Facioscapulohumeral muscular dystrophy(FSHD) is a disorder characterized by muscle weakness and wasting (atrophy). This disease is typically inherited as autosomal dominant and has a complex genetic and epigenetic etiology. Our collaborator had differentiated healthy human pluripotent stem cells(iPSC) into skeletal muscles and exploited ISO-Seq to explore cell gene expression and transcript alternative splicing usage profile during 8 differentiation stages. Later, stage specific gene differential expression, transcript alternative splicing, gene ontology and novel gene/transcript were analysed to characterize the feature of each stage during the differentiation. In terms of expressed genes with more than or equal to 5 transcripts, each stage had shown their own stage specific features. About transcripts, iPS, S1, ADM.D0, ADM.D4 have about 30% to 40% more total transcripts than the rest 4 stages. 4 kinds of alternative splicing events are generally distributed and S2 stage has the least alternative splicing events potentially due to technical reasons. As for gene differential expressions, ADM.D4 has considerable amount of differential expressed genes with 5 other stages and it has minor difference with ISM.D4 and S3 stages(they are all myotubes cells). The gene ontology analysis is performed according to the results of previous step, stage specific GO terms are revealed.

Facioscapulohumeral muscular dystrophy(FSHD) is a disorder characterized by muscle weakness and wasting (atrophy). This disease is typically inherited as autosomal dominant and has a complex genetic and epigenetic etiology. Our collaborator had differentiated healthy human pluripotent stem cells(iPSC) into skeletal muscles and exploited ISO-Seq to explore cell gene expression and transcript alternative splicing usage profile during 8 differentiation stages. Later, stage specific gene differential expression, transcript alternative splicing, gene ontology and novel gene/transcript were analysed to characterize the feature of each stage during the differentiation. In terms of expressed genes with more than or equal to 5 transcripts, each stage had shown their own stage specific features. About transcripts, iPS, S1, ADM.D0, ADM.D4 have about 30% to 40% more total transcripts than the rest 4 stages. 4 kinds of alternative splicing events are generally distributed and S2 stage has the least alternative splicing events potentially due to technical reasons. As for gene differential expressions, ADM.D4 has considerable amount of differential expressed genes with 5 other stages and it has minor difference with ISM.D4 and S3 stages(they are all myotubes cells). The gene ontology analysis is performed according to the results of previous step, stage specific GO terms are revealed.

Anopheles stephensi is a potent vector of malaria throughout the Indian subcontinent and Middle East. An. stephensi is emerging as a model for molecular and genetic studies of mosquito-parasite interactions. Here we conducted a series of genomic and transcriptomic studies to improve the understanding of the biology of Anopheles stephensi and mosquito in general. First we reported the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly was produced using a combination of 454, Illumina, and PacBio sequencing. This hybrid assembly method was significantly better than assemblies generated from a single data source. A total of 11,789 protein-encoding genes were annotated using a combination of homology and de novo prediction. Secondly, we demonstrated the presence of complete dosage compensation in An. stephensi by determining that autosomal and X-linked genes have very similar levels of expression in both males and females. The uniformity of average expression levels of autosomal and X-linked genes remained when An. stephensi gene expression was normalized by that of their Ae. aegypti orthologs, strengthening the conclusion of complete dosage compensation in Anopheles. Lastly, we investigated trans-splicing events in Anopheles stephensi. We identified six trans-splicing events and all the trans-splicing sites are conserved and present in Ae. aegypti. The proteins encoded by the trans-spliced mRNAs are also highly conserved and their orthologs are co-linearly transcribed in out-groups of family Culicidae. This finding indicates the need to preserve the intact mRNA and protein function of the broken-up genes by trans-splicing during evolution. In summary, we presented the first genome assembly of Anopheles stephensi and studied two interesting evolution events" dosage compensation and trans-splicing - via transcriptomic analysis. / Ph. D.