The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana

Cannon, Steven B.; Mitra, Arvind; Baumgarten, Andrew; Young, Nevin D.; May, Georgiana

doi:10.1186/1471-2229-4-10

Cited by 1,631 publications

(1,095 citation statements)

References 82 publications

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“…Among them, the segmental duplication associated with the salicoid duplication event that occurred 65 million years (Ma) ago significantly contribute to the amplification of many multi-gene families [61,69-71]. To determine the possible relationship between the NAC genes and potential segmental duplications, we mapped Populus NACs to the duplicated blocks established in the previous studies [5].…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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BackgroundNAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.ResultsIn the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.ConclusionBased on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.

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Section: Resultsmentioning

confidence: 99%

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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“…The much more numerous Group III WRKY genes in Arabidopsis and rice is explained by tandem duplication and recent duplication events, which has led to a large-scale expansion of the gene families in these genomes [31,35]. Recent gene duplication and tandem duplication events are the most important factors in the rapid expansion and evolution of gene families [35]. Previous research has demonstrated that the Arabidopsis Group III WRKY gene family expanded rapidly as a result of recent segmentaland tandem duplication events.…”

Section: Number and Type Of Sesame Wrky Genesmentioning

confidence: 99%

“…Table 3 shows that one key difference between the sesame, Arabidopsis, and rice genomes is the number of Group III WRKY genes in each. The much more numerous Group III WRKY genes in Arabidopsis and rice is explained by tandem duplication and recent duplication events, which has led to a large-scale expansion of the gene families in these genomes [31,35]. Recent gene duplication and tandem duplication events are the most important factors in the rapid expansion and evolution of gene families [35].…”

Section: Number and Type Of Sesame Wrky Genesmentioning

confidence: 99%

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

Liu

et al. 2017

BMC Plant Biol

111

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Background: Sesame (Sesamum indicum L.) is one of the world's most important oil crops. However, it is susceptible to abiotic stresses in general, and to waterlogging and drought stresses in particular. The molecular mechanisms of abiotic stress tolerance in sesame have not yet been elucidated. The WRKY domain transcription factors play significant roles in plant growth, development, and responses to stresses. However, little is known about the number, location, structure, molecular phylogenetics, and expression of the WRKY genes in sesame.

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“…Our results suggest that the current ncRNA annotation of plant genomes, which is still based in a large part on comparative genomics, may miss several thousand ncRNA families that appeared more recently than the divergence time from species used for comparison. The fact that 80% of the ncRNA families detected in our intragenome screen are associated to tandem rather than segmental duplications further supports a recent occurrence of many ncRNA repeats, as there are more recent events of tandem duplications than of segmental duplications (Cannon et al 2004).…”

Section: Discussionmentioning

confidence: 79%

Plant noncoding RNA gene discovery by “single-genome comparative genomics”

Chen¹,

Zhou²,

Chen³

et al. 2011

RNA

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Plant genomes have undergone multiple rounds of duplications that contributed massively to the growth of gene families. The structure of resulting families has been studied in depth for protein-coding genes. However, little is known about the impact of duplications on noncoding RNA (ncRNA) genes. Here we perform a systematic analysis of duplicated regions in the rice genome in search of such ncRNA repeats. We observe that, just like their protein counterparts, most ncRNA genes have undergone multiple duplications that left visible sequence conservation footprints. The extent of ncRNA gene duplication in plants is such that these sequence footprints can be exploited for the discovery of novel ncRNA gene families on a large scale. We developed an SVM model that is able to retrieve likely ncRNA candidates among the 100,000+ repeat families in the rice genome, with a reasonably low false-positive discovery rate. Among the nearly 4000 ncRNA families predicted by this means, only 90 correspond to putative snoRNA or miRNA families. About half of the remaining families are classified as structured RNAs. New candidate ncRNAs are particularly enriched in UTR and intronic regions. Interestingly, 89% of the putative ncRNA families do not produce a detectable signal when their sequences are compared to another grass genome such as maize. Our results show that a large fraction of rice ncRNA genes are present in multiple copies and are species-specific or of recent origin. Intragenome comparison is a unique and potent source for the computational annotation of this major class of ncRNA.

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The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana

Cited by 1,631 publications

References 82 publications

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

Plant noncoding RNA gene discovery by “single-genome comparative genomics”

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