Fungal genomes

Third-generation Sequencing
 

Service Overview

In fungal genome studies, genome survey, fine genome and pene-complete genome of fungal can be provided depending on specific research goal. Genome sequencing, assembly and functional annotation can be achieved by combining NGS and TGS or NGS, TGS and Hi-C technologies.




Project Workflow

Sample delivery
Library construction and sequencing
Data analysis
Final report
After-sale technical support
Service specifications

Service Sequencing platform conc. Total
Genome survey xten/nova PE150 ≥30 ng/μl ≥2 μg
Fine genome xten/nova PE150
+Pacbio/Nanopore
≥20 ng/μl ≥15 μg
Pene-complete genome xten/nova PE150
+Pacbio/Nanopore+Hi-C
35-200 ng/μl ≥10 μg
Sample requirements

Service Sequencing platform conc. Total
Genome survey xten/nova PE150 ≥30 ng/μl ≥2 μg
Fine genome xten/nova PE150
+Pacbio/Nanopore
≥20 ng/μl ≥15 μg
Pene-complete genome xten/nova PE150
+Pacbio/Nanopore+Hi-C
35-200 ng/μl ≥10 μg

Bioinformatic Analysis


Analysis Contents
Standard Analysis Genome assembly Raw data quality control, data evaluation, assembled genome evaluation
Gene analysis CDS prediction, repetitive sequence annotation, lncRNA prediction, pseugogene analysis
Functional annotation

Gene annotation via database: GO, KEGG, COG, Swissprot, Nr, TrEMBL, pfam;signal peptide prediction, 

transmembrane proteins, transport proteins, secretory proteins analysis; 

annotation against CAZyme, PHI

Epigenetic analysis 6mA, 4mC identification, specific motif analysis
Advanced Analysis Comparative genomics

Gene family classfication, common and unique gene identification, rapid evolving gene identification,

 rapid evolving gene functional analysis, phylogenetic analysis, collinearity analysis.


Results Demo







KOG analysis

Predicted genes from assembled fungal genome is annotated against KOG database in order to classify gene products into orthologous groups.








Common and unique gene analysis

In comparative genomics analysis, unique gene family of the fungi is identified by protein sequence based classification on OrthoMCL.






Signal peptide prediction
Signal peptide is a short peptide on newly synthesized proteins, which guides protein towards secretory pathways. The existence of signal peptide is predicted based on the protein sequences.








Collinearity analysis

Orthologous genes and protein sequences of a closely related species are identified by blastn mapping between the two genomes. Collinearity at nucleus-level is obtained based on the loci of each orthologous gene on both genomes.

FAQ

1How to assemble fungi genome data from NGS and TGS?
Answer: There are three assembly strategies. The best assembled genome will be chosen from the three as final outcome of genome assembly. (1) Mixing sequenced fragments from NGS and TGS for assembly. (2) Assembling reads from NGS and TGS to contigs separately and mixing the contigs for further genome assembly. (3) Assembling reads from NGS to contigs and assembling tht contigs into scaffold based on TGS data.
2What is complete genome of fungus?
Answer: Pene-complete genome of fungus is achieved by assembly of NGS, TGS and Hi-C data, where sequences can be assembled into chromosome-level. It doesn't include anchoring scaffolds onto chromosomes based on optical maps. However, the number of assembled scaffolds from this analysis is very close to the number of chromosomes.
3Is there any cautions in sampling for this analysis?
Answer: Firstly, there shouldn't be any contaminated microbials. Nucleus staining is required to identify if the fungi is mononucleus or poly nucleus. Genome survey is recommended to find out the heterozygosity and repetitive ratio to guide sequencing strategy for fine genome.