ArticleBMC evolutionary biology2007
Transposable element distribution, abundance and role in genome size variation in the genus Oryza.
Article in BMC evolutionary biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed, 111 citations in OpenAlex.
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- Genome Size Variation and Evolution Driven by Transposable Elements in the GenusFrontiers in plant science · 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
- The first draft genome of feather grasses using SMRT sequencing and its implications in molecular studies of Stipa.Scientific reports · 2021Article
- Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice.Genome biology · 2020Article
- Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice.Frontiers in plant science · 2020Review
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- Genome size, chromosome number determination, and analysis of the repetitive elements inPeerJ · 2019Article
- Draft genome sequence of first monocot-halophytic species Oryza coarctata reveals stress-specific genes.Scientific reports · 2018Article
- Retroelements and DNA Methylation Could Contribute to Diversity of 5S rDNA in Agave L.Journal of molecular evolution · 2018Article
- De novo genome assembly ofCommunications biology · 2018Article
- Red Clover (Frontiers in plant science · 2018Article
- Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii.Molecular genetics and genomics : MGG · 2017Article
- Domestication of rice has reduced the occurrence of transposable elements within gene coding regions.BMC genomics · 2017Article
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation.
resultsWe identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial.
conclusionLong Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.
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