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. 2021 Feb 27;11(3):148. doi: 10.1007/s13205-021-02695-x

A highly contiguous reference genome assembly for Colletotrichum falcatum pathotype Cf08 causing red rot disease in sugarcane

Amaresh Chandra 1,✉, Dinesh Singh 1, Deeksha Joshi 1, Ashwini D Pathak 1, Ram K Singh 1,2, Sanjeev Kumar 1,✉
PMCID: PMC7914311  PMID: 33732569

Abstract

Among the biotic factors, which affect the productivity and quality of sugarcane, red rot disease caused by the fungal pathogen, Colletotrichum falcatum is the most devastating that cause enormous loss to millers as well as cane growers. We present a highly contiguous genome assembly of C. falcatum pathotype Cf08 which is virulent to popular sugarcane varieties grown in more than 3 million hectares in sub-tropical India. By performing long read sequencing on PacBio RSII system, 56.06 Mb assemblies with 238 contigs having N50 of 0.51 Mb and L50 of 34 was produced. A BUSCO completeness score of 97.24% (including 4.1% fragmented) of the entire C. falcatum Cf08 nuclear genome, greatly improved contiguity compared to an existing highly fragmented draft of C. falcatum Cf671 genome (48.13 Mb) was obtained. This Cf08 assembly had 54.14% GC content and possessed < 1% repetitive elements. A total of 18,635 protein-coding genes were predicted compared with 12,270 for Cf671. Among 617 CAZymes predicted, glycoside hydrolases were the predominant (298), and among 7264 genes associated with pathogenicity/virulence, 77 genes having effector functions were identified. The assembled genome showed its similarity with the genome of C. graminicola and C. higginsianum, the causal organisms of anthracnose in maize and in members of Brassicaceae, respectively. A total of 94 large sequences (> 100 kb) of Cf08 were mapped over C. higginsianum 10 of 12 chromosomes with 106 synteny blocks. Results discussed here would provide an important tool for future studies of evolutionary and functional genomics in C. falcatum.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-021-02695-x.

Keywords: Colletotrichum falcatum Cf08, Plant pathogen, PacBio RSII, Red rot, Sugarcane

Colletotrichum falcatum Went (Perfect state: Glomerella tucumanensis (Speg.) Arx and Muller) is a hemi-biotrophic concealed ascomycete that causes one of the most devastating diseases of sugarcane, i.e., red rot (Singh and Lal 1996). The huge damage potential of red rot disease was documented between 1895 and 1900 when this disease in the Godavari delta of India pushed sugarcane cultivation to verge of extinction. Breeding superior sugarcane varieties with durable resistance to red rot has been hampered by frequent emergence of new pathotypes of C. falcatum. In India, 12 pathotypes of C. falcatum have been reported till now (Viswanathan et al. 2020) and, since every new pathotype show more virulence, in a very short period, it result in resistance breakdown (Viswanathan 2017). In many of the plant pathogenic fungal species, colonization and host interaction is facilitated by pathogen-encoded small, secreted effector proteins. Through such effectors, the pathogen is able to manipulate host metabolism and evade host immune responses. Studies to identify effector proteins in commercially important phytopathogenic Colletotrichum species have lagged behind experiments on pathogen biochemistry, including the analysis of metabolites produced by these fungi, and only a few effector proteins have been characterized so far (Gan et al. 2013). In the case of red rot disease in sugarcane, only limited information is available about fungal pathogenesis and its molecular components that are involved in disease initiation and spread, and without complete genome information, the identification of pathogenic determinants/virulence factors and the underlying molecular mechanism(s) are not possible. Barring few reports on pathogen variability at molecular level (Suman et al. 2006; Malathi et al. 2010), not much effort has been made to understand the molecular basis of pathogenicity in C. falcatum. Analysis of conserved inverted terminal repeat (ITR) regions and other molecular techniques including loop-mediated isothermal amplification (LAMP) have been developed to detect the presence of fungi in cane stalk (Nithya et al. 2012; Chandra et al. 2015). Next-generation sequencing (NGS) tools have been employed to study the pathogenicity in Colletotrichum species (Gan et al. 2013, 2016; O’Connell et al. 2012). O’Connell et al. (2012) compared the genomes of C. higginsianum and C. graminicola and reported that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters, and peptidases are expanded in C. higginsianum. Moreover, genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions. Gan et al. (2016) did genus-wide comparative genome analyses using NGS tools and reported that Colletotrichum species have tailored profiles of their carbohydrate-degrading enzymes according to their infection lifestyles.

