isolate with nematicidal activity. The resulting 4.6 Mb B. firmus I-1582 and 5.3 Mb Bacillus sp. ZZV12-4809 genome assemblies contain respectively 18 and 19 homologs to nematode-virulent proteases, two nematode-virulent chitinase homologs in ZZV12-4809 and 28 and 36 secondary metabolite biosynthetic clusters, projected to encode antibiotics, small peptides, toxins and siderophores. The results of this study point to the genetic capability of B. firmus and related species for nematode virulence through a range of direct and indirect mechanisms.

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Uncovering dynamic evolution in the plastid genome of seven Ligusticum species provides insights into species discrimination and phylogenetic implications

Scientific Reports ◽

10.1038/s41598-020-80225-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Can Yuan ◽

Xiufen Sha ◽

Miao Xiong ◽

Wenjuan Zhong ◽

Yu Wei ◽

...

Keyword(s):

Plastid Genome ◽

Species Discrimination ◽

Chloroplast Genomes ◽

Genomic Arrangement ◽

Phylogenetic Implications ◽

Solid Foundation ◽

Conserved Gene ◽

Fine Resolution ◽

Genome Scale ◽

First Time

AbstractLigusticum L., one of the largest members in Apiaceae, encompasses medicinally important plants, the taxonomic statuses of which have been proved to be difficult to resolve. In the current study, the complete chloroplast genomes of seven crucial plants of the best-known herbs in Ligusticum were presented. The seven genomes ranged from 148,275 to 148,564 bp in length with a highly conserved gene content, gene order and genomic arrangement. A shared dramatic decrease in genome size resulted from a lineage-specific inverted repeat (IR) contraction, which could potentially be a promising diagnostic character for taxonomic investigation of Ligusticum, was discovered, without affecting the synonymous rate. Although a higher variability was uncovered in hotspot divergence regions that were unevenly distributed across the chloroplast genome, a concatenated strategy for rapid species identification was proposed because separate fragments inadequately provided variation for fine resolution. Phylogenetic inference using plastid genome-scale data produced a concordant topology receiving a robust support value, which revealed that L. chuanxiong had a closer relationship with L. jeholense than L. sinense, and L. sinense cv. Fuxiong had a closer relationship to L. sinense than L. chuanxiong, for the first time. Our results not only furnish concrete evidence for clarifying Ligusticum taxonomy but also provide a solid foundation for further pharmaphylogenetic investigation.

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Genome Assembly of the Canadian Two-row Malting Barley Cultivar AAC Synergy

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab031 ◽

2021 ◽

Author(s):

Wayne Xu ◽

James R Tucker ◽

Wubishet A Bekele ◽

Frank M You ◽

Yong-Bi Fu ◽

...

Keyword(s):

Reference Genome ◽

Single Copy ◽

Barley Cultivar ◽

Malting Barley ◽

Orthologous Genes ◽

Hordeum Vulgare L ◽

Chromosome Conformation ◽

Mate Pair ◽

Genome Assemblies ◽

First Time

Abstract Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

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Efficient TALEN-mediated gene knockin at the bovine Y chromosome and generation of a sex-reversal bovine

Cellular and Molecular Life Sciences ◽

10.1007/s00018-021-03855-1 ◽

2021 ◽

Author(s):

Ming Wang ◽

ZhaoLin Sun ◽

Fangrong Ding ◽

Haiping Wang ◽

Ling Li ◽

...

Keyword(s):

Y Chromosome ◽

Nuclear Transfer ◽

Sex Reversal ◽

Practical Application ◽

Transcription Activator ◽

New Methods ◽

Fetal Fibroblasts ◽

Male Phenotype ◽

Solid Foundation ◽

First Time

AbstractFunctional elucidation of bovine Y-chromosome genes requires available genome editing technologies. Meanwhile, it has yet to be proven whether the bovine Sry gene is the main or single factor involved in the development of the male phenotype in bovine. Here, we efficiently knocked out four Y-linked genes (Sry, ZFY, DDX3Y, and EIF2S3Y) in bovine fetal fibroblasts (BFFs) with transcription activator-like effector nucleases (TALENs) individually. Furthermore, we used TALEN-mediated gene knockin at the Sry gene and generated a sex-reversal bovine by somatic cell nuclear transfer (SCNT). The resulting bovine had only one ovary and was sterile. We demonstrate, for the first time, that the Sry gene is an important sex-determining gene in bovine. Our method lays a solid foundation for detecting the biology of the bovine Y chromosome, as it may provide an alternative biological model system for the study of mammalian sex determination, and new methods for the practical application in agricultural, especially for sex predetermination.

