From coconut to cassava: the coconut lethal yellowing phytoplasma is worsening the threat to food security in C\uf4te d\u2019Ivoire

Background. Cassava (Manihot esculenta Crantz) is a major staple food in the developing countries whose total world production reached approximately 278 million metric tonnes in 2017. C\uf4te d'Ivoire produces around three million tonnes of cassava every year and reached 4.54 metric tonnes in 2017. It is typically consumed as 'attiek\ue9', which is currently exported on regional and international markets. Cassava crop is now threaten by the C\uf4te d'Ivoire lethal yellowing disease (CILY) first reported and associated with a phytoplasma in Grand-Lahou in 2013. CILY destroyed over 400 ha of coconut groves in smallholder coconut farms where women farmers started planting cassava as an alternative food and cash crop in coconut lands devastated by the disease. Methods. Symptoms of leaf mosaic, curling and yellowing were observed in cassava orchards intwo coconut-growing villages located in the south coastal littoral of Grand-Lahou. Leaf samples were collected from symptom-bearing and symptomless cassava plants and subjected to total DNA extraction. PCR with phytoplasma universal 16S rRNA primers, and group-specific primers for subgroup 16SrXXII-B, \u2018Candidatus Phytoplasma palmicola\u2019-related strains; and with specific primers for African/Eastern cassava mosaic viruses (ACMV, EACMV). Amplicons were purified, cloned and sequenced. Sequences were compared to those of reference in NCBI (https://www.ncbi.nlm.nih.gov) and used for phylogeny analysis of phytoplasma and virus strains, respectively. Results. Phytoplasma DNA was amplified from six out of 12 symptom-bearing samples, five of which co-amplified virus DNA. Phytoplasma sequences showed 99% identity to those of 16SrXXII-B phytoplasmas as confirmed through phylogeny analysis. One cassava plant was co-infected with ACMV, closely related to the Angola strain, while the other four showed co-infection with both the ACMV (Angola) and an EACMV strain from Madagascar. All cassava varieties were phytoplasma-begomovirus co-infected, except the Yac\ue9 variety. Conclusions. Cassava plants in Grand-Lahou orchards were found infected by CILY phytoplasma (group 16SrXXII-B) and ACMV/EACMV virus strains. Results indicate that cassava may be an alternative host for the CILY phytoplasma, which may play a role spreading and worsening CILY epidemic. Prompt actions are required while waiting for a suitable resistant coconut cultivar. Short-term solutions may include replanting cassava yards with newly developed cassava varieties that enhance plant resilience against the coconut phytoplasma and ACMV/EACMV viruses to help supporting food production and improve livelihoods of smallholder coconut farmers in Grand-Lahou

Acremonium phylogenetic overview and revision of Gliomastix, Sarocladium, and Trichothecium

AbstractOver 200 new sequences are generated for members of the genus Acremonium and related taxa including ribosomal small subunit sequences (SSU) for phylogenetic analysis and large subunit (LSU) sequences for phylogeny and DNA-based identification. Phylogenetic analysis reveals that within the Hypocreales, there are two major clusters containing multiple Acremonium species. One clade contains Acremonium sclerotigenum, the genus Emericellopsis, and the genus Geosmithia as prominent elements. The second clade contains the genera Gliomastix sensu stricto and Bionectria. In addition, there are numerous smaller clades plus two multi-species clades, one containing Acremonium strictum and the type species of the genus Sarocladium, and, as seen in the combined SSU/LSU analysis, one associated subclade containing Acremonium breve and related species plus Acremonium curvulum and related species. This sequence information allows the revision of three genera. Gliomastix is revived for five species, G. murorum, G. polychroma, G. tumulicola, G. roseogrisea, and G. masseei. Sarocladium is extended to include all members of the phylogenetically distinct A. strictum clade including the medically important A. kiliense and the protective maize endophyte A. zeae. Also included in Sarocladium are members of the phylogenetically delimited Acremonium bacillisporum clade, closely linked to the A. strictum clade. The genus Trichothecium is revised following the principles of unitary nomenclature based on the oldest valid anamorph or teleomorph name, and new combinations are made in Trichothecium for the tightly interrelated Acremonium crotocinigenum, Spicellum roseum, and teleomorph Leucosphaerina indica. Outside the Hypocreales, numerous Acremonium-like species fall into the Plectosphaerellaceae, and A. atrogriseum falls into the Cephalothecaceae

