bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.08.22.607543

Hybrid Genome Sequence of Cryptococcus neoformans of Indian origin and comparative genome analysis

Sathiyamoorthy, J.·Ramakrishnan, J.
View original source ↗Export metadata ↓

Abstract

ObjectivesThe Indian isolate of Cryptococcus neoformans underwent complete genome sequencing to elucidate its genomic architecture and functional characteristics. Furthermore, this study aimed to comprehensively characterize the virulence factors (virulome), antibiotic resistance genes (resistome), and the pan-genome of C. neoformans spp. through a comparative genomic analysis, providing insights into the genetic diversity and evolutionary relationships among strains. MethodsThe genomic data of a clinical strain of C. neoformans was assembled and annotated by MaSuRCA5 and Braker tool. Along with this, the assembled genomic data of the 11 strains were retrieved from NCBI datasets. The comparative virulome, resistome, phylogeny and of the 12 C. neoformans genomes were analyzed using DFVF, AFRbase, BLAST, CLUSTAL Omega, MEGAX, and Orthovenn3, respectively. ResultsThe sequenced isolate was identified as a member of the Cryptococcus neoformans var. grubii subspecies. Notably, virulence-related genes comprise approximately 4.8% of the total genome. A comparative genomic analysis of 12 study genomes revealed variations in virulence patterns, including differences in melanization, immune evasion, blood-brain barrier evasion, transcriptional regulation, and oxidative stress response. The phylogenetic study using MLST and orthologous clusters categorized the subspecies grubii and neoformans in different clades. Pan-genome analysis showed that 73.6% of orthologous gene clusters and 77.72% of orthologous proteins were conserved across all 12 study genomes, indicating a shared core genome. Furthermore, the evolutionary relatedness study of the pan-genome revealed gene expansion and contraction events among the study strains. ConclusionThis pioneering study presents the first comprehensive genomic and comparative genomic analysis of Cryptococcus sp., incorporating data on virulence genes, antibiotic resistance, and pan-genome dynamics. Key findings reveal that strains Cn, H99, and JEC21 harbor crucial virulence genes associated with infection severity. While all study strains possess genes promoting antifungal resistance (AFR), most lack specific single nucleotide polymorphisms defining AFR. Consistent with pan-genome analysis, our results show significant gene expansion and contraction events in these strains. This study underscores the importance of bioinformatic tools for efficient whole-genome analysis and large-scale comparative genomics research.

Explore related subjects

genomicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sathiyamoorthy, J., Ramakrishnan, J.. 2024-08-22. Hybrid Genome Sequence of Cryptococcus neoformans of Indian origin and comparative genome analysis. https://doi.org/10.1101/2024.08.22.607543

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Structural variation in repeat elements is widespread in normal human tissues and in tumorigenesis

Somatic mosaicism contributes to genomic variation, yet postzygotic structural variants remain under-characterized. We performed long- and short-read WGS from multiple individuals (n=47 normal tissues; n=168 samples) and identified mosaic structural variants in all individuals and germ layers, impacting a median 285.2 kb/genome. Nearly half of breakpoints were independently validated, with tissue distributions reflecting both early and late developmental origins. Most mosaic variants were repeat-mediated and 8.3% overlapped functional elements, an enrichment compared to germline variants. To extend these analyses in samples where long-read sequencing is infeasible, we measured repeat alterations from short-read sequencing, recapitulating mosaic tissue-specific differences. We characterized tumor- and tissue- specific variation in repeats across 15 cancer types and found tumor-related repeat variation to be similar in scale to that of normal mosaic variation. Tracking repeat changes in cell-free DNA provided a noninvasive approach for tumor monitoring. Our analyses revealed widespread repeat-driven structural variation in health and disease.

genomics↗
bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗
bioRxiv2026

Structural polymorphism and population-variable coding capacity of HERV-K(HML-2) in human pangenomes

Approximately 8% of the human genome is derived from ancient retroviral infections. The most recently integrated of these endogenous retroviruses is the HERV-K(HML-2) clade, whose expression has been associated with cancer, amyotrophic lateral sclerosis, and embryogenesis. Studies of HERV expression, particularly HML-2, have relied predominantly on short-read sequencing. However, the high similarity among HML-2 proviruses prevents many short reads from being assigned uniquely to individual loci. We therefore compared haplotype-resolved long-read genome assemblies from 292 donors to resolve variation in proviral structure and coding capacity. Several loci previously thought to be fixed were structurally polymorphic. Tandem arrays occurred at 13 loci and contained up to six proviral copies in a single array. At 8q11.23, we identified a previously undescribed full-length provirus in one haplotype. All 583 other haplotypes carried a solo-LTR. We found that standard reference genomes failed to represent the coding capacity retained in many individuals, whose proviruses contained intact open reading frames despite disruptive mutations in the reference sequences. Short-read genotypes left 32.5% of the tested donor-variant pairs unresolved at sites associated with viral reading frames. These findings show why HML-2 expression must be interpreted in the context of the structural and coding alleles each individual carries.

genomics↗