Fractionization of Polyploid Duplicated Genes: Gene Loss, Expression Divergence, and Epigenetic Regulation in Brassica napus

2018 ◽  
pp. 149-158
Author(s):  
Chaobo Tong ◽  
Rafaqat Ali Gill ◽  
Yang Xiang ◽  
Lixin Ma ◽  
Xiaohui Cheng ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Epigenetic Regulation ◽  
Gene Loss ◽  
Duplicated Genes ◽  
Expression Divergence

scholarly journals Altered Transcription and Neofunctionalization of Duplicated Genes Rescue the Harmful Effects of a Chimeric Gene in Brassica napus

2016 ◽  
Vol 28 (9) ◽  
pp. 2060-2078 ◽  
Author(s):  
Shengqian Xia ◽  
Zhixin Wang ◽  
Haiyan Zhang ◽  
Kaining Hu ◽  
Zhiqiang Zhang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Chimeric Gene ◽  
Duplicated Genes ◽  
Harmful Effects

scholarly journals Comparable Rates of Gene Loss and Functional Divergence After Genome Duplications Early in Vertebrate Evolution

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1259-1266 ◽  
Author(s):  
Joseph H Nadeau ◽  
David Sankoff
Keyword(s):  
Gene Family ◽  
Protein Function ◽  
Gene Loss ◽  
Functional Divergence ◽  
Gene Families ◽  
High Rate ◽  
Vertebrate Evolution ◽  
Duplicated Genes ◽  
Apparent Contradiction ◽  
Genome Duplications

Duplicated genes are an important source of new protein functions and novel developmental and physiological pathways. Whereas most models for fate of duplicated genes show that they tend to be rapidly lost, models for pathway evolution suggest that many duplicated genes rapidly acquire novel functions. Little empirical evidence is available, however, for the relative rates of gene loss vs. divergence to help resolve these contradictory expectations. Gene families resulting from genome duplications provide an opportunity to address this apparent contradiction. With genome duplication, the number of duplicated genes in a gene family is at most 2n, where n is the number of duplications. The size of each gene family, e.g., 1, 2, 3,..., 2n, reflects the patterns of gene loss vs. functional divergence after duplication. We focused on gene families in humans and mice that arose from genome duplications in early vertebrate evolution and we analyzed the frequency distribution of gene family size, i.e., the number of families with two, three or four members. All the models that we evaluated showed that duplicated genes are almost as likely to acquire a new and essential function as to be lost through acquisition of mutations that compromise protein function. An explanation for the unexpectedly high rate of functional divergence is that duplication allows genes to accumulate more neutral than disadvantageous mutations, thereby providing more opportunities to acquire diversified functions and pathways.

scholarly journals Regulatory divergence of flowering time genes in the allopolyploid Brassica napus

2017 ◽  
Author(s):  
D. Marc Jones ◽  
Rachel Wells ◽  
Nick Pullen ◽  
Martin Trick ◽  
Judith A. Irwin ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Flowering Time ◽  
Gene Networks ◽  
Regulatory Elements ◽  
Duplicated Genes ◽  
Crop Species ◽  
Gene Copies ◽  
Gene Expression Dynamics ◽  
Flowering Time Gene ◽  
In Cis

AbstractPolyploidy is a recurrent feature of eukaryotic evolution and has been linked to increases in complexity, adaptive radiation and speciation. Within angiosperms, such events occur repeatedly in many plant lineages. We investigated the role of duplicated genes in the regulation of flowering in Brassica napus. This relatively young allotetraploid represents a snapshot of evolution and artificial selection in progress. In line with the gene balance hypothesis, we find preferential retention of expressed flowering time genes relative to the whole genome. Furthermore, gene expression dynamics across development reveal diverged regulation of many flowering time gene copies. This finding supports the concept of responsive backup circuits being key for the retention of duplicated genes. A case study of BnaTFL1 reveals differences in cis-regulatory elements downstream of these genes that could explain this divergence. Such differences in the regulatory dynamics of duplicated genes highlight the challenges for translating gene networks from model to more complex polyploid crop species.

scholarly journals Genomic asymmetry of the Brassica napus seed: Epigenetic contributions of DNA methylation and small RNAs to subgenome bias

2020 ◽  
Author(s):  
Dylan J. Ziegler ◽  
Deirdre Khan ◽  
Nadège Pulgar-Vidal ◽  
Isobel A.P. Parkin ◽  
Stephen J. Robinson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brassica Napus ◽  
Seed Development ◽  
Epigenetic Regulation ◽  
Small Rnas ◽  
Flowering Plants ◽  
Genetic History ◽  
History Of ◽  
Syntenic Regions

AbstractPolyploidy has predominated the genetic history of the angiosperms, and allopolyploidy is known to have contributed to the vast speciation of flowering plants. Brassica napus, one of the world’s most important oilseeds, is one such polyploid species originating from the interspecific hybridization of Brassica rapa (An) and Brassica oleracea (Cn). Nascent amphidiploids must balance progenitor genomes during reproduction, though the role of epigenetic regulation in subgenome maintenance is unknown. The seed is the pivotal developmental transition into the new sporophytic generation and as such undergoes substantial epigenetic modifications. We investigated subgenome bias between the An and Cn subgenomes as well as across syntenic regions by profiling DNA methylation and siRNAs characteristic of B. napus seed development. DNA methylation and siRNA accumulation were prevalent in the Cn subgenome and most pronounced early during seed morphogenesis. Hypermethylation during seed maturation was most pronounced on non-coding elements, including promoters, repetitive elements, and siRNAs. Methylation on siRNA clusters was more prevalent in syntenic regions of the Cn subgenome and implies selective silencing of genomic loci of the seed. Together, we find compelling evidence for the asymmetrical epigenetic regulation of the An and Cn subgenomes of Brassica napus across seed development.

scholarly journals Expression divergence of FRUITFULL homeologs enhanced pod shatter resistance in Brassica napus

2015 ◽  
Vol 14 (1) ◽  
pp. 871-885 ◽  
Author(s):  
P.F. Peng ◽  
Y.C. Li ◽  
D.S. Mei ◽  
J. Colasanti ◽  
L. Fu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Divergence ◽  
Pod Shatter

scholarly journals Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes

2010 ◽  
Vol 107 (47) ◽  
pp. 20417-20422 ◽  
Author(s):  
Y. Mizuta ◽  
Y. Harushima ◽  
N. Kurata
Keyword(s):  
Gene Loss ◽  
Duplicated Genes ◽  
Hybrid Incompatibility
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