First report of a phytoplasma affecting cassava orchards in Cote d'Ivoire

Annex 46 of 48 for CIFSRF-IDRC/GAC Final technical report: http://hdl.handle.net/10625/56415This work was carried out with the aid of a grant from Canada’s International Development Research Centre (IDRC), and with financial support from the Government of Canada, provided through Global Affairs Canada (GAC)This is the first report of a phytoplasma affecting cassava in Côte d'Ivoire. The findings suggest that cassava may be a potential alternative host for the Côte d'Ivoire lethal yellowing (CILY) phytoplasma, which poses a serious threat for the food security of smallholder coconut and cassava farmers, especially women, in Grand-Lahou, Côte d’Ivoire. Leaf samples were collected at random from 12 symptom-bearing and two symptomless cassava plants from two villages. Illustrations/ figures depict the symptoms of yellowing. Cassava (Manihot esculenta) is one of the staple foods in Africa, cultivated in 40 countries and producing more than three million tonnes per year

Genetic diversity of phytoplasmas identified in peach (Prunus persica) accessions at the Canadian Clonal Genebank.

Peach [Prunus persica (L.) Bastch] is mainly cultivated in Canada in Ontario province (82% of national production). A variety of symptoms typical of a phytoplasma infection were observed some of the 83 P. persica accessions during June-August 2009 at the Canadian Clonal Genebank. PRU0430 (‘HW274’, from Canada), PRU0380 (‘GF305’ from France), PRU0334 (‘RedSkin’ from USA), PRU0155 (‘Harblaze’, from Canada) and PRU0375 (‘Babygold #5’, from USA) showed decline, leaf reddening, yellowing, shortening of internodes, witches’ broom and reduced fruit size; while ‘PRU0382’ (peach-almond ‘Kando’ from the Czech Republic) and PRU0445 (peach ‘HW271’ from Canada) exhibited peach rosette-like symptoms. Leaf samples from symptomatic and symptomless plants were collected and total DNA was extracted. Phytoplasma universal 16S rRNA primers, R16mF2/R1 and R16F2n/R2 and fU5/rU3 were used in nested PCR assays. R16F2n/R2 nested PCR products were obtained for ‘PRU0430’, ‘PRU0380’, ‘PRU0155’, ‘PRU0334’ and ‘PRU0375’; while fU5/rU3 PCR products were obtained for ‘PRU0382’ and ‘PRU0445’. Plants lacking symptoms yielded no PCR products. Amplicons were purified, cloned, and sequenced. BLAST analysis showed that R16F2n/R2 sequences (GU223903) were 99% identical to 16S rRNA phytoplasma sequences for group 16SrVII ‘Candidatus Phytoplasma fraxini’, while those from fU5/rU3 amplicons (GU223904) shared 99% identity with those of group 16SrI ‘Candidatus Phytoplasma asteris’. AluI, RsaI and MseI RFLP analysis yielded profiles consistent with those of phytoplasma in subgroups 16SrVII-A and 16SrI-B, respectively. To our knowledge, this is the first report of a 16SrI-related phytoplasma in peach in Canada, and the first world report of a 16SrVII-related phytoplasma strain identified in peach after a case in southern Italy

First report of 'Candidatus Phytoplasma fraxini' (group 16SrVII phytoplasma) associated with a peach disease in Canada.

