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

Wang, Yi; Xu, Limei; Thilmony, Roger; You, Frank M.; Gu, Yong; Coleman‐Derr, Devin

doi:10.1093/nar/gkw935

Cited by 24 publications

(17 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In order to determine the intron/exon distribution in the GPAT genes of plants and understand the rules and possible consequences of gene structure and organization on protein functionality and evolutionary changes among species ( Wang et al , 2013 ), a comparative analysis of exon/intron organization was performed from genomic DNA sequences deposited in the Piece2.0 databases ( Wang et al , 2016 ). Basically, we submitted a query sequence set (in multi-FASTA format) consisting of genomic and CDS for GPATs and putative GPATs from seven representative species ( A. thaliana , G. max , O. sativa , B. distachyon, S. moellendorffii , P. patens and V. carteri ) to GSDraw and retrieved the gene structures with conserved protein motifs and phylogenetic trees.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide analysis of the Glycerol-3-Phosphate Acyltransferase (GPAT) gene family reveals the evolution and diversification of plant GPATs

et al. 2018

View full text Add to dashboard Cite

sn-Glycerol-3-phosphate 1-O-acyltransferase (GPAT) is an important enzyme that catalyzes the transfer of an acyl group from acyl-CoA or acyl-ACP to the sn-1 or sn-2 position of sn-glycerol-3-phosphate (G3P) to generate lysophosphatidic acids (LPAs). The functional studies of GPAT in plants demonstrated its importance in controlling storage and membrane lipid. Identifying genes encoding GPAT in a variety of plant species is crucial to understand their involvement in different metabolic pathways and physiological functions. Here, we performed genome-wide and evolutionary analyses of GPATs in plants. GPAT genes were identified in all algae and plants studied. The phylogenetic analysis showed that these genes group into three main clades. While clades I (GPAT9) and II (soluble GPAT) include GPATs from algae and plants, clade III (GPAT1-8) includes GPATs specific from plants that are involved in the biosynthesis of cutin or suberin. Gene organization and the expression pattern of GPATs in plants corroborate with clade formation in the phylogeny, suggesting that the evolutionary patterns is reflected in their functionality. Overall, our results provide important insights into the evolution of the plant GPATs and allowed us to explore the evolutionary mechanism underlying the functional diversification among these genes.

show abstract

Section: Methodsmentioning

confidence: 99%

Genome-wide analysis of the Glycerol-3-Phosphate Acyltransferase (GPAT) gene family reveals the evolution and diversification of plant GPATs

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Additional time and cost savings may be achieved by using amplicons larger than ones reported here. For example, while gene sizes vary, median gene length in plants such as barley can be thousands of base pairs 25,26 . Long PCR, however, can be more challenging to optimize, and careful testing should be performed to avoid unforeseen biases and to ensure that PCR amplification produces and equal representation of molecules from complex pooled genomic DNAs.…”

Section: Discussionmentioning

confidence: 99%

Fragmentation of pooled PCR products for highly multiplexed TILLING

Tramontano

Jarc

Jankowicz-Cieślak

et al. 2018

Preprint

View full text Add to dashboard Cite

Improvements to massively parallel sequencing have allowed the routine recovery of natural and induced sequence variants. A broad range of biological disciplines have benefited from this, ranging from plant breeding to cancer research. The need for high sequence coverage to accurately recover single nucleotide variants and small insertions and deletions limits the applicability of whole genome approaches. This is especially true in organisms with a large genome size or for applications requiring the screening of thousands of individuals, such as the reverse-genetic technique known as TILLING, where whole genome approaches become cost prohibitive. Using PCR to target and sequence chosen genomic regions provides an attractive alternative as the vast reduction in interrogated bases means that sample size can be dramatically increased through amplicon multiplexing and multidimensional sample pooling while maintaining suitable coverage for recovery of small mutations. Direct sequencing of PCR products is limited, however, due to limitations in read lengths of many next generation sequencers. In the present study we show the optimization and use of ultrasonication for the simultaneous fragmentation of multiplexed PCR amplicons for TILLING highly pooled samples. Thirty-two PCR products were produced from genomic DNA pools representing 265 pooled barley mutant lines. Mutant lines were produced with the chemical mutagen ethyl methanesulfonate. Samples were subjected to 2x300PE illumina sequencing. Evaluation of read coverage and base quality across amplicons suggests this approach is suitable for high-throughput TILLING and other applications employing highly pooled complex sampling schemes. Induced mutations previously identified in a traditional TILLING screen were recovered in this dataset further supporting the efficacy of the approach.

show abstract

“…Correlation analysis of SF1 exons were performed by using the piece2 webserver (http://www.bioinfogenome.net/piece/search.php? tdsourcetag=s_pctim_aiomsg) [76]. SF1 protein sequences were used to search for matching Pfam families using the HMMER website (https://www.ebi.ac.uk/Tools/hmmer/) [14].…”

Section: Gene Structure Protein Domain and Multiple Em For Motif Elimentioning

confidence: 99%

Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses

et al. 2020

View full text Add to dashboard Cite

Background: Among eukaryotic organisms, alternative splicing is an important process that can generate multiple transcripts from one same precursor messenger RNA, which greatly increase transcriptome and proteome diversity. This process is carried out by a super-protein complex defined as the spliceosome. Specifically, splicing factor 1/ branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting the 5′ and 3′ splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoa and mammals. However, its counterpart in plants has been seldomly reported. Results: To this end, we conducted a systematic characterization of the SF1 gene family across plant lineages. In this work, a total of 92 sequences from 59 plant species were identified. Phylogenetic relationships of these sequences were constructed, and subsequent bioinformatic analysis suggested that this family likely originated from an ancient gene transposition duplication event. Most plant species were shown to maintain a single copy of this gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this gene family in comparison to their animal and yeast counterparts, indicating that their potential role was preserved in the plant lineage. Conclusion: Our analysis presents general features of the gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.

show abstract

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

Cited by 24 publications

References 30 publications

Genome-wide analysis of the Glycerol-3-Phosphate Acyltransferase (GPAT) gene family reveals the evolution and diversification of plant GPATs

Genome-wide analysis of the Glycerol-3-Phosphate Acyltransferase (GPAT) gene family reveals the evolution and diversification of plant GPATs

Fragmentation of pooled PCR products for highly multiplexed TILLING

Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses

Contact Info

Product

Resources

About