Phylogenetic diversity of Calonectria ilicicola causing Cylindrocladium black rot of peanut and red crown rot of soybean in southern China

Gai, Yunpeng; Deng, Q.; Chen, Xinglong; Guan, M.; Xiao, Xiang; Xu, Donglin; Deng, M.; Pan, R.

doi:10.1007/s10327-017-0724-9

Cited by 17 publications

(18 citation statements)

References 36 publications

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“…2005 ) are important causal agents of Calonectria leaf blight (CLB) in Eucalyptus plantations. Calonectria ilicicola is known as a common pathogen responsible for the red crown rot of soybeans in China, Japan and USA ( Gai et al. 2017 , Yamamoto et al.…”

Section: Introductionmentioning

confidence: 99%

Reconsideration of species boundaries and proposed DNA barcodes for Calonectria

Liu

Wingfield

et al. 2020

Studies in Mycology

123

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Calonectria represents a genus of phytopathogenic ascomycetous fungi with a worldwide distribution. In recent years, there has been an increase in the number of taxonomic studies on these fungi. Currently, there are 169 described species of Calonectria based on comparisons of DNA sequence data, combined with morphological characteristics. However, for some of these species, the sequence data utilised at the time of their description were relatively limited. This has justified an urgent need to reconsider the species boundaries for Calonectria based on robust genus-wide phylogenetic analyses. In this study, we utilised 240 available isolates including the ex-types of 128 Calonectria species, and re-sequenced eight gene regions ( act , cmdA , his3 , ITS, LSU, rpb2, tef1 and tub2 ) for them. Sequences for 44 Calonectria species, for which cultures could not be obtained, were downloaded from GenBank. DNA sequence data of all the 169 Calonectria species were then used to determine their phylogenetic relationships. As a consequence, 51 species were reduced to synonymy, two new species were identified, and the name Ca. lauri was validated. This resulted in the acceptance of 120 clearly defined Calonectria spp. The overall data revealed that the genus includes 11 species complexes, distributed across the Prolate and Sphaero-Naviculate Groups known to divide Calonectria . The results also made it possible to develop a robust set of DNA barcodes for Calonectria spp. To accomplish this goal, we evaluated the outcomes of each of the eight candidate DNA barcodes for the genus, as well as for each of the 11 species complexes. No single gene region provided a clear identity for all Calonectria species. Sequences of the tef1 and tub2 genes were the most reliable markers; those for the cmdA , his3 , rpb2 and act gene regions also provided a relatively effective resolution for Calonectria spp., while the ITS and LSU failed to produce useful barcodes for species discrimination. At the species complex level, results showed that the most informative barcodes were inconsistent, but that a combination of six candidate barcodes ( tef1 , tub2 , cmdA , his3 , rpb2 and act ) provided stable and reliable resolution for all 11 species complexes. A six-gene combined phylogeny resolved all 120 Calonectria species, and revealed that tef1 , ...

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Section: Introductionmentioning

confidence: 99%

Reconsideration of species boundaries and proposed DNA barcodes for Calonectria

Liu

Wingfield

et al. 2020

Studies in Mycology

123

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“…Species of Calonectria have been isolated from soils, fruits, leaves, stems, and roots [1,4,[7][8][9][10][11][12][13][14]. The fungi are best known as foliar, shoot, and root pathogens [1,2,4,5], and they are commonly associated with disease symptoms, including seedling damping-off, seedling rot, cutting rot, leaf spots, leaf blight, shoot blight, crown cankers, stem lesions, collar and root rots, and tuber rot [1,[14][15][16][17][18][19][20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

“…Some species of Calonectria isolated from soils are important plant pathogens. Calonectria ilicicola is a soil-borne fungal pathogen of worldwide importance that causes black rot disease in peanut and red crown rot in soybean [21,[24][25][26][27][28]. Recently, we isolated five Calonectria species, namely C. aconidialis, C. auriculiformis, C. hongkongensis, C. pseudoreteaudii, and C. reteaudii, from soils in a plantation of Eucalyptus trees [14].…”

Section: Introductionmentioning

confidence: 99%

Species Diversity and Distribution Characteristics of Calonectria in Five Soil Layers in a Eucalyptus Plantation

