Imprecise intron losses are less frequent than precise intron losses but are not rare in plants

Ma, Ming-Yue; Zhu, Τao; Li, Xue-Nan; Lan, Xin-Ran; Liu, Heng-Yuan; Yang, Yufei; Niu, Deng-Ke

doi:10.1186/s13062-015-0056-7

Cited by 14 publications

(13 citation statements)

References 25 publications

(16 reference statements)

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“…Manuscript to be reviewed present paper, we confine our discussion of intron gain to the creation of new introns rather than the propagation of preexisting introns. By comparing the orthologous genes of Solanum lycopersicum, Solanum tuberosum, and other Solanaceae plants, we found 11 cases of precise intron loss and six cases of imprecise intron loss (Ma et al 2015b). Moreover, we found indications of an intron gain in one of the potato RNA-dependent RNA polymerase (RdRp) genes, PGSC0003DMG402000361 (Fig.…”

Section: Introductionmentioning

confidence: 92%

Peer Review #2 of "Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase (v0.2)"

2016

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The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp) gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3 ′ splicing site, two putative exonic splicing enhancers, and the GC contents differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals.

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Section: Introductionmentioning

confidence: 92%

Peer Review #2 of "Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase (v0.2)"

2016

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“…W przypadku pomidora (Solanum lycopersicum) i ziemniaka (S. tuberosum), których genomy różnią się o mniej niż 10%, opisano 17 delecji intronów w genach ortologicznych. Z kolei w wyniku porównania Arabidopsis thaliana oraz jego niedalekiego przodka, Arabidopsis lyrata (których linie oddzieliły się niecałe 10 milionów lat temu), opisano aż 114 delecji intronów [52]. Trzecią przyczyną utraty intronów są działania mechanizmów naprawy pęknięć obu nici DNA w obszarze intronu.…”

Section: Podsumowanieunclassified

“…Z badań nad blisko spokrewnionymi przedstawicielami rodzaju Solanum wynika, że wspomniana duplikacja nie występowała u ostatniego wspólnego przodka tych roślin. Dodatkowa sekwencja zawierająca intron pojawiła się dopiero u S. tuberosum [52].…”

Section: Nabywanie Intronów Przez Tandemową Duplikację W Genomieunclassified

Mechanizmy utraty i nabywania intronów spliceosomalnych

2019

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Introny to wewnątrzgenowe sekwencje niekodujące. Dawniej były uznawane za „śmieciowy” DNA, jednak obecnie uważa się, że są ważnymi elementami wpływającymi na funkcjonowanie genomu. Udowodniono, że introny zwiększają różnorodność transkryptomu i proteomu, spełniają w komórce role regulatorowe, wpływają na ekspresję genów oraz obróbkę, translację i degradację mRNA. Ze względu na sposób powstawania dzielą się na trzy główne kategorie: spliceosomalne, samowycinające się oraz introny tRNA. Introny spliceosomalne są charakterystyczne dla organizmów eukariotycznych. Analizy sekwencji genów ortologicznych w rożnych grupach eukariontów pozwoliły zidentyfikować wiele przypadków nabywania oraz utraty intronów. Niektóre z tych zdarzeń miały miejsce w dalekiej przeszłości, do innych doszło stosunkowo niedawno. Uważa się, że procesy te mogą działać jako jedna z sił napędowych w ewolucji genów eukariotycznych.

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“…Nonetheless the distribution of introns among different species and different genes are quite different (Ma et al, 2015b), studying the evolutionary dynamics of introns may provide clues to the evolution of eukaryotic genome. However, there are still controversies on the evolution forces that cause the present distribution of introns, which can be divided into neutral evolution (also known as genetic drift) and selective evolution.…”

Section: Introductionmentioning

confidence: 99%

The Evolution Force of Genome Reduction in Carnivorous Plants

Ma¹,

Tan²,

Yin³

et al. 2018

American Journal of Biochemistry and Biotechnology

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Abstract:The introns are widely present in the genome of eukaryotes and the distribution of intron varies greatly among different organisms or different genes. Generally, introns loss is an important way for uneven distribution of intron during genome evolution. In this study, two closely related carnivorous plants (Genlisea aurea and Utricularia gibba) were chosen, their genome were relatively integrity and high quality, especially, the large difference in genome size between them. We detected intron loss events, then investigated the relationship between the genome size, intron density, intron loss and the mutation rate in the carnivorous plants. Finally, a total of 752 and 124 intron loss positions were identified in G. aurea and U. gibba, respectively. In carnivorous plants, we found that the region around lost site had high mutation rate, the genes of intron loss had high mutation rate. Besides, for the species with more intron losses, the genome size was smaller and the mutation rate was higher. Thus, we propose that the mutation rate was positively correlated with intron losses, but negatively correlated with intron number and genome size. These could be explained by the selection to minimize mutational hazards.

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Imprecise intron losses are less frequent than precise intron losses but are not rare in plants

Cited by 14 publications

References 25 publications

Peer Review #2 of "Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase (v0.2)"

Peer Review #2 of "Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase (v0.2)"

Mechanizmy utraty i nabywania intronów spliceosomalnych

The Evolution Force of Genome Reduction in Carnivorous Plants

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