Peach (Prunus persica), family Rosaceae, is native to China. In Canada, the province of Ontario produces 82% of the nation\u2019s peach crop. The Canadian Clonal Genebank, also located in Ontario, currently holds 83 accessions of peach. The collection is routinely monitored for symptoms of phytoplasma including decline (Fig. 1), leaf reddening (Fig. 2), yellowing, shortening of internodes, witches\u2019 broom and reduced fruit size. Leaf samples from trees exhibiting symptoms and symptomless trees representing sixteen accessions were collected from June to August 2009. Total DNA was extracted (DNeasy plant extraction kit, QIAGEN). Phytoplasma universal primers specific for 16S rDNA (R16mF2/R1 and R16F2n/R2; Gundersen & Lee, 1996) were used in a nested PCR assay. Nested PCR products of expected size (~1250 bp) were obtained for accessions PRU0430 (cv. HW274, from Canada), PRU0380 (cv. GF 305 from France), PRU0334 (cv. RedSkin from USA), PRU0155 (cv. Harblaze from Canada) and PRU0375 (cv. Babygold #5 from USA). Symptomless plants yielded no PCR products. Amplicons were purified (Wizard PCR Clean-up, Promega), cloned (pGEM-T Easy Vector, Promega), and sequenced (Robarts Institute, London, Canada). The obtained sequences shared 100% identity with each other and a representative corresponding to PRU0430 was deposited in GenBank (Accession No. GU223903). BLAST analysis showed that the Prunus phytoplasma shared 99% 16S rDNA sequence identity with those of phytoplasmas in the group 16SrVII (ash yellows) for which \u2018Candidatus Phytoplasma fraxini\u2019 is the reference strain. Restriction fragment length polymorphism analysis (RFLP) of amplicons using AluI, RsaI and MseI yielded profiles similar to those of 16SrVII-A phytoplasma subgroup. Phytoplasmas of group 16SrVII have been reported in different hosts in Colombia, Argentina, Brazil and Chile (Fiore et al., 2007). Particularly in North America, including Canada, 16SrVII phytoplasmas have been associated with ash yellows and lilac witches\u2019 broom diseases (Sinclair et al., 1996; Griffiths et al., 1999). To our knowledge, this is the first report of a 16SrVII-related phytoplasma strain identified in peach after an incidental report in peach in Southern Italy (Paltrineri et al., 2003). The 16SrVII phytoplasma has caused devastating effects in ornamentals. Therefore its presence in peach is of great phytosanitary significance due to its commercial interest, and represents a potential threat for disease spread to other fruit crops, particularly Prunus sp

First Report of \u2018Candidatus Phytoplasma asteris\u2019-Related Strain Associated with Peach Rosette in Canada.

Prunus persica (L.) Bastch (family Rosaceae) is currently represented by 83 accessions at the Canadian Clonal Genebank. Approximately 3,200 ha are devoted to peach cultivation in Canada where Ontario Province accounts for 82% of the national production. The clonal peach accessions, also located in Ontario, are monitored routinely for symptoms of phytoplasma infection, including rosette-like symptoms (3) that are characterized by new shoots with very short internodes, loss of older shoot leaves leaving only bunches of young leaves on the tips of naked shoots, and flowers that rarely set fruit. From June to August 2009, peach accessions PRU0382 and PRU0445 showed typical peach rosette symptoms, while another 14 accessions exhibited either short internodes or no symptoms. Leaf midrib samples were collected from 16 peach accessions, including 17 symptomatic (from which 8 corresponded to accession PRU0382, 6 for PRU0445, 1 for PRU0335, 1 for PRU0179, and 1 for PRU0451) and 16 asymptomatic (from which 5 corresponded to a representative of each accession PRU0382, PRU0445, PRU0335, PRU0179, and PRU0451 and 11 to other peach accessions). Total DNA was extracted (DNeasy Plant Extraction Mini Kit, QIAGEN, Valencia, CA) from 100 mg of each sample and used as a template in a nested PCR with phytoplasma universal primers R16mF2/R1 (1) and fU5/rU3 (2). Nested PCR products of the expected size (~880 bp) were obtained from all symptomatic samples (14 of 14) of accessions PRU0382 (peach-almond cv. Kando from the Czech Republic) and PRU0445 (peach cv. HW271 from Canada) only. All other plants with or without symptoms yielded no PCR products. Amplicons were purified (Wizard PCR Clean-up, Promega, Madison, WI), cloned in pGEM-T Easy Vector (Promega), and sequenced (Robarts Institute, London, Canada). The resulting 16S rDNA sequences were identical; one of each was archived in GenBank as Accession No. GU223904. BLAST analysis determined that the P. persica phytoplasma sequence shared 99% identity with 16S rDNA sequences of \u2018Candidatus Phytoplasma asteris\u2019-related strains. This relationship was also supported by restriction fragment length polymorphism analysis (RFLP) of rDNA amplicons using AluI, RsaI, and MseI endonucleases that yielded fragment profiles indicative of phytoplasmas belonging to group 16SrI (Aster Yellows), subgroup B (16SrI-B). Among phytoplasma diseases, those attributed to group 16SrI strains are most numerous and affect the widest plant host range. They include peach rosette in the United States and Europe (3) as well as diseases of various horticultural crops in Canada, including grapevine (4). To our knowledge, this is the first report of a subgroup 16SrI-B phytoplasma affecting peach in Canada. Early detection of phytoplasmas by PCR in accessions with both European and Canadian origins underscores the importance of prompt identification of infected plants for subsequent thermotherapy treatment to maintain the health of the collection and prevent further disease spread

