Journal: Nature Genetics

Article Title: Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction

doi: 10.1038/ng.3010

Figure Lengend Snippet: ( a ) Normalized transcript levels of the 44 genes encoding WAP domain–containing proteins in T. muris , comparing the parasite anterior region with the posterior regions of adult female (F) and male (M) parasites. Indication of significant transcriptional upregulation in a particular pairwise comparison (Up) refers to false discovery rate (FDR) % 0.01 and FDR % 1 × 10 −5 when denoted by one asterisk and to FDR % 1 × 10 −5 when denoted by two asterisks. SP, signal peptide; WAP, whey acidic protein (Interpro, IPR008197 ); WR1, cysteine-rich repeat ( IPR006150 ); TIL, trypsin inhibitor–like ( IPR002919 ). For a full version of this figure, see . ( b ) Sequence logos show the conserved and distinct sequence characteristics of the WAP domains (Interpro, IPR008197 ) found in proteins from H. sapiens , T. trichiura and T. muris . The four canonical disulfide bonds formed by eight cysteine residues are highlighted at the top of the sequence logo for human WAP domains. The sequence logos representing the different species are aligned around the central CXXDXXC motif (where X is any amino acid). For a full version of this figure, see .

Article Snippet: Functional gene annotation including the assignment of gene product descriptions and GO terms was based on Interpro protein domain analysis and BLAST searches against annotated genomes.

Techniques: Comparison, Sequencing

Journal: BMC Genomics

Article Title: Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera

doi: 10.1186/s12864-024-10636-0

Figure Lengend Snippet: Analysis of gene polymorphism in P. margaritifera . ( A ) Redundancy analysis (RDA) performed with 1,824 SNPs called for 19 individuals using growth phenotype as the constraining variable on the first ordination axis. Grey points in the center of the plot represent SNPs, while colored diamonds represent individuals with orange and purple colors indicating Fast- (F) and Slow- (S) growing phenotypes respectively. ( B ) RDA biplot focusing on SNPs, where candidates for significant association (± 2.75 SD; P < 0.006) with growth phenotype are colored in red. ( C ) Genotype distribution vs. gene expression for the candidate SNP observed in the SR-F1 gene (scaffold4300size113025; base position 20,247) and associated with a high impact effect due to a stop codon gained mutation (see Table ). Colored diamonds represent individuals, with orange and purple colors indicating Fast- (F) and Slow- (S) growing phenotypes, respectively. ( D ) Structural representation and motif composition of the SR-F1 like protein. Functional domains are based on Interpro protein predictive model database . EGF: epidermal growth factor-like domain. Sequence base localization of domains are indicated below each scheme

Article Snippet: Functional domains are based on Interpro protein predictive model database [ ].

Techniques: Gene Expression, Mutagenesis, Functional Assay, Sequencing

Journal: Nucleic Acids Research

Article Title: The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

doi: 10.1093/nar/gkr875

Figure Lengend Snippet: AspGD curation statistics

Article Snippet: Features with protein-domain (InterPro)-based GO annotations , 5748 , 5226 , 6348.

Techniques: