ArticleBMC genomics2012
Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns.
Article in BMC genomics, 2012. 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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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed, 64 citations in OpenAlex.
- A Gypsy LTR retrotransposon insertion in BrNYC1-A04 causes the stay-green phenotype by inhibiting chlorophyll b degradation in Chinese cabbage (Brassica rapa L. ssp. pekinensis).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Chromosome distribution of four LTR retrotransposons and 18 S rDNA in coffea eugenioides.Scientific reports · 2025Article
- A target cultivar-specific identification system based on the chromatographic printed array strip method for eight prominent Japanese citrus cultivars.Breeding science · 2023Article
- Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Full-length LTR retroelements in Capsicum annuum revealed a few species-specific family bursts with insertional preferences.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2021Article
- Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic SpeciesBiotech (Basel (Switzerland)) · 2021Article
- Article
- The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability.Annals of botany · 2021Article
- Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference inInternational journal of molecular sciences · 2020Article
- Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis.Molecular biology reports · 2019Article
- Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop.GigaScience · 2019Article
- Comparative analysis of miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species.BMC plant biology · 2019Article
- The control of endopolygalacturonase expression by the sugarcane RAV transcription factor during aerenchyma formation.Journal of experimental botany · 2019Article
- The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages.PloS one · 2019Article
- Genomic abundance and transcriptional activity of diverse gypsy and copia long terminal repeat retrotransposons in three wild sunflower species.BMC plant biology · 2018Article
- Comparative Analysis of Homologous Sequences ofFrontiers in plant science · 2018Article
- Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.Genetica · 2017Article
- Distribution of Divo in Coffea genomes, a poorly described family of angiosperm LTR-Retrotransposons.Molecular genetics and genomics : MGG · 2017Article
- sRNAs as possible regulators of retrotransposon activity in Cryptococcus gattii VGII.BMC genomics · 2017Article
- Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii.Molecular genetics and genomics : MGG · 2017Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out.
resultsSixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements.
conclusionsIndividual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.