The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species.

Background: Metarhizium anisopliae is an important fungal biocontrol agent of insect pests of agricultural crops. Genomics can aid the successful commercialization of biopesticides by identification of key genes differentiating closely related species, selection of virulent microbial isolates which are amenable to industrial scale production and formulation and through the reduction of phenotypic variability. The genome of Metarhizium isolate ARSEF23 was recently published as a model for M. anisopliae, however phylogenetic analysis has since re-classified this isolate as M. robertsii. We present a new annotated genome sequence of M. anisopliae (isolate Ma69) and whole genome comparison to M. robertsii (ARSEF23) and M. acridum (CQMa 102).Results: Whole genome analysis of M. anisopliae indicates significant macrosynteny with M. robertsii but with some large genomic inversions. In comparison to M. acridum, the genome of M. anisopliae shares lower sequence homology. While alignments overall are co-linear, the genome of M. acridum is not contiguous enough to conclusively observe macrosynteny. Mating type gene analysis revealed both MAT1-1 and MAT1-2 genes present in M. anisopliae suggesting putative homothallism, despite having no known teleomorph, in contrast with the putatively heterothallic M. acridum isolate CQMa 102 (MAT1-2) and M. robertsii isolate ARSEF23 (altered MAT1-1). Repetitive DNA and RIP analysis revealed M. acridum to have twice the repetitive content of the other two species and M. anisopliae to be five times more RIP affected than M. robertsii. We also present an initial bioinformatic survey of candidate pathogenicity genes in M. anisopliae.Conclusions: The annotated genome of M. anisopliae is an important resource for the identification of virulence genes specific to M. anisopliae and development of species- and strain- specific assays. New insight into the possibility of homothallism and RIP affectedness has important implications for the development of M. anisopliae as a biopesticide as it may indicate the potential for greater inherent diversity in this species than the other species. This could present opportunities to select isolates with unique combinations of pathogenicity factors, or it may point to instability in the species, a negative attribute in a biopesticide

Pathogenicity of Botryosphaeria species isolated from declining grapevines in sub tropical regions of Eastern Australia

From 2002 to 2004, vines from 11 vineyards in the Hunter Valley region and from 4 vineyards in Mudgee (New South Wales, Australia) were inspected for foliar and wood symptoms of Eutypa dieback and Botryosphaeria canker. Eutypa lata was not isolated, however species of Botryosphaeria were frequently isolated from dead and declining spurs, cordons and trunks. Two species conforming to the anamorphs of Diplodia and Fusicoccum were isolated. Cultures on PDA producing a yellow pigment, and hyaline aseptate conidia (14-23.5 x 8-13 μm in size) were identified as B. lutea. Cultures with dark brown, 1-septate, ornamented conidia (15-25 x 8-14 μm in size) at maturity were identified as B. obtusa. Pathogenicity tests were conducted on detached green shoots, detached one-year-old canes and glasshouse-grown grapevines. In all situations, disease symptoms were reproduced and Koch’s postulates were fulfilled. The results demonstrate the potential of B. obtusa and B. lutea as primary pathogens of Vitis vinifera.

Models of spatiotemporal variation in rabbit abundance reveal management hot spots for an invasive species

First published: 25 January 2020The European rabbit (Oryctolagus cuniculus) is a notorious economic and environmental pest species in its invasive range. To better understand the population and range dynamics of this species, 41 years of abundance data have been collected from 116 unique sites across a broad range of climatic and environmental conditions in Australia. We analyzed this time series of abundance data to determine whether inter‐annual variation in climatic conditions can be used to map historic, contemporary, and potential future fluctuations in rabbit abundance from regional to continental scales. We constructed a hierarchical Bayesian regression model of relative abundance that corrected for observation error and seasonal biases. The corrected abundances were regressed against environmental and disease variables in order to project high spatiotemporal resolution, continent‐wide rabbit abundances. We show that rabbit abundance in Australia is highly variable in space and time, being driven primarily by inter‐annual variation in temperature and precipitation in concert with the prevalence of a non‐pathogenic virus. Moreover, we show that inter‐annual variation in local spatial abundances can be mapped effectively at a continental scale using highly resolved spatiotemporal predictors, allowing “hotspots” of persistently high rabbit abundance to be identified. Importantly, cross‐validated model performance was fair to excellent within and across distinct climate zones. Long‐term monitoring data for invasive species can be used to map fine‐scale spatiotemporal fluctuations in abundance patterns when accurately accounting for inherent sampling biases. Our analysis provides ecologists and pest managers with a clearer understanding of the determinants of rabbit abundance in Australia, offering an important new approach for predicting spatial abundance patterns of invasive species at the near‐term temporal scales that are directly relevant to resource management.Stuart C Brown, Konstans Wells, Emilie Roy-Dufresne, Susan Campbell, Brian Cooke, Tarnya Cox, Damien A. Fordha

Genetic diversity of carotenoid-rich bananas evaluated by Diversity Arrays Technology (DArT)

