PIGD: a database for intronless genes in the Poaceae

Yan, Hanwei; Jiang, Cuiping; Li, Xiaoyü; Sheng, Lei; Dong, Qing; Peng, Xiaojian; Li, Qian; Zhao, Yang; Jiang, Haiyang; Cheng, Beijiu

doi:10.1186/1471-2164-15-832

Cited by 23 publications

(20 citation statements)

References 28 publications

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“…Chiifu-401 (BRAD). The detection of intronless Brassica SOC1 in eukaryotic genomes provides important insights into the evolution of gene structure as well as retroposition (Yan et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas

2015

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Whole genome sequence analyses allow unravelling such evolutionary consequences of meso-triplication event in Brassicaceae (∼14-20 million years ago (MYA)) as differential gene fractionation and diversification in homeologous sub-genomes. This study presents a simple gene-centric approach involving microsynteny and natural genetic variation analysis for understanding SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1) homeolog evolution in Brassica. Analysis of microsynteny in Brassica rapa homeologous regions containing SOC1 revealed differential gene fractionation correlating to reported fractionation status of sub-genomes of origin, viz. least fractionated (LF), moderately fractionated 1 (MF1) and most fractionated (MF2), respectively. Screening 18 cultivars of 6 Brassica species led to the identification of 8 genomic and 27 transcript variants of SOC1, including splice-forms. Co-occurrence of both interrupted and intronless SOC1 genes was detected in few Brassica species. In silico analysis characterised Brassica SOC1 as MADS intervening, K-box, C-terminal (MIKC(C)) transcription factor, with highly conserved MADS and I domains relative to K-box and C-terminal domain. Phylogenetic analyses and multiple sequence alignments depicting shared pattern of silent/non-silent mutations assigned Brassica SOC1 homologs into groups based on shared diploid base genome. In addition, a sub-genome structure in uncharacterised Brassica genomes was inferred. Expression analysis of putative MF2 and LF (Brassica diploid base genome A (AA)) sub-genome-specific SOC1 homeologs of Brassica juncea revealed near identical expression pattern. However, MF2-specific homeolog exhibited significantly higher expression implying regulatory diversification. In conclusion, evidence for polyploidy-induced sequence and regulatory evolution in Brassica SOC1 is being presented wherein differential homeolog expression is implied in functional diversification.

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Section: Discussionmentioning

confidence: 99%

Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas

2015

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“…Intronless genes have gained increasing attention because of their implication in understanding evolutionary patterns of related genes and genomes (13). Currently, there are only two specialized database named PIGD (13) and IGDD (14) for plant intronless genes. PIGD only contains five species from the Poaceae family and IGDD only provides the data set of intronless genes from five eudicot species.…”

Section: New Featurementioning

confidence: 99%

PIECE 2.0: an update for the plant gene structure comparison and evolution database

Wang

Thilmony

et al. 2016

Nucleic Acids Res

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PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.

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“…We compared the list of maize intron-less genes with our mapping data and found 7 152 of them actually had an intron or introns that were directly supported by PUTs mapping (Supplementary Table 1 -file: false_intronless.ids). Thus, the intron-less gene lists collected by Yan et al (2014) need to be examined thoroughly with gene expression data for other types of analysis. The transcripts mapping to genome information generated in the work can be further used to improve the predicted gene structures in maize.…”

Section: Detection and Classification Of Alternative Splicing Eventsmentioning

confidence: 99%

“…Recently Yan et al (2014) developed a database of intron-less genes of Poaceae (PIGD, http://pigd.ahau.edu.cn), which collected 14 623 intron-less maize genes. We compared the list of maize intron-less genes with our mapping data and found 7 152 of them actually had an intron or introns that were directly supported by PUTs mapping (Supplementary Table 1 -file: false_intronless.ids).…”

Section: Detection and Classification Of Alternative Splicing Eventsmentioning

confidence: 99%

Comprehensive Cataloging and Analysis of Alternative Splicing in Maize

Min

2017

cmb

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Gene expression is a key step in developmental regulation and responses in changing environments in plants. Alternative splicing (AS) is a process generating multiple RNA isoforms from a single gene pre-mRNA transcript that increases the diversity of functional proteins and RNAs. Identification and analysis of alternatively splicing events are critical for crop improvement and understanding regulatory mechanisms. In maize large numbers of transcripts generated by RNA-seq technology are available, we incorporated these data with data assembled with ESTs and mRNAs to comprehensively catalog all genes having pre-mRNAs undergoing AS. A total of 192 624 AS events were detected and classified, including 103 566 (53.8%) basic events and 89 058 (46.2%) complex events which were formed by combination of various types of basic events. Intron retention was the dominant type of basic AS event, accounting for 24.1%. These AS events were identified from 91 128 transcripts which were generated from 26 669 genomic loci, of which consisted of 20 860 gene models. It was estimated that 55.3% maize genes may be subjected to AS. The transcripts mapping information can be used to improve the predicted gene models in maize. The data can be accessed at Plant Alternative Splicing Database

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PIGD: a database for intronless genes in the Poaceae

Cited by 23 publications

References 28 publications

Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas

Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas

PIECE 2.0: an update for the plant gene structure comparison and evolution database

Comprehensive Cataloging and Analysis of Alternative Splicing in Maize

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