Liu

Chen

2021

JoF

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The genus Calonectria includes pathogens of various agricultural, horticultural, and forestry crops. Species of Calonectria are commonly collected from soils, fruits, leaves, stems, and roots. Some species of Calonectria isolated from soils are considered as important plant pathogens. Understanding the species diversity and distribution characteristics of Calonectria species in different soil layers will help us to clarify their long-term potential harm to plants and their patterns of dissemination. To our knowledge, no systematic research has been conducted concerning the species diversity and distribution characteristics of Calonectria in different soil layers. In this study, 1000 soil samples were collected from five soil layers (0–20, 20–40, 40–60, 60–80, and 80–100 cm) at 100 sampling points in one 15-year-old Eucalyptus urophylla hybrid plantation in southern China. A total of 1037 isolates of Calonectria present in all five soil layers were obtained from 93 of 100 sampling points. The 1037 isolates were identified based on DNA sequence comparisons of the translation elongation factor 1-alpha (tef1), β-tubulin (tub2), calmodulin (cmdA), and histone H3 (his3) gene regions, as well as the combination of morphological characteristics. These isolates were identified as C. hongkongensis (665 isolates; 64.1%), C. aconidialis (250 isolates; 24.1%), C. kyotensis (58 isolates; 5.6%), C. ilicicola (47 isolates; 4.5%), C. chinensis (2 isolates; 0.2%), and C. orientalis (15 isolates; 1.5%). With the exception of C. orientalis, which resides in the C. brassicae species complex, the other five species belonged to the C. kyotensis species complex. The results showed that the number of sampling points that yielded Calonectria and the number (and percentage) of Calonectria isolates obtained decreased with increasing depth of the soil. More than 84% of the isolates were obtained from the 0–20 and 20–40 cm soil layers. The deeper soil layers had comparatively lower numbers but still harbored a considerable number of Calonectria. The diversity of five species in the C. kyotensis species complex decreased with increasing soil depth. The genotypes of isolates in each Calonectria species were determined by tef1 and tub2 gene sequences. For each species in the C. kyotensis species complex, in most cases, the number of genotypes decreased with increasing soil depth. The 0–20 cm soil layer contained all of the genotypes of each species. To our knowledge, this study presents the first report of C. orientalis isolated in China. This species was isolated from the 40–60 and 60–80 cm soil layers at only one sampling point, and only one genotype was present. This study has enhanced our understanding of the species diversity and distribution characteristics of Calonectria in different soil layers.

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“…The fungus Calonectria ilicicola Boedijin & Reitsma (anamorph: Cylindrocladium parasiticum Crous, Wingfield and Alfennas) is an economically important plant pathogen, which cause Cylindrocladium black rot (CBR) on peanut (Arachis hypogaea L.) and Red crown rot (RCR) on soybean [Glycine max (L.) Merr.] (Gai et al 2017). Calonectria ilicicola is a soil-borne fungal pathogen of global importance, which was first recorded in Georgia, the USA in 1965 and has since spread throughout peanut production areas in the southeastern United States (Bell and Sobers 1966;Wright et al 2010).…”

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confidence: 99%

“…In order to understand mitogenomic background and genetic evolution relationship of C. ilicicola, we sequenced the complete mitochondrial genome of three strains isolated from diseased peanut showing symptom of CBR in Boluo County, Huizhou City, Guangdong (23 27 0 31 00 N, 114 31 0 53 00 E, GDBL02); Longnan County, Ganzhou City, Jiangxi Province (24 38 0 10 00 N, 114 45 0 33 00 E, JXLN31), and Longyan City, Fujian Province (25 7 0 23 00 N, E116 48 0 7 00 E, FJLY41), respectively, and two strains isolated from diseased soybean showing symptom of RCR in Boluo County, Huizhou City, Guangdong (23 27 0 31 00 N o , 114 31 0 53 00 E, GDBL60), and Tonglu County, Hangzhou City, Zhejiang Province (29 50 0 43 00 N, 119 27 0 59 00 E, ZJHZ01), respectively. The taxonomic position of these strains have been identified based on ribosomal DNA internal transcribed spacer (rDNA-ITS), beta-tubulin gene, translation elongation factor 1-a gene sequences, and the pathogenicity has been confirmed by inoculation experiment (Gai et al 2017). The DNA was extracted from the hyphae of C. ilicicola using a fungal DNA extraction kit (OMEGA BioTek, Beijing, China) according to the manufacturer's instructions.…”

mentioning

confidence: 99%

A phylogenomic tree of fungi: evolutionary relationships among Calonectria ilicicola and 586 fungal mitochondrial genomes

Gai

Pan

Peng

2020

Mitochondrial DNA Part B

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The mitochondrial genomes have the potential to be 'molecular clock' due to its high mutation rate and low DNA recombination rate. Here, we sequenced the complete mitochondrial genome of three strains of Calonectria ilicicola (anamorph Cylindrocladium parasiticum) isolated from diseased peanut showing symptoms of Cylindrocladium black rot (CBR) and two C. ilicicola strains isolated from diseased soybean showing symptoms of Red crown rot (RCR). The complete mitogenome of C. ilicicola ranged from 41,187 bp to 64,421 bp in length, 22-34 protein-coding genes, 19-20 tRNA genes, 2 rRNA genes, and a control region. Besides, we used a phylogenomic approach to infer evolutionary relationships among 591 mitochondrial genomes that span the diversity of 294 fungal species, including C. ilicicola. Our results underline the potential importance of mitochondrial genomes in comparative genomic analyses and provide a robust evolutionary insight across the tree of life.

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Phylogenetic diversity of Calonectria ilicicola causing Cylindrocladium black rot of peanut and red crown rot of soybean in southern China

Cited by 17 publications

References 36 publications

Reconsideration of species boundaries and proposed DNA barcodes for Calonectria

Reconsideration of species boundaries and proposed DNA barcodes for Calonectria

Species Diversity and Distribution Characteristics of Calonectria in Five Soil Layers in a Eucalyptus Plantation

A phylogenomic tree of fungi: evolutionary relationships among Calonectria ilicicola and 586 fungal mitochondrial genomes

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