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Characterization of Fusarium oxysporum Isolates Obtained from Cucumber in China by Pathogenicity, VCG, and RAPD

Plant Disease ◽

10.1094/pdis.2004.88.6.645 ◽

2004 ◽

Vol 88 (6) ◽

pp. 645-649 ◽

Cited By ~ 45

Author(s):

D. J. Vakalounakis ◽

Z. Wang ◽

G. A. Fragkiadakis ◽

G. N. Skaracis ◽

D.-B. Li

Keyword(s):

Fusarium Oxysporum ◽

Random Amplified Polymorphic Dna ◽

Vegetative Compatibility ◽

Stem Rot ◽

Chinese Isolate ◽

Vegetative Compatibility Group ◽

Group I ◽

Compatibility Group ◽

First Time

Thirty-four isolates of Fusarium oxysporum, obtained in China from cucumber plants showing either Fusarium wilt (F. oxysporum f. sp. cucumerinum) or root and stem rot (F. oxysporum f. sp. radicis-cucumerinum) symptoms, were characterized by pathogenicity, vegetative compatibility, and random amplified polymorphic DNA (RAPD). Of these, 23 isolates were identified by pathogenicity as F. oxysporum f. sp. cucumerinum, and one as F. oxysporum f. sp. radicis-cucumerinum, while 10 isolates were avirulent on cucumber, melon, sponge gourd, and pumpkin. The Chinese isolates of F. oxysporum f. sp. cucumerinum were assigned to RAPD groups III and XXI and to vegetative compatibility group (VCG) 0183, four new VCGs, 0184 to 0187, and a single-member VCG included in the artificial VCG 018-. The Chinese isolate of F. oxysporum f. sp. radicis-cucumerinum was assigned to RAPD group I and bridging VCG 0260/0261. The occurrence of F. oxysporum f. sp. radicis-cucumerinum on cucumber is reported for the first time in China.

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European Mail Armour

10.5117/9789463721264 ◽

2021 ◽

Author(s):

Martijn A. Wijnhoven

Keyword(s):

Early Modern ◽

Middle Ages ◽

Iron Age ◽

Early Modern Period ◽

Vital Role ◽

Military Technology ◽

Roman Army ◽

Solid Foundation ◽

First Time

Mail armour (commonly mislabelled 'chainmail') was used for more than two millennia on the battlefield. After its invention in the Iron Age, mail rapidly spread all over Europe and beyond. The Roman army, keen on new military technology, soon adopted mail armour and used it successfully for centuries. Its history did not stop there and mail played a vital role in warfare during the Middle Ages up to the Early Modern Period. Given its long history, one would think mail is a well-documented material, but that is not the case. For the first time, this books lays a solid foundation for the understanding of mail armour and its context through time. It applies a long-term multi-dimensional approach to extract a wealth of as yet untapped information from archaeological, iconographic and written sources. This is complemented with technical insights on the mail maker’s chaîne opératoire.

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Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

Genome Research ◽

10.1101/gr.097501.109 ◽

2009 ◽

Vol 19 (12) ◽

pp. 2231-2244 ◽

Cited By ~ 151

Author(s):

A. P. Jackson ◽

J. A. Gamble ◽

T. Yeomans ◽

G. P. Moran ◽

D. Saunders ◽

...

