Phylogenetic Analysis and Genetic Diversity of Colletotrichum falcatum Isolates Causing Sugarcane Red Rot Disease in Bangladesh

Abstract

Colletotrichum falcatum Went causes red rot disease in sugarcane farming in the tropical and sub-tropical regions. This disease causes significant economic loss to the sugarcane production industry. Successful disease management strategies depend on understanding the evolutionary relationship between pathogens, genetic diversity, and population structure, particularly at the intra-specific level. Forty-one isolates of C. falcatum were collected from different sugarcane farms across Bangladesh for molecular identification, phylogeny and genetic diversity study. The four genes namely, ITS-rDNA, β-tubulin, Actin and GAPDH sequences were conducted. All the 41 C. falcatum isolates showed a 99–100% similarity index to the conserved gene sequences in the GenBank database. The phylogram of the four genes revealed that C. falcatum isolates of Bangladesh clustered in the same clade and no distinct geographical structuring were evident within the clade. The four gene sequences revealed that C. falcatum isolates from Bangladesh differed from other countries´ isolates because of nucleotides substitution at different loci. The genetic structure of C. falcatum isolates were determined using ISSR marker generated 404 polymorphic loci from 10 selected markers. The percentage of polymorphic loci was 99.01. The genetic variability at species level was slightly higher than at population level. Total mean gene diversity at the species level was 0.1732 whereas at population level it was 0.1521. The cluster analysis divided 41 isolates into four main genetic groups and the principal component analysis was consistent with cluster analysis. To the best of our knowledge, this is the first finding on characterizing C. falcatum isolates infesting sugarcane in Bangladesh. The results of this present study provide important baseline information vis a vis C. falcatum phylogeny analysis and genetic diversity study.

Dry Rot Caused by the Complex Colletotrichum falcatum and Thielaviopsis paradoxa Emerges as a Key Stalk Disorder in Newly Expanded Sugarcane Plantations from Northwestern São Paulo, Brazil

“…Appressoria and perithecia were not observed. The morphological characteristics observed for C. falcatum strains aligned with those formerly described by Costa et al [22] and Hossain et al [50]. Similarly, the specific characteristics of T. paradoxa strains resembled those in the description of the pathogen in the CABI Compendium [28].…”

Highly Diverse Phytophthora infestans Populations Infecting Potato Crops in Pskov Region, North-West Russia

“…The coefficient of genetic differentiation (GST) at population level was estimated as GST = ( H T − H S )/H T , where H T corresponds to the total gene diversity, and H S corresponds to the gene diversity within sub-populations [ 51 , 52 ]. Gene flow is defined as the average per generation of migrants transferred across populations and it is estimated indirectly based on the formula: Nm = 0.5 (1 − GST)/GST [ 53 ].…”

Identification and Characterization of Colletotrichum Species Causing Tea-Oil Camellia (Camellia oleifera C.Abel) Anthracnose in Hainan, China

“…A previous report showed that C. fructicola is a non-host-specific pathogen infecting fruit, vegetables, and economic crops, including apple (Malus pumila) [37], sugarcane (Saccharum officinarum) [38], blueberry (Vaccinium corymbosum) [53], and Camellia yuhsienensis [54]. C. fructicola was described as a common species existing on the leaves of tea-oil camellia [35].…”

“…Interestingly, C. siamense showed broad variation in cultural appearance [21]. Although 11 isolates of Colletotrichum Group 2 and six isolates of Colletotrichum Group 4, isolated from different locations, were slightly different on the morphology of colony and conidia, they were all identified to be the species of C. siamense by phylogenetic analyses, which showed the unreliability and inconsistency of Colletotrichum identification methods relying only on colonial and morphological characteristics because fungal colony and morphological characteristics are affected by environmental factors [38]. In the present study, a new Colletotrichum species, C. cordylinicola, was reported causing anthracnose on tea-oil camellia in China.…”

“…2.4. Fungal DNA Extraction, PCR Amplification, and DNA Sequencing After 6 days of incubation at 25 • C, the total genomic DNA of each Colletotrichum isolates was extracted for PCR amplification using an SDS extraction method described by Hossain [38]. The concentration of the extracted DNA was determined by using a spectrophotometer and adjusted to 15 ng/L with ultrapure water.…”