In 2016, an Illumina short-read draft genome sequence of C. falcatum pathotype Cf671 that causes red rot predominantly in sugarcane varieties in tropical zone of India was published (Viswanathan et al. 2016a), but, the details of contigs, genome assembly, and coverage were not provided. This genome draft sequence reported 48.16 Mb genome with 12,270 predicted genes of which 9891 were annotated (Viswanathan et al. 2016a). The transcriptome analysis of host–pathogen interaction between sugarcane and C. falcatum revealed 10,038 differentially expressing transcripts from resistance response library (RRL) and 4022 from susceptible response (SRL) library (Viswanathan et al. 2016b). Strong induction of WRKY transcription factors has been also reported during such interaction (Rahul et al. 2016). The presence of transcripts homologous to CEBiP and STPK in both RRL and SRL, and MAPKKK1 and MAPKK1 kinases from MAPK cascade only in RRL (Viswanathan et al. 2016b), clearly demonstrates that host–pathogen interaction and red rot disease development takes place through complex regulatory pathways. The genome sequence of C. falcatum Cf671 revealed a high level of similarity of the annotated genes with C. graminicola (8902 genes, 90%) and C. sublineola (8308 genes, 84%). Thus far, the draft genome sequence reported for C. falcatum succinctly inconclusive and warrant enrichment by sequencing predominant pathotypes associated with sub-tropical sugarcane varieties as > 60% sugarcane and > 50% sugar come from sub-tropical region of the country. In present study, a genome assembly for C. falcatum pathotype Cf08 is presented that was produced by PacBio Single Molecule Real-Time (SMRT) sequencing. This assembly comprises 238 contigs, of which 94 (> 100 kb) were mapped on to 10 out of 12 chromosomes of C. higginsianum with 106 synteny blocks. This genome assembly represents 97.24% nuclear genome coverage with 282 BUSCO genes. The total assembled genome length was 56.06 Mb with 18,635 predicted genes encompassing 617 carbohydrate-associated enzymes and 77 genes having effector functions.

The C. falcatum pathotype Cf08 (Acc no. NAIMCC-F-03384) isolated from infected stalk of sugarcane variety CoJ 64 following tissue segment method (Rangaswami 1958) was used for whole genome sequencing (Supplementary file 1). The C. falcatum pathotype Cf08 was deposited to National Agriculturally Important Culture Collection Repository at ICAR—National Bureau of Agriculturally Important Microorganisms, Mau, India as accession number NAIMCC-F-03384 (http://nbaim.org.in/pages/services-culture-collectionnaimccculture-collectionnaimcc). The vegetative mycelium of the fungus was obtained by culturing single spore on oat meal agar for 5–6 days (Choi et al. 1999). Genomic DNA was isolated from fungal mycelium by phenol–chloroform method as described by Lee et al. (1988) with little modifications. Briefly, fungal mycelia (~ 100 mg) were snap frozen in liquid nitrogen, crushed with the help of pestle-mortar to fine powder. It was incubated with 10 ml lysis buffer (200 mM Tris–HCl pH 8.5, 250 mM NaCl, 25 mM EDTA, 0.5% SDS) at 65 °C for 10 min in water bath. The RNA was removed by adding 20 mgmL−1 DNase-free RNase-A and was incubated at 37 °C for 30 min. Finally, it was purified using AMPure PB beads (Beckman Coulter, CA, USA) according to manufacturer’s protocol. The quality of genomic DNA was determined using a nanodrop spectrophotometer (DS-11, Denovix, USA), Qubit fluorometer (Thermo Fisher), and by electrophoresis in 0.7% agarose gel.

