Sequence-based identification and characterisation of cultivated filamentous fungi in the Alan Bunga peat ecosystems of Sarawak, Malaysia

The identification of cultivated fungal isolates using multiple primer set approaches reveals a lot of information on how soil fungi change as land use changes in tropical peat swamp forest ecosystems. This study aimed to identify the cultivated species of fungi from three different Alan Bunga peat swamp forest ecosystems: secondary forest, logged-over secondary forest, and 3.5 years after oil palm planting. A total of 45 fungal isolates were cultivated on two different types of media (potato dextrose agar [PDA] and malt extract agar [MEA]), and subsequently amplified using two different primer sets, namely ITS (ITS1/ITS4) and 18S rDNA (EF4/fung5). The morphological characteristics of fungal isolates were examined under a light microscope. Forty-two fungal isolates were successfully verified by PCR and DNA sequencing. The majority of the cultivated fungal species belonged to the phylum Ascomycota; one was from the Basidiomycota. Trichoderma asperellum (34 %) was the commonest fungal species detected in secondary forest using ITS primer whereas Aspergillus fumigatus (22 %) was the commonest using 18S rDNA primer. In conclusion, the ITS1/ITS4 primer set showed greater accuracy than the EF4/fung5 primer set in identification of the fungal taxonomic groups to species level

Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.

Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of intervening in pathways underlying lung function. We highlight new putative causal variants, genes, proteins and pathways, including those targeted by existing drugs. These findings bring us closer to understanding the mechanisms underlying lung function and COPD, and should inform functional genomics experiments and potentially future COPD therapies