Higher frequency of intron loss from the promoter proximally paused genes of<i>Drosophila melanogaster</i>

Jiang, Li; Li, Xue-Nan; Niu, Deng-Ke

doi:10.4161/fly.29489

Cited by 3 publications

(3 citation statements)

References 57 publications

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“…S9). Intron losses and smaller transcript sizes are reported to enable regulation of expression timing in Drosophila and mouse 69 , 70 . It is not clear whether ‘gene-only’ tr–d events (Fig.…”

Section: Discussionmentioning

confidence: 99%

Landscape of gene transposition–duplication within the Brassicaceae family

Dassanayake

2018

DNA Research

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We developed the CLfinder-OrthNet pipeline that detects co-linearity among multiple closely related genomes, finds orthologous gene groups, and encodes the evolutionary history of each orthologue group into a representative network (OrthNet). Using a search based on network topology, we identified 1,394 OrthNets that included gene transposition–duplication (tr–d) events, out of 17,432 identified in six Brassicaceae genomes. Occurrences of tr–d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr–d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. These were derived from older tr–d events and had a higher chance of being expressed. We also found an enrichment of tr–d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr–d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr–d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3 that relate to their adaptive evolution. CLfinder-OrthNet provides a flexible toolkit to compare gene order, visualize evolutionary paths among orthologues as networks, and identify gene loci that share an evolutionary history.

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Section: Discussionmentioning

confidence: 99%

Landscape of gene transposition–duplication within the Brassicaceae family

Dassanayake

2018

DNA Research

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“…8B and S6). Intron losses and smaller transcript sizes are thought to enable rapid responses and regulation of expression timing in Drosophila and mouse [91,92] as well as in yeast [93]. It may also indicate variations in DNA methylation landscapes among duplicated paralogs, which facilitate intron losses [94].…”

Section: Comparisonsmentioning

confidence: 99%

Landscape of gene transposition-duplication within the Brassicaceae family

Dassanayake

2017

Preprint

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8Gene duplication, deletion, and transposition erode co-linearity between genomes over time, 9providing a substantial source of genomic structural variations. We developed CLfinder-OrthNet 10 pipeline to systematically trace gene duplication and transposition events by building networks based on 11 co-linearity among orthologs (OrthNets) from multiple closely related genomes. Using this pipeline, we 12 explored evolutionary events that result in erosion of co-linearity among six genomes in Brassicaceae, 13 including the model plant Arabidopsis thaliana and two extremophyte wild-relatives of Brassica crops 14 adapted to highly saline habitats. Out of 17,432 OrthNets derived from the six Brassicaceae genomes, 15 7,034 consisted of six co-linear orthologs, one from each genome, while the remaining included various 16 degrees and combinations of gene duplication, deletion, and transposition. We focused on 17 transposition-duplication (tr-d) events that lead to variations in both gene copy number and co-linearity. 32 peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/236299 doi: bioRxiv preprint first posted online Dec. 18,

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“…Small populations are more likely to gain introns because deleterious introns can become fixed, whereas even slightly deleterious introns are more likely to be eliminated in larger populations due to the higher efficiency of selection (Lynch, , ; Omilian et al ., ). IL is more prevalent in fast‐growing unicellular species due to selection for small genome size and rapid gene expression (Jeffares et al ., ; Jiang et al ., ), whereas IG is tolerated in slow‐growing metazoans in stable environments. In such environments, different mating strategies have pleiotropic effects on IL/IG rates, e.g.…”

Section: Introductionmentioning

confidence: 99%

The dynamic loss and gain of introns during the evolution of the Brassicaceae

et al. 2015

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SUMMARYSequence comparison allows the detailed analysis of evolution at the nucleotide and amino acid levels, but much less information is known about the structural evolution of genes, i.e. how the number, length and distribution of introns change over time. We constructed a parsimonious model for the evolutionary rate of intron loss (IL) and intron gain (IG) within the Brassicaceae and found that IL/IG has been highly dynamic, with substantial differences between and even within lineages. The divergence of the Brassicaceae lineages I and II marked a dramatic change in the IL rate, with the common ancestor of lineage I losing introns three times more rapidly than the common ancestor of lineage II. Our data also indicate a subsequent declining trend in the rate of IL, although in Arabidopsis thaliana introns continue to be lost at approximately the ancestral rate. Variations in the rate of IL/IG within lineage II have been even more remarkable. Brassica rapa appears to have lost introns approximately 15 times more rapidly than the common ancestor of B. rapa and Schenkiella parvula, and approximately 25 times more rapidly than its sister species Eutrema salsugineum. Microhomology was detected at the splice sites of several dynamic introns suggesting that the nonhomologous end-joining and double-strand break repair is a common pathway underlying IL/IG in these species. We also detected molecular signatures typical of mRNA-mediated IL, but only in B. rapa.

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Higher frequency of intron loss from the promoter proximally paused genes ofDrosophila melanogaster

Cited by 3 publications

References 57 publications

Landscape of gene transposition–duplication within the Brassicaceae family

Landscape of gene transposition–duplication within the Brassicaceae family

Landscape of gene transposition-duplication within the Brassicaceae family

The dynamic loss and gain of introns during the evolution of the Brassicaceae

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