A MITE Insertion in the Promoter Region of Anthocyanidin Synthase from Morus alba L.

Li, Jun; Liu, Changying; Zhao, Aichun; Yu, Maode; Liu, Xiaoqing; Chen, Xiangyun; Li, Yaofeng

doi:10.1007/s11105-018-1069-z

Cited by 4 publications

(3 citation statements)

References 37 publications

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“…TEs play important roles in the evolution of new genes and transcriptome diversity. TE insertions have potential impact on host gene expression through cis - or trans- regulatory activities [ 24 , 30 , 39 , 53 , 54 ]. Studies have implicated MITEs as negative transcription regulators of nearby genes [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

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Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

Lin

Sharma

2021

BMC Plant Biol

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Background Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. Results We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. Conclusions Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.

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Section: Discussionmentioning

confidence: 99%

“…Studies have implicated MITEs as negative transcription regulators of nearby genes [ 40 ]. However, MITEs may also upregulate gene expression by introducing regulatory motifs [ 39 , 53 , 54 ]. ml-MITEs showed a higher level of methylation than mt-MITEs.…”

Section: Discussionmentioning

confidence: 99%

Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

Lin

Sharma

2021

BMC Plant Biol

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“…MITEs may also carry transcription factor binding sites (TFBS) [18,19] or cis-acting DNA regulatory elements, e.g., new splice sites [20], transcription start sites, TATA boxes, and polyadenylation signals [21]. Insertions of MITEs into 3' UTRs may considerably affect post-transcriptional gene regulation, through modulation of RNA stability or translation [21][22][23], while insertion into the upstream region of a gene may result in its up-regulation [24,25]. However, in order to investigate the impact of MITEs on host genes, their genome-wide identification and characterization is an essential prerequisite.…”

Section: Introductionmentioning

confidence: 99%

A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome

Macko-Podgórni

Machaj

Grzebelus

2021

Genes

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Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack of coding capacity, the identification of MITEs has been demanding. However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes. We mined MITEs in the carrot reference genome DH1 using MITE-hunter and developed a curated carrot MITE repository comprising 428 families. Of the 31,025 MITE copies spanning 10.34 Mbp of the carrot genome, 54% were positioned in genic regions. Stowaways and Tourists were frequently present in the vicinity of genes, while Mutator-like MITEs were relatively more enriched in introns. hAT-like MITEs were relatively more frequently associated with transcribed regions, including untranslated regions (UTRs). Some carrot MITE families were shared with other Apiaceae species. We showed that hAT-like MITEs were involved in the formation of new splice variants of insertion-harboring genes. Thus, carrot MITEs contributed to the accretion of new diversity by altering transcripts and possibly affecting the regulation of many genes.

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Candidate genes in red pigment biosynthesis of a red-fleshed radish cultivar (Raphanus sativus L.) as revealed by transcriptome analysis

Liu

Chen

2019

Biochemical Systematics and Ecology

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A MITE Insertion in the Promoter Region of Anthocyanidin Synthase from Morus alba L.

Cited by 4 publications

References 37 publications

Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome

Candidate genes in red pigment biosynthesis of a red-fleshed radish cultivar (Raphanus sativus L.) as revealed by transcriptome analysis

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