Genetic Variability and Host Specialization in the Latin American Clade of Ceratocystis fimbriata

The Ceratocystis fimbriata complex includes many undescribed species that cause wilt and canker diseases of many economically important plants. Phylogenetic analyses of DNA sequences have delineated three geographic clades within Ceratocystis fimbriata. This study examined host specialization in the Latin American clade, in which a number of lineages were identified using sequences of the internal transcribed spacer (ITS) region of the rDNA. Three host-associated lineages were identified from cacao (Theobroma cacao), sweet potato (Ipomoea batatas), and sycamore (Platanus spp.), respectively. Isolates from these three lineages showed strong host specialization in reciprocal inoculation experiments on these three hosts. Six cacao isolates from Ecuador, Trinidad, and Columbia differed genetically from other cacao isolates and were not pathogenic to cacao in inoculation tests. Further evidence of host specialization within the Latin American clade of Ceratocystis fimbriata was demonstrated in inoculation experiments in growth chambers using sweet potato, sycamore, Colocasia esculenta, coffee (Coffea arabica), and mango (Mangifera indica) plants; inoculation experiments in Brazil using Brazilian isolates from cacao, Eucalyptus spp., mango, and Gmelina arborea; and inoculation experiments in Costa Rica using Costa Rican isolates from cacao, coffee, and Xantho-soma sp. Hosts native to the Americas appeared to be colonized by only select pathogen genotypes, whereas nonnative hosts were colonized by several genotypes. We hypothesize that local populations of Ceratocystis fimbriata have specialized to different hosts; some of these populations are nascent species, and some host-specialized genotypes have been moved to new areas by humans.

Download Full-text

Species or Genotypes? Reassessment of Four Recently Described Species of the Ceratocystis Wilt Pathogen, Ceratocystis fimbriata, on Mangifera indica

Phytopathology ◽

10.1094/phyto-03-15-0065-r ◽

2015 ◽

Vol 105 (9) ◽

pp. 1229-1244 ◽

Cited By ~ 39

Author(s):

Leonardo S. S. Oliveira ◽

Thomas C. Harrington ◽

Maria A. Ferreira ◽

Michelle B. Damacena ◽

Abdullah M. Al-Sadi ◽

...

Keyword(s):

New Species ◽

Dna Sequences ◽

Ipomoea Batatas ◽

Phylogenetic Analyses ◽

Mangifera Indica ◽

Ceratocystis Fimbriata ◽

Ceratocystis Wilt ◽

Nursery Stock ◽

Internal Transcribed Spacer Sequences ◽

Mating Type Genes

Ceratocystis wilt is among the most important diseases on mango (Mangifera indica) in Brazil, Oman, and Pakistan. The causal agent was originally identified in Brazil as Ceratocystis fimbriata, which is considered by some as a complex of many cryptic species, and four new species on mango trees were distinguished from C. fimbriata based on variation in internal transcribed spacer sequences. In the present study, phylogenetic analyses using DNA sequences of mating type genes, TEF-1α, and β-tubulin failed to identify lineages corresponding to the four new species names. Further, mating experiments found that the mango isolates representing the new species were interfertile with each other and a tester strain from sweet potato (Ipomoea batatas), on which the name C. fimbriata is based, and there was little morphological variation among the mango isolates. Microsatellite markers found substantial differentiation among mango isolates at the regional and population levels, but certain microsatellite genotypes were commonly found in multiple populations, suggesting that these genotypes had been disseminated in infected nursery stock. The most common microsatellite genotypes corresponded to the four recently named species (C. manginecans, C. acaciivora, C. mangicola, and C. mangivora), which are considered synonyms of C. fimbriata. This study points to the potential problems of naming new species based on introduced genotypes of a pathogen, the value of an understanding of natural variation within and among populations, and the importance of phenotype in delimiting species.

Download Full-text

Genetic Variation and Variation in Aggressiveness to Native and Exotic Hosts Among Brazilian Populations of Ceratocystis fimbriata

Phytopathology ◽

10.1094/phyto-08-10-0228 ◽

2011 ◽

Vol 101 (5) ◽

pp. 555-566 ◽

Cited By ~ 37

Author(s):

Thomas C. Harrington ◽

Daniel J. Thorpe ◽

Acelino C. Alfenas

Keyword(s):

