Biology subjects

Cano, L. M.

Publications and source records attributed to Cano, L. M..

5 recordsLinked to original sources

bioRxiv2026

Phytophthora cinnamomi populations collected from avocado in the United States exhibit high adaptive capacity to climate and disease control methods

Phytophthora cinnamomi, the causal agent of Phytophthora root rot (PRR), poses a persistent threat to the United States avocado industry, the top domestic producer and consumer. Avocado growers are facing clonal A2 P. cinnamomi populations challenging their current PRR control methods. In this study, we characterized 125 isolates collected from orchards in California, Florida, Hawaii, Texas, and Puerto Rico for radial growth per day, optimal growth temperature, in vitro fungicide sensitivity, and virulence on DAnjou pear fruit and UC2001 avocado seedlings. Across all isolates, optimal growth occurred most frequently at a range from 22 to 25{degrees}C; however, a subset of isolates from Hawaii, Florida, and California exhibited higher optimal growth temperatures (28{degrees}C and 30{degrees}C) suggesting thermal adaptation in warmer regions. Potassium phosphite EC50 values spanned from 4.61 to 763.13 {micro}g/ml, with significantly higher insensitivity in isolates from California and Florida, reflecting the continued overuse of this fungicide in these major production states. In contrast, baseline sensitivities to ethaboxam, mandipropamid, mefenoxam, fluopicolide, and oxathiapiprolin were uniformly high, with narrow, unimodal EC50 distributions across states. Finally, a wide range of virulence among isolates was detected using avocado seedlings and DAnjou pear fruits with isolates from California and Puerto Rico being the most virulent. Together, this data documents extensive phenotypic diversity within clonal A2 P. cinnamomi populations including heat-adapted and phosphite-insensitive lineages, establishes multi-state fungicide sensitivity baselines, and underscores the need for continued surveillance, integrated fungicide stewardship (especially phosphonates), and rootstock screening against phenotypically diverse populations to sustain avocado PRR management and ensure the United States avocado industry sustainability and profitability.

microbiology↗

bioRxiv2025

Rapid and reproducible haplotyping of complete mitochondrial genomes using split k-mers

Accurate phylogenetic analysis of mitochondrial haplotypes underpins a wide spectrum of biological inquiry. While multilocus sequence-based phylogenies are standard, inconsistent gene selection and trimming limit network reproducibility and disregard non-coding sequence. To examine alternative approaches, we tested split k-mer analysis (SKA) to reassess published mitogenome datasets of one mammalian and two insect species. SKA accurately haplotyped each dataset, improved polymorphism detection in the hemipteran Diaphorina citri and aided in the identification of D. citri haplotypes associated with the titer of "Candidatus Liberibacter asiaticus", the bacterium associated with citrus greening disease. We present a new mitogenome haplotyping method and script, ska-mtdna.py.

bioinformatics↗

bioRxiv2018

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, cultured from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of Clade 1A and 1C. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from Clade 1 and will facilitate effector informed breeding strategies in other crops.

pathology↗

bioRxiv2017

nQuire: A Statistical Framework For Ploidy Estimation Using Next Generation Sequencing

SummarynQuire is a statistical framework that distinguishes between diploids, triploids and tetraploids using next generation sequencing. The command-line tool models the distribution of base frequencies at variable sites using a Gaussian Mixture Model, and uses maximum likelihood to select the most plausible ploidy model.\n\nAvailability and ImplementationThe model is implemented as a stand-alone Linux command line tool in the C programming language and is available at github under the MIT licence. Please also refer to github.com/clwgg/nQuire for usage instructions. Contact: clemens.weiss@tuebingen.mpg.de or hernan.burbano@tuebingen.mpg.de

bioinformatics↗

bioRxiv2017

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012,Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Cooke et al. 2012, Yoshida et al. 2013,Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.

plant biology↗