First report of ‘Candidatus Phytoplasma fraxini’ (group 16SrVII phytoplasma) associated with a peach disease in Canada

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First Report of ‘Candidatus Phytoplasma asteris’-Related Strain Associated with Peach Rosette in Canada

Prunus persica (L.) Bastch (family Rosaceae) is currently represented by 83 accessions at the Canadian Clonal Genebank. Approximately 3,200 ha are devoted to peach cultivation in Canada where Ontario Province accounts for 82% of the national production. The clonal peach accessions, also located in Ontario, are monitored routinely for symptoms of phytoplasma infection, including rosette-like symptoms (3) that are characterized by new shoots with very short internodes, loss of older shoot leaves leaving only bunches of young leaves on the tips of naked shoots, and flowers that rarely set fruit. From June to August 2009, peach accessions PRU0382 and PRU0445 showed typical peach rosette symptoms, while another 14 accessions exhibited either short internodes or no symptoms. Leaf midrib samples were collected from 16 peach accessions, including 17 symptomatic (from which 8 corresponded to accession PRU0382, 6 for PRU0445, 1 for PRU0335, 1 for PRU0179, and 1 for PRU0451) and 16 asymptomatic (from which 5 corresponded to a representative of each accession PRU0382, PRU0445, PRU0335, PRU0179, and PRU0451 and 11 to other peach accessions). Total DNA was extracted (DNeasy Plant Extraction Mini Kit, QIAGEN, Valencia, CA) from 100 mg of each sample and used as a template in a nested PCR with phytoplasma universal primers R16mF2/R1 (1) and fU5/rU3 (2). Nested PCR products of the expected size (~880 bp) were obtained from all symptomatic samples (14 of 14) of accessions PRU0382 (peach-almond cv. Kando from the Czech Republic) and PRU0445 (peach cv. HW271 from Canada) only. All other plants with or without symptoms yielded no PCR products. Amplicons were purified (Wizard PCR Clean-up, Promega, Madison, WI), cloned in pGEM-T Easy Vector (Promega), and sequenced (Robarts Institute, London, Canada). The resulting 16S rDNA sequences were identical; one of each was archived in GenBank as Accession No. GU223904. BLAST analysis determined that the P. persica phytoplasma sequence shared 99% identity with 16S rDNA sequences of ‘Candidatus Phytoplasma asteris’-related strains. This relationship was also supported by restriction fragment length polymorphism analysis (RFLP) of rDNA amplicons using AluI, RsaI, and MseI endonucleases that yielded fragment profiles indicative of phytoplasmas belonging to group 16SrI (Aster Yellows), subgroup B (16SrI-B). Among phytoplasma diseases, those attributed to group 16SrI strains are most numerous and affect the widest plant host range. They include peach rosette in the United States and Europe (3) as well as diseases of various horticultural crops in Canada, including grapevine (4). To our knowledge, this is the first report of a subgroup 16SrI-B phytoplasma affecting peach in Canada. Early detection of phytoplasmas by PCR in accessions with both European and Canadian origins underscores the importance of prompt identification of infected plants for subsequent thermotherapy treatment to maintain the health of the collection and prevent further disease spread. References: (1) D. E Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:1441, 1996. (2) K. H. Lorenz et al. Phytopathology 85:771, 1995. (3) C. Marcone et al. Acta Hortic. 386:471, 1995. (4) C. Y. Olivier et al. Plant Dis. 93:669, 2009