Approximately 10 µg of purified high-quality genomic DNA (gDNA) was taken for generating long read sequencing libraries. Genomic DNA was sheared with g-TUBES (Covaris, Woburn, MA, USA) as per manufacturer’s protocol for generating ~ 20 kb fragments. To prepare SMRT bell-template libraries, fragmented gDNA was subjected to damage repair, end repair, and blunt end ligation with hairpin adaptors at both ends using the PacBio DNA template preparation kit 2.0 (Pacific Biosciences, CA, USA) following manufacturer’s instructions. Sequencing libraries were purified by 0.45 × AMPure beads (Beckman Coulter, CA, USA) to remove short inserts (< 1.5 kb size). SMRT bell-template libraries of > 10 kb size were selected (BP start = 10 kb, BP end = 50 kb) using the S1 marker on Blue-Pippin size selection system (Sage Science, MA, USA). The size selected SMRT bell-template libraries were further purified with 1 × AMPure beads and quantified using Qubit fluorometer (Thermo Fisher). Sequencing of size selected SMRT bell-template libraries was performed on PacBio RS II system using P6-C4 chemistry (Pacific Biosciences, CA, USA). DNA polymerase binding kit P6 v2 was used to bind DNA polymerase and primers to template and reagent kit 4.0 was used for sequencing. To optimize the loading concentration of SMRT complex template on SMRT cell, three titrations sequencing run at 0.01, 0.04, and 0.08 nM library concentration were performed. Thereafter, sequencing reactions was run at optimized loading concentrations of template using 8 SMRT cells with 360 min collection protocol. The raw data obtained were processed through Falcon v0.3 (Pacific Bioscience) to generate reference assembly of C. falcatum Cf08. Falcon-derived draft assembly was polished three rounds using Quiver algorithm (Pacific Bioscience) with parameters of minimum sub-read length of 1000 bp, minimum polymerase read length of 1000 bp, and polymerase read quality of 85 to improve consensus accuracy of C. falcatum reference assembly (Chin et al. 2013). The genome completeness of C. falcatum assembly was assessed by Benchmarking Universal Single Copy Orthologs ver. 3.0.1. (BUSCO v3; Simao et al. 2015) with fungal dataset on all the contigs and assembly statistics was generated by Quality Assessment Tool for Genome Assemblies (QUAST; Gurevich et al. 2013).

The protein-coding genes in assembled genome of C. falcatum were identified taking gene models from Aspergillus nidulans as a reference and complete gene models as parameter using the gene predictions program, AUGUSTUS ver. 3.2.3 (Stanke and Morgenstern 2005). To characterize the predicted genes of C. falcatum, functional annotation was performed by running Blast2GO (Gotz et al. 2008). For this, BLASTx search was done against NCBI non-redundant database with E value cut-off of ≤ le−5 and identity ≥ 40%. Further, the predicted genes were classified into functional pathways using BLASTp search against a KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways using KAAS annotation server (Moriya et al. 2007). The non-coding RNA, rRNA were predicted using RNAmmer ver. 1.2 (Lagesen et al. 2007), while tRNA was predicted using tRNAscan-SE-1.23 (Lowe and Eddy 1997), respectively.

Carbohydrate-active enzymes (CAZymes) protein families were screened through local BLASTp search in CAZy database (Lombard et al. 2014). The candidate virulence-associated genes were identified by performing BLASTp search of the C. falcatum draft against pathogen-host interaction database ver. 4.8 (PHI, Urban et al. 2020). Protein families were further screened to identify genes involved in metabolism, genetic information processing, signalling and cellular processes, and novel genes were identified by BLASTp search against KEGG database. Homologs of structural RNA sequences present in C. falcatum genome assembly were classified using software package Infernal ver. 1.1 (INFERence of RNA Alignment; Nawrocki and Eddy 2013).