Keyword(s):

Candida Albicans ◽

Comparative Genomics ◽

Fungal Pathogens ◽

Candida Dubliniensis

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Finding of Agr Phase Variants in Staphylococcus aureus

mBio ◽

10.1128/mbio.00796-19 ◽

2019 ◽

Vol 10 (4) ◽

Cited By ~ 3

Author(s):

Vishal Gor ◽

Aya J. Takemura ◽

Masami Nishitani ◽

Masato Higashide ◽

Veronica Medrano Romero ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Virulence Factors ◽

Phase Variation ◽

Accessory Gene ◽

Content Type ◽

Accessory Gene Regulator ◽

Immune Mediated ◽

A Minor ◽

First Time ◽

Phase Variants

ABSTRACT Staphylococcus aureus is an important human pathogen whose success is largely attributed to its vast arsenal of virulence factors that facilitate its invasion into, and survival within, the human host. The expression of these virulence factors is controlled by the quorum sensing accessory gene regulator (Agr) system. However, a large proportion of clinical S. aureus isolates are consistently found to have a mutationally inactivated Agr system. These mutants have a survival advantage in the host but are considered irreversible mutants. Here we show, for the first time, that a fraction of Agr-negative mutants can revert their Agr activity. By serially passaging Agr-negative strains and screening for phenotypic reversion of hemolysis and subsequent sequencing, we identified two mutational events responsible for reversion: a genetic duplication plus inversion event and a poly(A) tract alteration. Additionally, we demonstrate that one clinical Agr-negative methicillin-resistant S. aureus (MRSA) isolate could reproducibly generate Agr-revertant colonies with a poly(A) tract genetic mechanism. We also show that these revertants activate their Agr system upon phagocytosis. We propose a model in which a minor fraction of Agr-negative S. aureus strains are phase variants that can revert their Agr activity and may act as a cryptic insurance strategy against host-mediated stress. IMPORTANCE Staphylococcus aureus is responsible for a broad range of infections. This pathogen has a vast arsenal of virulence factors at its disposal, but avirulent strains are frequently isolated as the cause of clinical infections. These isolates have a mutated agr locus and have been believed to have no evolutionary future. Here we show that a fraction of Agr-negative strains can repair their mutated agr locus with mechanisms resembling phase variation. The agr revertants sustain an Agr OFF state as long as they exist as a minority but can activate their Agr system upon phagocytosis. These revertant cells might function as a cryptic insurance strategy to survive immune-mediated host stress that arises during infection.

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The emergence of cereal fungal diseases and the incidence of leaf spot diseases in Finland

Agricultural and Food Science ◽

10.2137/145960611795163015 ◽

2008 ◽

Vol 20 (1) ◽

pp. 62 ◽

Cited By ~ 7

Author(s):

M. JALLI ◽

P. LAITINEN ◽

S. LATVALA

Keyword(s):

Spring Wheat ◽

Leaf Spot ◽

Fungal Pathogens ◽

Plant Pathogens ◽

Field Survey ◽

Fungal Diseases ◽

Cochliobolus Sativus ◽

Pyrenophora Tritici Repentis ◽

Fungal Plant Pathogens ◽

First Time

Fungal plant pathogens causing cereal diseases in Finland have been studied by a literature survey, and a field survey of cereal leaf spot diseases conducted in 2009. Fifty-seven cereal fungal diseases have been identified in Finland. The first available references on different cereal fungal pathogens were published in 1868 and the most recent reports are on the emergence of Ramularia collo-cygni and Fusarium langsethiae in 2001. The incidence of cereal leaf spot diseases has increased during the last 40 years. Based on the field survey done in 2009 in Finland, Pyrenophora teres was present in 86%, Cochliobolus sativus in 90% and Rhynchosporium secalis in 52% of the investigated barley fields. Mycosphaerella graminicola was identified for the first time in Finnish spring wheat fields, being present in 6% of the studied fields. Stagonospora nodorum was present in 98% and Pyrenophora tritici-repentis in 94% of spring wheat fields. Oat fields had the fewest fungal diseases. Pyrenophora chaetomioides was present in 63% and Cochliobolus sativus in 25% of the oat fields studied.;

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