Identifying interstitial lung disease associated chemicals by integrating transcriptome-wide association study and chemical-gene interaction networks.

Interstitial lung diseases (ILD) comprise a heterogeneous group of lung disease characterized by common clinical syndromes and patterns of lung injury which poses growing burden on the health and social economic consequences. Its etiology remains elusive. By integrating transcriptome-wide association studies analysis of ILD and chemical-gene interaction networks implemented by CGSEA software, we systematically evaluated the association between ILD and 11,190 chemicals in this study. We detected several chemicals significantly associated with ILD (permutated empirical P values < 0.05). Briefly, a total of 56 chemicals were detected for ILD in lung tissue, 121 in whole blood respectively. Among the chemicals identified for ILD in lung tissue and whole blood, we found 7 common chemicals, including St. Thomas' Hospital cardioplegic solution, cytarabine, ginsenoside Rg3, cholecalciferol, fluoxetine, oxidized-L-alpha-1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine and excitatory amino acid agonists. Our findings shed lights on the underlying impact of chemical exposure on the development and progression of ILD, which will pave the way for more effective prevention and treatment strategies, ultimately improving the health outcomes and quality of life of those affected by ILD.

Genome assembly of Erythrophleum Fordii, a special "ironwood" tree in China.

OBJECTIVES: Erythrophleum is a genus in the Fabaceae family. The genus contains only about 10 species, and it is best known for its hardwood and medical properties worldwide. Erythrophleum fordii Oliv. is the only species of this genus distributed in China. It has superior wood and can be used in folk medicine, which leads to its overexploitation in the wild. For its effective conservation and elucidation of the distinctive genetic traits of wood formation and medical components, we present its first genome assembly. DATA DESCRIPTION: This work generated ~ 160.8 Gb raw Nanopore whole genome sequencing (WGS) long reads, ~ 126.0 Gb raw MGI WGS short reads and ~ 29.0 Gb raw RNA-seq reads using E. fordii leaf tissues. The de novo assembly contained 864,825,911 bp in the E. fordii genome, with 59 contigs and a contig N50 of 30,830,834 bp. Benchmarking Universal Single-Copy Orthologs (BUSCO) revealed 98.7% completeness of the assembly. The assembly contained 471,006,885 bp (54.4%) repetitive sequences and 28,761 genes that coded for 33,803 proteins. The protein sequences were functionally annotated against multiple databases, facilitating comparative genomic analysis.