Predicted genes and proteins of C. falcatum were compared with that of genome sequences of C. gloeosporioides, C. higginsianum, C. orbiculare, Glomerella graminicola (C. graminicola), and Verticillium dahliae using OrthoVenn web server (Wang et al. 2015) which is a web-based platform for comparison and annotation of orthologous gene clusters among multiple species. An unrelated pathogen V. dahliae which is a causal agent of wilt and leaf mottle in sunflower was added to identify orthologus clusters, if any with such species. Within OrthoVenn, UBLAST and orthAgogue were utilized to classify putative orthology and in paralogy relations. A synteny analysis taking > 100 kb sequences of C. falcatum (Cf08) was performed using SyMAPv4.0 program (http://www.symapdb.org/) with C. higginsianum IMI 349,063 as this was the only assembly among Colletotrichum species which is fully assembled at chromosome level.

The present study reports a highly contiguous reference genome of C. falcatum pathotype Cf08 assembled using long read data generated on PacBio RSII sequencing system. The earlier short read sequence-based assembly of C. falcatum Cf671 reported 48.13 Mb assembled scaffold size (Viswanathan et al. 2016a). The SMRT cells sequencing libraries produced ~ 7.24 Gb polymerase raw read data with 124.8 × coverage which was initially analysed using RS Subread1 protocol on SMRT portal. A total of 5.21 Gb filtered polymerase read data comprised 2,42,298 raw reads were assembled through Falcon that produced 62.39784 Mb primary (253 contigs) and 22 kb alternate (4 contigs) assembly, found well within the predicated genome size but more than those reported by Viswanathan et al. (2016a). FALCON usually generates alternate assembly in the form of alternate haplotypes, along with the main genomic (primary) assembly, and, therefore, further analysis of the assembled genome was carried out with primary assembly. After polishing and removing the alternate contigs, an assembly of 238 contigs was generated. The final primary assembly showed a N50 of 506.4 kb with longest contig length of 2.23 Mb, L50 of 34 contigs and GC content of 54.14% (Table 1). A wide variation in GC content (37.3–54.4%) has been reported in different species of Colletotrichum. The short-read sequence assembly of C. falcatum Cf671 as reported by Viswanathan et al. (2016a) had a GC content of 51.6%.

Table 1.

Assembly and annotation statistics of C. falcatum Cf08 estimated using QUAST and C. falcatum Cf671 genome

Assembly statistics C. falcatumCf08a C. falcatum cf671b
Sequencing platform PacBio SMRT Illumina
Genome size (bp) 56,062,448 48,130,062
Total sequence bases

 ~ 7.24 Gb polymerase read data/

 ~ 5.21 Gb filtered read data

(242,298 reads)

 9 Gb
Coverage 124 ×  150 × 
Number of contigs 238 6400
Size of the largest contig (bp) 22,32,291 Not available
N50 (bp) 5,06,431 16,629
N75 (bp) 3,17,938 Not available
L50 34 763
L75 72 Not available
GC content (%) 54.14 51.6
#N’s per 100 kbp 0 2042 (Spanned gaps)
Annotation statistics
 Number of protein-coding genes 18,635 12,270
 Predicated effectors 77 Not available
 Predicted number of CAZymes 617 Not available
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aPresent study, bViswanathan et al. (2016a)

The genome completeness analysis of the final reference assembly of C. falcatum against fungal BUSCO database revealed 97.24% genome completeness (93.1% complete + 4.1% fragmented BUSCOs), with only 2.8% missing BUSCOs. A total 290 BUSCO groups were searched against fungi_odb9 database which categorized 269 as complete and single-copy BUSCOs, a single complete and duplicated BUSCO, 12 fragmented BUSCOs, while 8 were classified as missing. This C. falcatum Cf08 genome assembly (56.062448 Mb) featuring highly contiguous contigs, does not contain any missing bases, has a high N50, and is larger than that of earlier assembly of C. falcatum Cf671 (48.13 Mb including 2042 Spanned gaps) in scaffolds status (Table 1).