Dna Sequences ◽

Phylogenetic Analyses ◽

Mangifera Indica ◽

Storage Roots ◽

Ceratocystis Fimbriata ◽

Internal Transcribed Spacer Region ◽

Mating Type Gene ◽

Type Gene ◽

Pathogen Populations ◽

Brazilian Populations

Ceratocystis fimbriata is a complex of many species that cause wilt and cankers on woody plants and rot of storage roots or corms of many economically important crops worldwide. In Brazil, C. fimbriata infects different cultivated crop plants that are not native to Brazil, including Gmelina arborea, Eucalyptus spp., Mangifera indica (mango), Ficus carica (fig), and Colocasia esculenta (inhame). Phylogenetic analyses and inoculation studies were performed to test the hypothesis that there are host-specialized lineages of C. fimbriata in Brazil. The internal transcribed spacer region ribosomal DNA sequences varied greatly but there was little resolution of lineages based on these sequences. A portion of the MAT1-2 mating type gene showed less variation, and this variation corresponded more closely with host of origin. However, mango isolates were found scattered throughout the tree. Inoculation experiments on the five exotic hosts showed substantial variation in aggressiveness within and among pathogen populations. Native hosts from the same families as the exotic hosts tended to be less susceptible than the cultivated hosts, but there was little correlation between aggressiveness to the cultivated and native hosts of the same family. Cultivation and vegetative propagation of exotic crops may select for strains that are particularly aggressive on those crops.

Download Full-text

First report of black rot of Colocasia esculenta caused by Ceratocystis fimbriata in Brazil

Fitopatologia Brasileira ◽

10.1590/s0100-41582005000100017 ◽

2005 ◽

Vol 30 (1) ◽

pp. 88-89 ◽

Cited By ~ 15

Author(s):

Thomas C. Harrington ◽

Daniel J. Thorpe ◽

Vera Lucia A. Marinho ◽

Edson L. Furtado

Keyword(s):

Latin American ◽

Mangifera Indica ◽

Sao Paulo ◽

Colocasia Esculenta ◽

Ficus Carica ◽

Black Rot ◽

São Paulo ◽

Ceratocystis Fimbriata ◽

Distrito Federal ◽

American Clade

Ceratocystis fimbriata was found sporulating in gray to black discolored areas on edible corms of Colocasia esculenta found in supermarkets in the states of São Paulo, Rio de Janeiro, Bahia, Rondônia and the Distrito Federal. In most cases the corms were grown in the state of São Paulo. The black rot appeared to occur post-harvest. Sequences of rDNA indicated that the Colocasia sp. isolates belong to the Latin American clade of the C. fimbriata complex, but the isolates were more aggressive than isolates from Ficus carica and Mangifera indica, in pseudopetioles of C. esculenta.

Download Full-text

Baorangia duplicatopora (Boletaceae, Boletales), a new bolete from tropical China

Phytotaxa ◽

10.11646/phytotaxa.508.1.4 ◽

2021 ◽

Vol 508 (1) ◽

Author(s):

XU ZHANG ◽

ZHI-QUN LIANG ◽

SHUAI JIANG ◽

CHANG XU ◽

XIN-HUA FU ◽

...

Keyword(s):

New Species ◽

Dna Sequences ◽

Phylogenetic Analyses ◽

Elongation Factor ◽

Its Region ◽

Tropical Region ◽

Translation Elongation ◽

Line Drawings ◽

Microscopic Features ◽

Tropical China

Baorangia duplicatopora is described as a new species from Hainan Province, a tropical region of China. It is morphologically characterized by large to very large basidiomata with a dull rose red, rose pink to purplish red pileus, compound pores, pileus context near hymenophore and stipe context staining blue when injured, a red stipe, and cheilocystidia wider than those of other Baorangia species. Phylogenetic analyses of DNA sequences from part of the 28S gene, the nuc rDNA internal transcribed spacer (ITS) region, and part of the translation elongation factor 1-α gene (TEF1) also confirmed that B. duplicatopora forms an independent lineage within Baorangia. Detailed descriptions, color photographs of fresh basidiomata, and line drawings of microscopic features of the new species are presented. A key to species of Baorangia in the world is also provided.

Download Full-text

Phylogenetics of Taxus Using the Internal Transcribed Spacers of Nuclear Ribosomal DNA and Plastid trnL-F Regions

Horticulturae ◽

10.3390/horticulturae6010019 ◽

2020 ◽

Vol 6 (1) ◽

pp. 19

Author(s):

Patricia Coughlan ◽

James C. Carolan ◽

Ingrid L. I. Hook ◽

Lisa Kilmartin ◽

Trevor R. Hodkinson

Keyword(s):

Dna Sequences ◽

Phylogenetic Analyses ◽

Intergenic Spacer ◽

Its Region ◽

Single Species ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Trnl Intron ◽

