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XB-ART-59780
Dev Comp Immunol 2023 Aug 01;145:104734. doi: 10.1016/j.dci.2023.104734.
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Advances in the Xenopus immunome: Diversification, expansion, and contraction.

Dimitrakopoulou D , Khwatenge CN , James-Zorn C , Paiola M , Bellin EW , Tian Y , Sundararaj N , Polak EJ , Grayfer L , Barnard D , Ohta Y , Horb M , Sang Y , Robert J .


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Xenopus is a genus of African clawed frogs including two species, X. tropicalis and X. laevis that are extensively used in experimental biology, immunology, and biomedical studies. The availability of fully sequenced and annotated Xenopus genomes is strengthening genome-wide analyses of gene families and transgenesis to model human diseases. However, inaccuracies in genome annotation for genes involved in the immune system (i.e., immunome) hamper immunogenetic studies. Furthermore, advanced genome technologies (e.g., single-cell and RNA-Seq) rely on well-annotated genomes. The annotation problems of Xenopus immunome include a lack of established orthology across taxa, merged gene models, poor representation in gene pages on Xenbase, misannotated genes and missing gene IDs. The Xenopus Research Resource for Immunobiology in collaboration with Xenbase and a group of investigators are working to resolve these issues in the latest versions of genome browsers. In this review, we summarize the current problems of previously misannotated gene families that we have recently resolved. We also highlight the expansion, contraction, and diversification of previously misannotated gene families.

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Species referenced: Xenopus tropicalis Xenopus laevis
Genes referenced: cxcl8a cxcl8a.2 cxcl8b.2 ids il15 il18 il9 mhc1-uca mhc1-uda mhc1-uea mhc2-daal mhc2-dab mhc2-dma mhc2-dmb tlr1 tlr12 tlr13 tlr14.2 tlr14.3 tlr2 tlr21 tlr22 tlr3 tlr4 tlr5 tlr6 tlr7 tlr8 tlr9
GO keywords: immune system process [+]


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References [+] :
Alfonzo, A call for direct sequencing of full-length RNAs to identify all modifications. 2021, Pubmed