ArticlePlant physiology2005
Computational identification of 69 retroposons in Arabidopsis.
Article in Plant physiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 57 citations in OpenAlex.
- Article
- RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization.Frontiers in genetics · 2021Article
- Rapid Genome Evolution and Adaptation ofFrontiers in plant science · 2021Article
- A member of wheat class III peroxidase gene family, TaPRX-2A, enhanced the tolerance of salt stress.BMC plant biology · 2020Article
- A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature inFrontiers in plant science · 2020Article
- Distinct Evolutionary Origins of Intron Retention Splicing Events inFrontiers in plant science · 2020Article
- Evolutionary patterns of chimeric retrogenes in Oryza species.Scientific reports · 2019Article
- The cyclin-dependent kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A.The Plant journal : for cell and molecular biology · 2018Article
- A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing inRNA (New York, N.Y.) · 2017Article
- The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?Genome biology and evolution · 2017Article
- Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii.Biology direct · 2016Article
- LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots.Scientific reports · 2016Article
- "Out of pollen" hypothesis for origin of new genes in flowering plants: study from Arabidopsis thaliana.Genome biology and evolution · 2014Article
- Pollen-specific activation of Arabidopsis retrogenes is associated with global transcriptional reprogramming.The Plant cell · 2014Article
- Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes.Plant physiology · 2014Article
- Article
- High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences.Genome biology and evolution · 2013Article
- Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum.PloS one · 2013Article
- RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity.International journal of evolutionary biology · 2013Article
- New gene evolution: little did we know.Annual review of genetics · 2013Review
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Retroposition is a shot-gun strategy of the genome to achieve evolutionary diversities by mixing and matching coding sequences with novel regulatory elements. We have identified 69 retroposons in the Arabidopsis (Arabidopsis thaliana) genome by a computational approach. Most of them were derivatives of mature mRNAs, and 20 genes contained relics of the reverse transcription process, such as truncations, deletions, and extra sequence additions. Of them, 22 are processed pseudogenes, and 52 genes are likely to be actively transcribed, especially in tissues from apical meristems (roots and flowers). Functional compositions of these retroposon parental genes imply that not the mRNA itself but its expression in gamete cells defines a suitable template for retroposition. The presence/absence patterns of retroposons can be used as cladistic markers for biogeographic research. Effects of human and the Mediterranean Pleistocene refugia in Arabidopsis biogeographic distributions were revealed based on two recent retroposons (At1g61410 and At5g52090). An evolutionary rate of new gene creation by retroposition was calculated as 0.6 genes per million years. Retroposons can also be used as molecular fossils of the parental gene expressions in ancient time. Extensions of 3' untranslated regions for those expressed parental genes are revealed as a possible trend of plant transcriptome evolution. In addition, we reported the first plant functional chimeric gene that adapts to intercompartmental transport by capturing two additional exons after retroposition.
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