Group Status ◽

Haplotype Networks

Taxus is a genus of trees and shrubs with high value in horticulture and medicine as a source of the anticancer drug paclitaxel. The taxonomy of the group is complex due to the lack of diagnostic morphological characters and the high degree of similarity among species. Taxus has a wide global geographic distribution and some taxonomists recognize only a single species with geographically defined subgroups, whereas others have described several species. To address these differences in taxonomic circumscription, phylogenetic analyses were conducted on DNA sequences using Maximum Likelihood, Bayesian Inference and TCS haplotype networks on single and combined gene regions obtained for the nuclear ribosomal ITS region and the plastid trnL intron and trnL-F intergenic spacer. Evidence is presented for the sister group status of Pseudotaxus to Taxus and the inclusion of Amentotaxus, Austrotaxus, Cephalotaxus and Torreya within Taxaceae. Results are consistent with the taxonomic recognition of nine species: T. baccata, T. brevifolia, T. canadensis, T. cuspidata, T. floridana, T. fuana, T. globosa, T. sumatrana and T. wallichiana, but evidence is found for less species distinction and considerable reticulation within the T. baccata, T. canadensis and T. cuspidata group. We compare the results to known taxonomy, biogeography, present new leaf anatomical data and discuss the origins of the hybrids T. ×media and T. ×hunnewelliana.

Download Full-text

Phylogeny of Subtribe Aeridinae (Orchidaceae) Inferred from DNA Sequences Data : Advanced Analyses Including Australasian Genera

Jurnal Teknologi ◽

10.11113/jt.v59.1591 ◽

2012 ◽

Vol 59 (1) ◽

Cited By ~ 1

Author(s):

Topik Hidayat ◽

Peter H. Weston ◽

Tomohisa Yukawa ◽

Motomi Ito ◽

Rod Rice

Keyword(s):

Dna Sequences ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Its Region ◽

Classification Systems ◽

Genus Level ◽

Preliminary Work ◽

Secondary Center ◽

Generic Position ◽

Australasian Region

Advanced phylogenetic analyses of the orchid subtribe Aeridinae has been conducted using DNA sequences of ITS region of nrDNA andmatK of cpDNA. In the preliminary work, we only involved the most representative Asian genera of the subtribe. Further, to establish more robust relationships in the Aeridinae, in this study we have extended the sampling to include Australasian specimens. Our analyses revealed that: (1) the subtribe is reorganised by four major groups with 11 subgroups (This is inconsistent with previous classification systems of the subtribe); (2) the Australasian region is a secondary center of diversification of the subtribe; (3) vegetative features have shown to have greater value than reproductive one in determining major groups in the subtribe; and (4) at genus level, some genera, i.e. Phalaenopsis,Cleisostoma, Sarcochilus, and Aerides are shown to be non-monophyletic. This study also resolved the taxonomic status ofAerides flabellata Rolve ex Downie, a species with a debatable generic position.

Download Full-text

Pathogenicity, Internal Transcribed Spacer-rDNA Variation, and Human Dispersal of Ceratocystis fimbriata on the Family Araceae

Phytopathology ◽

10.1094/phyto-95-0316 ◽

2005 ◽

Vol 95 (3) ◽

pp. 316-323 ◽

Cited By ~ 35

Author(s):

Daniel J. Thorpe ◽

Thomas C. Harrington ◽

Janice Y. Uchida

Keyword(s):

Internal Transcribed Spacer ◽

Mangifera Indica ◽

Its Region ◽

Colocasia Esculenta ◽

Caribbean Region ◽

Herbarium Specimens ◽

Storage Roots ◽

Ceratocystis Fimbriata ◽

The Family ◽

The Caribbean

Ceratocystis fimbriata is a complex of many cryptic, host-specialized species that causes wilt and canker of woody species and rot diseases of storage roots and corms of many economically important plants worldwide. With the exception of the family Araceae, all confirmed hosts of C. fimbriata are dicotyledonous plants. We hypothesized that the isolates from members of the family Araceae would form a monophyletic lineage specialized to infect these unique hosts. Analyses of sequences of the internal transcribed spacer (ITS) region of nuclear rDNA indicate that isolates and herbarium specimens of C. fimbriata from the family Araceae represent three different groups: an Xanthosoma/Syngonium group on corms of Xanthosoma spp. from the Caribbean region and on ornamental S. podophyllum from greenhouses in Florida, Hawaii, Australia, and Brazil; an inhame group on corms of Colocasia esculenta in Brazil; and a distantly related taro group on Colocasia esculenta in Hawaii and China and on X. sagittifolium in Fiji. Inoculations of three species of Araceae (Caladium bicolor, S. podophyllum, and Colocasia esculenta) showed that isolates from all three groups are pathogenic to these three hosts. Brazilian isolates from Mangifera indica and Ficus carica were only weakly pathogenic to Caladium and Syngonium sp. and were not pathogenic to Colocasia sp. Syngonium plants appeared to be most susceptible to isolates of the Xanthosoma/Syngonium group, and Colocasia plants were least susceptible to isolates from Syngonium spp. Thus, it appears that adaptations to the family Araceae have evolved more than once in the C. fimbriata complex. It is hypothesized that the three groups of C. fimbriata on the family Araceae are native to the Caribbean, Brazil, and Asia, respectively, but they have been spread elsewhere by humans.