A total of 8113 repetitive elements (Repeat Modeller) were identified in C. falcatum Cf08 genome, consisting of DNA/TcMar-Fot1 (341), LTR (500), LTR/Copia (642), LTR/Gypsy (1265), Simple repeats (220) and Unknown (5145). A total of 196 contigs contained 13,168 simple sequence repeats of which 6540 were di-, 5490 tri-, 815 tetra-, 165 penta- and 158 were hexa-nucleotide repeats. Kumar et al. (2017) also reported a predominance of di-nucleotide repeats in many fungal genomes. In addition, TR finder identified 6279 tandem repeats, while tRNA scan identified 417 tRNA. In general, fungal genome of ascomycetes has been reported to contain lesser number of repetitive elements, and their proportions, rarely exceed 5% of the genome (Wostemeyer and Kreibich 2002), possibly due to the presence of repeat-induced point mutation (defense mechanism) which save fungal genomes against highly repeated sequences (Hood et al. 2005). The C. falcatum Cf08 genome contained > 1% repetitive elements, which is in agreement to general assertion about ascomycetes, although, some fungal species, e.g., Phycomyces blakesleeanus, Absidia glauca do possess > 35% repetitive DNA content (Wostemeyer and Kreibich 2002).

Ab initio approach with Augustus predicted 18,635 protein-coding genes, which is significantly higher than those predicted in other Colletotrichum species (NCBI database) including the earlier reported C. falcatum Cf671 genome (12,270 predicted genes; Viswanathan et al. 2016a). Of the 18,635 predicted protein-coding genes, 10,013 (53.73%) exhibited homologies with known function in NCBI non-redundant (NR), while 8289 (44.48%) and 8602 (46.10%) of the predicted genes exhibited homologies with known function in Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Gene ontology (GO) terms for three categories as biological process, cellular component, and molecular function were annotated for predicted genes. A major proportion (80.39%; 6664) of the protein-coding genes were assigned GO term for molecular functions followed by cellular components (62.44%; 5176) and biological processes (60.02%; 4975). Under the molecular function category, catalytic (28%) and binding (22%) activities were most dominant, whereas, cell (19.4%) and cell parts (19.4%) were dominant under cellular component category. Metabolic processes (38.30%), cellular processes (35.93%), and single organism processes (22.47%) were predominant in biological process category. Pathogen–Host Interactions database (PHI-base) which comprises experimentally validated pathogenesis genes from 76 organisms revealed a total of 7264 (38.9%) pathogenesis-associated genes in Cf08 genome, which could be crucial for the virulence (Table 2). The majority of these genes belong to the category having no effect on pathogenicity on mutagenesis (1997 with unaffected pathogenicity), while others belong to different functional categories, indirectly relevant for pathogenicity including secreted proteases, CAZymes, P450s, and transporters. Of the 7264 genes, 3573 were associated with reduced virulence, 393 with loss of pathogenicity, 646 with mixed phenotype, 316 with hyper-virulence, 252 with lethality, 77 with having effector functions, 9 with resistance to chemical, and 1 gene with enhanced antagonism function.

Table 2.

