The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

Aims:  To type the staphylococcal cassette chromosome (SCC) in coagulase‐negative staphylococci (CoNS) from animal sources. Methods and Results:  A total of 92 CoNS isolates recovered from farm animals was analysed. The top three staphylococcal species were Staphylococcus lentus (34), S. sciuri (31), and S. xylosus (13). The presence of the cassette chromosome recombinase (ccr) genes ccrA1, ccrB1, ccrA2, ccrB2, ccrA3, ccrB3 and ccrC, the mec regulatory genes mecI and mecR1, and Tn554 was used to differentiate the SCC. A total of 60 of the 92 isolates were methicillin resistant. Among the 60 methicillin‐resistant Staphylococcus spp. isolates, SCCmec (mecA‐carrying SCC) types I, III, IV and V were identified in 24 isolates based on the combinations of the ccr genes and the mec regulatory genes, with type III being predominant. The single S. epidermidis carried SCCmec type IV. SCC type III was also identified in two of 32 methicillin‐susceptible isolates. Identical SCCmec types were present in different species of CoNS. Pulsed‐field gel electrophoresis (PFGE) generated 64 patterns out of 81 PFGE typeable isolates. Indistinguishable clones were detected in animals from different farms. Conclusions:  Heterogeneous SCC existed in CoNS of diverse genetic background. Both clonal transmission of methicillin‐resistant CoNS and horizontal transfer of SCCmec occurred in the animal production environment. Significance and Impact of the Study:  This study adds to our knowledge of SCCmec type and the diversity of SCC in CoNS.

Aims To study the antimicrobial resistance of coagulase‐negative staphylococci (CoNS) in animals. Methods and Results In the present study, a total of 87 CoNS recovered from food animals were characterized by antimicrobial susceptibility testing, resistance gene identification and conjugation. Of the seven species studied, Staphylococcus lentus, Staphylococcus sciuri, Staphylococcus xylosus and Staphylococcus haemolyticus accounted for over 96% of the isolates. In addition to β‐lactam resistance (100%), high percentages of CoNS were resistant to tetracycline (67·8%), erythromycin (36·7%), clindamycin (27·5%) and quinopristin/dalfopristin (14·9%). Importantly, 47 (54%) isolates were resistant to at least three antimicrobial classes, including six CoNS resistant to six antimicrobial classes. The common genes for the above‐mentioned resistance phenotypes were mec(A), tet(M), erm(A) and vga(A)LC, which were identified from 68·7%, 61%, 56·2% and 69·2% of the isolates, respectively. tet(M) was conjugatively transferable from 10 tetracycline‐resistant CoNS to a Enterococcus strain, underlining the potential of antimicrobial resistance transfer from Staphylococcus to the commensal bacteria in human. Conclusions Multidrug resistance and resistance to non‐β‐lactam antimicrobials are common in CoNS in animals. Significance and Impact of the Study The data improve our understanding on the extent to which CoNS contribute to the dissemination of antimicrobial resistance in the food production environment.