The aim of this work was to evaluate the carotenoid content and genetic variability of banana accessions from the Musa germplasm collection held at Embrapa Cassava and Tropical Fruits, Brazil. Forty-two samples were analyzed, including 21 diploids, 19 triploids and two tetraploids. The carotenoid content was analyzed spectrophotometrically and genetic variability was estimated using 653 DArT markers. The average carotenoid content was 4.73 μg.g -1 , and ranged from 1.06 μg.g -1 for the triploid Nanica (Cavendish group) to 19.24 μg.g -1 for the triploid Saney. The diploids Modok Gier and NBA-14 and the triploid Saney had a carotenoid content that was, respectively, 7-fold, 6-fold and 9-fold greater than that of cultivars from the Cavendish group (2.19 μg.g -1). The mean similarity among the 42 accessions was 0.63 (range: 0.24 to 1.00). DArT analysis revealed extensive genetic variability in accessions from the Embrapa Musa germplasm bank

Beyond Refugia: New insights on Quaternary climate variation and the evolution of biotic diversity in tropical South America

Haffer’s (Science 165: 131–137, 1969) Pleistocene refuge theory has provided motivation for 50 years of investigation into the connections between climate, biome dynamics, and neotropical speciation, although aspects of the orig- inal theory are not supported by subsequent studies. Recent advances in paleocli- matology suggest the need for reevaluating the role of Quaternary climate on evolutionary history in tropical South America. In addition to the many repeated large-amplitude climate changes associated with Pleistocene glacial-interglacial stages (~40 kyr and 100 kyr cyclicity), we highlight two aspects of Quaternary climate change in tropical South America: (1) an east-west precipitation dipole, induced by solar radiation changes associated with Earth’s precessional variations (~20 kyr cyclicity); and (2) periods of anomalously high precipitation that persisted for centuries-to-millennia (return frequencies ~1500 years) congruent with cold “Heinrich events” and cold Dansgaard-Oeschger “stadials” of the North Atlantic region. The spatial footprint of precipitation increase due to this North Atlantic forcing extended across almost all of tropical South America south of the equator. Combined, these three climate modes present a picture of climate change with different spatial and temporal patterns than envisioned in the original Pleistocene refuge theory. Responding to these climate changes, biomes expanded and contracted and became respectively connected and disjunct. Biome change undoubtedly influenced biotic diversification, but the nature of diversification likely was more complex than envisioned by the original Pleistocene refuge theory. In the lowlands, intermittent forest expansion and contraction led to species dispersal and subsequent isolation, promoting lineage diversification. These pulses of climate-driven biotic interchange profoundly altered the composition of regional species pools and triggered new evolutionary radiations. In the special case of the tropical Andean forests adjacent to the Amazon lowlands, new phylogenetic data provide abundant evidence for rapid biotic diversification during the Pleistocene. During warm interglacials and intersta- dials, lowland taxa dispersed upslope. Isolation in these disjunct climate refugia led to extinction for some taxa and speciation for others.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155561/1/Baker2020.pdfDescription of Baker2020.pdf : Main articl

Black scab of jojoba (simmondsia chinensis) in Australia caused by a putative new pathotype of elsinoë Australis

A new disease of jojoba in Australia is described. We have demonstrated that this disease is caused by Elsinoë australis, a pathogen which is normally associated with citrus. This pathogen has not been found previously in Australia on citrus or any other crop. The fungus causes a scab on leaves and stems of jojoba and is widely distributed in eastern Australia. Although molecular analysis of the pathogen indicates that it is closely related to the natsudaidai and the sweet orange pathotypes of E. australis, glasshouse and laboratory experiments demonstrate that it is not pathogenic to a range of citrus cultivars grown in Australia. The data indicate that the isolates from jojoba represent a new pathotype of E. australis

Implications of bacterial contaminated seed lots and endophytic colonization by Pseudomonas fuscovaginae on rice establishment

The economic impact of seedborne bacterial diseases on rice production provides a major motivation for research on seed health. This paper reports on the endophytic growth of a rifampicin-marked strain of the seedborne rice pathogen Pseudomonas fuscovaginae. The bacterium was found in most tested seeds indicating that, even without visible discolouration, seed transmission is possible. Crushed discoloured seeds contained more bacterial cells than did non-crushed discoloured seeds. These bacteria were released during seed soaking, contaminating clean seed and lowering seed germination. Cells of a rifampicin-resistant strain of P. fuscovaginae, which had been inoculated onto rice seeds, were subsequently recovered from different growth stages and from different rice tissues, thereby indicating endophytic colonization. These results have implications for seedling establishment, as symptomless seeds do not assure disease-free seeds, and the presence of seedborne bacteria results in poor germination and poor seedling establishment. Elimination of seedborne bacteria by soaking in sodium hypochlorite can increase seed germination. This could be used in developing control strategies, and, if practised regularly, reduce entry of seedborne disease- causing organisms into crops, resulting in lower disease pressure