Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

The chicken is a model animal for the study of evolution, immunity and development. In addition to their use as a model organism, chickens also represent an important agricultural product. Pathogen invasion has already been shown to modulate the expression of hundreds of genes, but the role of alternative splicing in avian virus infection remains unclear. We used RNA-seq data to analyze virus-induced changes in the alternative splicing of Gallus gallus, and found that a large number of alternative splicing events were induced by virus infection both in vivo and in vitro. Virus-responsive alternative splicing events preferentially occurred in genes involved in metabolism and transport. Many of the alternatively spliced transcripts were also expressed from genes with a function relating to splicing or immune response, suggesting a potential impact of virus infection on pre-mRNA splicing and immune gene regulation. Moreover, exon skipping was the most frequent AS event in chickens during virus infection. This is the first report describing a genome-wide analysis of alternative splicing in chicken and contributes to the genomic resources available for studying host–virus interaction in this species. Our analysis fills an important knowledge gap in understanding the extent of genome-wide alternative splicing dynamics occurring during avian virus infection and provides the impetus for the further exploration of AS in chicken defense signaling and homeostasis.

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Genome-wide analysis of alternative splicing evolution amongMussubspecies

Molecular Ecology ◽

10.1111/j.1365-294x.2009.04490.x ◽

2010 ◽

Vol 19 ◽

pp. 228-239 ◽

Cited By ~ 36

Author(s):

BETTINA HARR ◽

LESLIE M. TURNER

Keyword(s):

Alternative Splicing ◽

Genome Wide Analysis ◽

Genome Wide

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Abstract 4346: Genome-wide analysis of alternative splicing in pediatric medulloblastoma

10.1158/1538-7445.am10-4346 ◽

2010 ◽

Cited By ~ 1

Author(s):

Francesca Menghi ◽

Thomas S. Jacques ◽

Martino Barenco ◽

Mike Hubank ◽

Steven C. Clifford ◽

...

Keyword(s):

Alternative Splicing ◽

Genome Wide Analysis ◽

Pediatric Medulloblastoma ◽

Genome Wide

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Genome-Wide Analysis of Alternative Splicing in Zea mays during Maize Iranian Mosaic Virus Infection

Plant Molecular Biology Reporter ◽

10.1007/s11105-019-01169-y ◽

2019 ◽

Vol 37 (5-6) ◽

pp. 413-420 ◽

Cited By ~ 1

Author(s):

Abozar Ghorbani ◽

Ahmad Tahmasebi ◽

Keramatollah Izadpanah ◽

Alireza Afsharifar ◽

Ralf G. Dietzgen

Keyword(s):

Zea Mays ◽

Alternative Splicing ◽

Virus Infection ◽

Mosaic Virus ◽

Genome Wide Analysis ◽

Genome Wide ◽

Mosaic Virus Infection

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Genome-Wide Analysis of the Lateral Organ Boundaries Domain (LBD) Gene Family in Solanum tuberosum

International Journal of Molecular Sciences ◽

10.3390/ijms20215360 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5360 ◽

Cited By ~ 3

Author(s):

Hengzhi Liu ◽

Minxuan Cao ◽

Xiaoli Chen ◽

Minghui Ye ◽

Peng Zhao ◽

...

Keyword(s):

Drought Stress ◽

Plant Growth And Development ◽

Point Distribution ◽

Expression Levels ◽

Genome Wide Analysis ◽

Qrt Pcr ◽

Genome Wide ◽

Normal Metabolism ◽

Lateral Organ ◽

Organ Boundaries

Lateral organ boundaries domain (LBD) proteins belong to a particular class of transcription factors of lateral organ boundary (LOB) specific domains that play essential roles in plant growth and development. However, a potato phylogenetic analysis of the LBD family has not been fully studied by scholars and researchers. In this research, bioinformatics methods and the growth of potatoes were used to identify 43 StLBD proteins. We separated them into seven subfamilies: Ia, Ib, Ic, Id, Ie, IIa and IIb. The number of amino acids encoded by the potato LBD family ranged from 94 to 327. The theoretical isoelectric point distribution ranged from 4.16 to 9.12 Kda, and they were distributed among 10 chromosomes. The results of qRT-PCR showed that the expression levels of StLBD2-6 and StLBD3-5 were up-regulated under drought stress in the stem. The expression levels of StLBD1-5 and StLBD2-6 were down-regulated in leaves. We hypothesized that StLBD1-5 was down-regulated under drought stress, and that StLBD2-6 and StLBD3-5 up-regulation might help to maintain the normal metabolism of potato and enhance the potatoes’ resistance to drought.

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