Download Full-text

The genome of cultivated sweet potato containsAgrobacteriumT-DNAs with expressed genes: An example of a naturally transgenic food crop

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1419685112 ◽

2015 ◽

Vol 112 (18) ◽

pp. 5844-5849 ◽

Cited By ~ 140

Author(s):

Tina Kyndt ◽

Dora Quispe ◽

Hong Zhai ◽

Robert Jarret ◽

Marc Ghislain ◽

...

Keyword(s):

Sweet Potato ◽

Dna Sequences ◽

Ipomoea Batatas ◽

Pathogenic Bacteria ◽

Arable Land ◽

Artificial Chromosome ◽

Plant Genome ◽

Small Interfering Rnas ◽

Food Crop ◽

Transgenic Food

Agrobacterium rhizogenesandAgrobacterium tumefaciensare plant pathogenic bacteria capable of transferring DNA fragments [transfer DNA (T-DNA)] bearing functional genes into the host plant genome. This naturally occurring mechanism has been adapted by plant biotechnologists to develop genetically modified crops that today are grown on more than 10% of the world’s arable land, although their use can result in considerable controversy. While assembling small interfering RNAs, or siRNAs, of sweet potato plants for metagenomic analysis, sequences homologous to T-DNA sequences fromAgrobacteriumspp. were discovered. Simple and quantitative PCR, Southern blotting, genome walking, and bacterial artificial chromosome library screening and sequencing unambiguously demonstrated that two different T-DNA regions (IbT-DNA1 andIbT-DNA2) are present in the cultivated sweet potato (Ipomoea batatas[L.] Lam.) genome and that these foreign genes are expressed at detectable levels in different tissues of the sweet potato plant.IbT-DNA1 was found to contain four open reading frames (ORFs) homologous to the tryptophan-2-monooxygenase (iaaM), indole-3-acetamide hydrolase (iaaH), C-protein (C-prot), and agrocinopine synthase (Acs) genes ofAgrobacteriumspp.IbT-DNA1 was detected in all 291 cultigens examined, but not in close wild relatives.IbT-DNA2 contained at least five ORFs with significant homology to theORF14,ORF17n, rooting locus (Rol)B/RolC,ORF13, andORF18/ORF17ngenes ofA. rhizogenes.IbT-DNA2 was detected in 45 of 217 genotypes that included both cultivated and wild species. Our finding, that sweet potato is naturally transgenic while being a widely and traditionally consumed food crop, could affect the current consumer distrust of the safety of transgenic food crops.

Download Full-text

Genetic Bottlenecks for Two Populations of Ceratocystis fimbriata on Sweet Potato and Pomegranate in China

Plant Disease ◽

10.1094/pdis-03-16-0409-re ◽

2016 ◽

Vol 100 (11) ◽

pp. 2266-2274 ◽

Cited By ~ 16

Author(s):

Qian Li ◽

Thomas C. Harrington ◽

Douglas McNew ◽

Jianqiang Li ◽

Qiong Huang ◽

...

Keyword(s):

Sweet Potato ◽

Mating Type ◽

Ipomoea Batatas ◽

The United States ◽

Its Rdna ◽

Storage Roots ◽

Ceratocystis Fimbriata ◽

Rdna Sequences ◽

Mating Type Genes ◽

Microsatellite Alleles

Chinese isolates of Ceratocystis fimbriata from sweet potato (Ipomoea batatas) and pomegranate (Punica granatum) were genetically compared with a worldwide collection of isolates from a variety of hosts. Isolates from black-rotted storage roots of sweet potato in China, Japan, Australasia, and the United States had identical internal transcribed spacer (ITS) ribosomal DNA (rDNA) sequences and only minor variation in microsatellite alleles. Sequences of their mating type genes were most similar to those of isolates from various hosts in Ecuador, a center of diversity for sweet potato. Isolates from Colocasia esculenta (taro) and pomegranate from Yunnan and Sichuan had only one ITS rDNA sequence (haplotype ITS5). This haplotype, sequences of mating type genes, and microsatellite alleles linked these isolates to isolates from Eucalyptus stumps in South China and diseased Eucalyptus trees in Brazil, supporting the hypothesis that the pomegranate population originated from Brazil via cuttings of Eucalyptus. Isolates from sweet potato and pomegranate in China were interfertile with tester strains of C. fimbriata, confirming that the causes of the two epidemics in China belong to a single biological species. However, other isolates from Eucalyptus stumps were intersterile with the tester strains and had ITS rDNA sequences typical of the Asian species, C. cercfabiensis.

Download Full-text