Summary of predicted genes exhibiting homologies with known functions, pathogenicity genes, CAZyme genes and enzyme classes identified from the C. falcatum Cf08 genome assembly

Category Number
Total protein-coding genes 18,635
Predicted genes exhibiting homologies with known functions in:
 NCBI non-redundant data base 10,013 (53.73%)
 GO data base 8289 (44.48%)
 KEGG data base 8602 (46.10%)
Predicted genes associated with fungal pathogenicity and virulence (PHI-database) 7264
Antimicrobial resistance (AMR) genes 39
CAZymes 617
 Glycoside hydrolase (GH) 298
 Carbohydrate esterase (CE) 45
 Polysaccharide lyase (PL) 17
 Auxiliary activities (AA) 95
 Carbohydrate-binding module (CBM) 9
 Glycosyl transferase (GT) 153
Enzyme classes (sequence)
 Oxidoreductases 551
 Transferases 698
 Hydrolases 949
 Lyases 211
 Isomerases 87
 Ligases 164
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Carbohydrate-Active Enzymes (CAZymes) prediction by applying three algorithms, viz., Diamond, HMMER, and Hotpep in dbCAN Meta server resulted in the identification of 891 genes in different CAZymes class. Filtering of genes by applying a single algorithm, predicted 617 genes encoding 149 different CAZyme families. A total of 224 of C. falcatum genes from 78 CAZyme families were predicted to be associated with cell secretion. The important classes of CAZymes in Cf08 identified were glycoside hydrolases (GH; 298 genes), carbohydrate esterases (CE; 45 genes), polysaccharide lyases (PL; 17 genes), auxiliary activities (AA; 95 genes), carbohydrate-binding modules (CBMs; 9 genes), and glucoside transferase (GT; 153 genes) were the important classes of CAZymes identified in C. falcatum Cf08 (Table 2). The sufficient numbers of CAZymes identified in Cf08 genome being the key feature of fungus suggest their peculiar role in the degradation of fungal and plant cell wall components (chitin, cellulose, hemicellulose, pectin, etc.) and utilization of plant polysaccharides during the host colonization by C. falcatum. In general dicot pathogens possessed more polysaccharide lyases to degrade pectate and pectin found more abundant in cell wall of dicots than monocots (Zhao et al. 2013); Cf08 being pathogen of monocot (sugarcane), exhibited lesser number of PL (17) than those reported in A. rabiei ArME14 (31), pathogen of dicot chickpea (Shah et al. 2020). A total of 119 genes in Cf08 exhibited homologues with cytochrome P450 monooxygenase (P450s) and antimicrobial resistance (AMR) genes in KEGG database. The major P450 family identified were CYP3 (30 genes; cytochrome P450 family 3) and CYP4 (15 genes; cytochrome P450 family 4). Among the six classes of enzymes (2660) represented by Cf08 genome sequence, the majority (949) belong to hydrolases which help pathogen to survive in host cells by hydrolysis (Table 2). A total of 39 genes were identified with AMR function, of which 8 belong to multidrug efflux system. Among others, heavy metal sensor histidine kinase CusS (3 genes), outer membrane protein tolC (2), virginiamycin A acetyltransferase (2), and MFS transporter, DHA1 family, tetracycline resistance protein (2 genes) were also identified inCf08 genome. The presence of P450s which are diverse heme thiolate proteins that play important role in primary and secondary metabolism and fungal pathogenicity (Kelly and Kelly 2013; Qhanya et al. 2015), suggest their enriched gene pool in Cf08 genome augmenting its virulence.

Orthology analysis conducted with C. gloeosporioides, C. higginsianum, C. orbiculare, Glomerella graminicola, C. falcatum (present study), and V. dahliae showed formation of 14,479 clusters, 13,111 orthologous clusters (at least contains two species), and 5631 single-copy gene clusters. A total of 257 genes from C. falcatum were classified as co-orthologous, whereas, 1570 genes were classified as in-paralogous. A total of 6304 elements were shared by all six species used for genome-wide comparison (Supplementary file2). The synteny analysis of Cf08 genome (> 100 kb fragments) against scaffold level assembly of C. higginsianum (Dallery et al. 2017), resulted in mapping of 94 sequences from C. falcatum (Cf08) over C. higginsianum (10 of 12 chromosomes) with 106 synteny blocks (Fig. 1). Thus, in these two closely related species having approximately similar genome size, a high synteny/co-linearity was observed.

Fig. 1.

