Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

Jiang, Wenkai; Liu, Yunlong; Xia, Enhua; Gao, Li‐Zhi

doi:10.1104/pp.112.200147

Cited by 85 publications

(81 citation statements)

References 98 publications

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“…Intriguingly, Amborella genes that undergo AS produce the highest average number of isoforms/gene compared to other species (Table S3). Whether this feature reflects the evolutionary position of Amborella in angiosperm, or is the result of the absence of lineage specific whole genome duplication events-whereas species with additional lineage specific WGD events have lost or partitioned AS isoforms among paralogues through subfunctionalization (Jiang et al 2013)-remains to be investigated. Maize has the largest collection of RNA-Seq data among the nine species examined, and also has the largest number of AS events, but the percentage of multi-exon genes that undergo AS is similar to other species.…”

Section: Resultsmentioning

confidence: 99%

Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

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One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction-based conserved AS events from RNA-Seq data across nine plant species, including five grass monocots (maize, sorghum, rice, Brachpodium, and foxtail millet), plus two nongrass monocots (banana and African oil palm), the eudicot Arabidopsis, and the basal angiosperm Amborella. In total, 9804 AS events were found to be conserved between two or more species studied. In grasses containing large regions of conserved synteny, the frequency of conserved AS events is twice that observed for genes outside of conserved synteny blocks. In plant-specific RS and RS2Z subfamilies of the serine/arginine (SR) splicefactor proteins, we observe both conservation and divergence of AS events after the whole genome duplication in maize. In addition, plant-specific RS and RS2Z splice-factor subfamilies are highly connected with R2R3-MYB in STRING functional protein association networks built using genes exhibiting conserved AS. Furthermore, we discovered that functional protein association networks constructed around genes harboring conserved AS events are enriched for phosphatases, kinases, and ubiquitylation genes, which suggests that AS may participate in regulating signaling pathways. These data lay the foundation for identifying and studying conserved AS events in the monocots, particularly across grass species, and this conserved AS resource identifies an additional layer between genotype to phenotype that may impact future crop improvement efforts.

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Section: Resultsmentioning

confidence: 99%

Evolutionarily Conserved Alternative Splicing Across Monocots

et al. 2017

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“…Previous research examined the relationships between gene features and retention probability following WGD in six plant genomes, including soybean (Jiang et al, 2013). They concluded that retained WGD genes have either low evolutionary rates (K a ) and high and broad expression patterns (type I), high structural complexity, including longer gene length, greater number of introns, and gene isoforms (type II), or high GC/GC3 content (type III).…”

Section: Methylation May Have Contributed To Biased Retention Of Genementioning

confidence: 99%

“…Since retained duplicated genes are more prone to AS (type II; Jiang et al, 2013), CG body methylation could play a role in retention if there is an explicit link with AS. Further analysis of paralogous or orthologous gene pairs that have simultaneously lost both AS and CG body methylation could help to elucidate the role of gene-body methylation in transcript splicing and its role in the evolution of duplicated genes.…”

Section: Methylation May Have Contributed To Biased Retention Of Genementioning

confidence: 99%

“…Although a majority of duplicated genes are lost through nonfunctionalization or pseudogenization (Lynch and Conery, 2000), many can be retained through balancing gene dosage (Papp et al, 2003;Birchler et al, 2005;Innan and Kondrashov, 2010) and/or functional divergence (Ohno, 1970;Force et al, 1999;Zhang and Cohn, 2008). While biased retention of duplicated genes can occur (Seoighe and Gehring, 2004;Freeling, 2009;Jiang et al, 2013), generally one of the paralogs is selectively lost, resulting in single-copy genes due to both neutral and selective forces. An interesting subset is shared single-copy genes, those that are repeatedly restored to singleton status after independent WGDs between lineages (Paterson et al, 2006;Duarte et al, 2010;De Smet et al, 2013).…”

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confidence: 99%

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A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

et al. 2015

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Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a paleopolyploidy (whole-genome duplication [WGD]) event, approximately 56.5 million years ago, followed by a genus Glycine-specific polyploidy, approximately 10 million years ago. Cytosine methylation is an epigenetic mark that plays an important role in the regulation of genes and transposable elements (TEs); however, the role of DNA methylation in the fate/evolution of genes following polyploidy and speciation has not been fully explored. Whole-genome bisulfite sequencing was used to produce nucleotide resolution methylomes for soybean and common bean. We found that, in soybean, CG body-methylated genes were abundant in WGD genes, which were, on average, more highly expressed than single-copy genes and had slower evolutionary rates than unmethylated genes, suggesting that WGD genes evolve more slowly than single-copy genes. CG body-methylated genes were also enriched in shared single-copy genes (single copy in both species) that may be responsible for the broad and high expression patterns of this class of genes. In addition, diverged methylation patterns in non-CG contexts between paralogs were due mostly to TEs in or near genes, suggesting a role for TEs and non-CG methylation in regulating gene expression post polyploidy. Reference methylomes for both soybean and common bean were constructed, providing resources for investigating epigenetic variation in legume crops. Also, the analysis of methylation patterns of duplicated and single-copy genes has provided insights into the functional consequences of polyploidy and epigenetic regulation in plant genomes.

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“…Thus, many large enzyme families, such as aminotransferases (39), contain members that differ in function. Furthermore, plants have many paralogs resulting from wholegenome duplication events (10,40,41). To deal with these challenges, we use the Ensembl Compara protein families, which depend on phylogenetic trees to extract orthologous relationships (32,42).…”

Section: Organizing Biochemical Pathways and Protein Families Into Sumentioning

confidence: 99%

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

Seaver

Gerdes²,

Frelin

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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The increasing number of sequenced plant genomes is placing new demands on the methods applied to analyze, annotate, and model these genomes. Today's annotation pipelines result in inconsistent gene assignments that complicate comparative analyses and prevent efficient construction of metabolic models. To overcome these problems, we have developed the PlantSEED, an integrated, metabolism-centric database to support subsystems-based annotation and metabolic model reconstruction for plant genomes. PlantSEED combines SEED subsystems technology, first developed for microbial genomes, with refined protein families and biochemical data to assign fully consistent functional annotations to orthologous genes, particularly those encoding primary metabolic pathways. Seamless integration with its parent, the prokaryotic SEED database, makes PlantSEED a unique environment for crosskingdom comparative analysis of plant and bacterial genomes. The consistent annotations imposed by PlantSEED permit rapid reconstruction and modeling of primary metabolism for all plant genomes in the database. This feature opens the unique possibility of modelbased assessment of the completeness and accuracy of gene annotation and thus allows computational identification of genes and pathways that are restricted to certain genomes or need better curation. We demonstrate the PlantSEED system by producing consistent annotations for 10 reference genomes. We also produce a functioning metabolic model for each genome, gapfilling to identify missing annotations and proposing gene candidates for missing annotations. Models are built around an extended biomass composition representing the most comprehensive published to date. To our knowledge, our models are the first to be published for seven of the genomes analyzed.systems biology | computational biochemistry | plant metabolism | plant genomics

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Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

Cited by 85 publications

References 98 publications

Evolutionarily Conserved Alternative Splicing Across Monocots

Evolutionarily Conserved Alternative Splicing Across Monocots

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

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