Fig. 1

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Mapping of 94 sequences from C. falcatum (Cf08) over C. higginsianum (10 of 12 chromosomes) with 106 synteny blocks, depicting co-linearity between C. falcatum and C. higginsianum

Red rot being an important disease of sugarcane damages the cane stalk where sugar is stored and, therefore, developing an understanding of the mechanism of virulence of C. falcatum pathotype Cf08 is critical to the effective control of disease leading to improved cane yield and sugar recovery. The publication of near-complete and contiguous genome assembly for C. falcatum provides the basis for further research on sugarcane red rot disease. Genome sequencing of major pathotypes identified both from tropical and sub-tropical regions where sugarcane is widely grown will further comprehend evolutionary and population genetic study and varietal specificity of the pathotype. The genomic information generated in this study would be a valuable resource to correlate data from functional studies and genetics of C. falcatum. This could be especially significant as a deeper understanding of C. falcatum genome and host–pathogen biology will help in developing strategies for targeted red rot disease control.

Supplementary Information

Below is the link to the electronic supplementary material.

13205_2021_2695_MOESM1_ESM.docx (13.4KB, docx)

Supplementary file1 Supplementary file1 Information pertaining to Cf08 pathotype of C. falcatum isolated from CoJ 64 sugarcane variety (DOCX 13 KB)

13205_2021_2695_MOESM2_ESM.jpg (42.5KB, jpg)

Supplementary file2 Supplementary file2 Venn diagram depicting the distribution of shared gene families (orthologous clusters) among C. gloeosporioides, C. higginsianum, C. orbiculare, Glomerella graminicola, C. falcatum (present study) and V. dahliae (JPG 43 KB)

Acknowledgements

This work is supported by the institute (ICAR-IISR Lucknow, India) core grant budget. The facilities utilized developed under SERB projects (SR/SO/PS/36/2012 and CRG/2018/000659) is duly acknowledged. Authors are thankful to the Director, ICAR—National Bureau of Fish Genetic Resources, Lucknow for allowing to use PacBio RSII System for sequencing. Accession number(s): the PacBio generated genome sequence data for C. falcatum pathotype Cf08 described herein, and the reference genome assembly have been deposited in the Sequence Read Archive and NCBI database, under the BioProject accession number PRJNA509540. C. falcatum Cf08 BioSample number is SAMN10584380. SRA entries are deposited as accessions SRR8375625-SRR8375634. The version described in this manuscript is SWKJ00000000.

Author contributions

AC, ADP, and RKS were involved in planning and execution of the work. AC has contributed in data collection and submission of sequence to database. DS and DJ were involved in growth and maintenance of C. falcatum pathotypes, while, SK was involved in isolation and purification of fungal DNA. AC and SK prepared and edited the draft manuscript. All authors read and approved the final manuscript.

Declarations

Conflict of interest

The authors declare that they have no competing interest in the publication.

Contributor Information

Amaresh Chandra, Email: amaresh_chandra@rediffmail.com.

Dinesh Singh, Email: Dinesh.Singh3@icar.gov.in.

Deeksha Joshi, Email: Deeksha.Joshi@icar.gov.in.

Ashwini D. Pathak, Email: Ashwini.Pathak@icar.gov.in

Ram K. Singh, Email: Ram.Singh8@icar.gov.in

Sanjeev Kumar, Email: sanjeeviivr@gmail.com.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

13205_2021_2695_MOESM1_ESM.docx (13.4KB, docx)

Supplementary file1 Supplementary file1 Information pertaining to Cf08 pathotype of C. falcatum isolated from CoJ 64 sugarcane variety (DOCX 13 KB)

13205_2021_2695_MOESM2_ESM.jpg (42.5KB, jpg)

Supplementary file2 Supplementary file2 Venn diagram depicting the distribution of shared gene families (orthologous clusters) among C. gloeosporioides, C. higginsianum, C. orbiculare, Glomerella graminicola, C. falcatum (present study) and V. dahliae (JPG 43 KB)

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