ArticleChromosoma2005
In-depth sequence analysis of the tomato chromosome 12 centromeric region: identification of a large CAA block and characterization of pericentromere retrotranposons.
Article in Chromosoma, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Cloning and Bioinformatics Analysis ofFrontiers in plant science · 2022Article
- Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress.Frontiers in plant science · 2022Review
- Genome relationships and LTR-retrotransposon diversity in three cultivated Capsicum L. (Solanaceae) species.BMC genomics · 2020Article
- Diversity, distribution and dynamics of full-length Copia and Gypsy LTR retroelements in Solanum lycopersicum.Genetica · 2017Article
- Natural and induced loss of function mutations in SlMBP21 MADS-box gene led to jointless-2 phenotype in tomato.Scientific reports · 2017Article
- Molecular cytogenetic analysis and genomic organization of major DNA repeats in castor bean (Ricinus communis L.).Molecular genetics and genomics : MGG · 2016Article
- Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis.Frontiers in plant science · 2016Article
- Development and regulation of pedicel abscission in tomato.Frontiers in plant science · 2015Review
- The AP2/ERF transcription factor SlERF52 functions in flower pedicel abscission in tomato.Journal of experimental botany · 2014Article
- Transcriptome analysis of tomato flower pedicel tissues reveals abscission zone-specific modulation of key meristem activity genes.PloS one · 2013Article
- MACROCALYX and JOINTLESS interact in the transcriptional regulation of tomato fruit abscission zone development.Plant physiology · 2012Article
- Article
- Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements.BMC genomics · 2011Article
- Divergence in centromere structure distinguishes related genomes in Coix lacryma-jobi and its wild relative.Chromosoma · 2010Article
- FISH mapping and molecular organization of the major repetitive sequences of tomato.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2008Article
- Terminal repeat retrotransposon in miniature (TRIM) as DNA markers in Brassica relatives.Molecular genetics and genomics : MGG · 2007Article
- Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species.BMC plant biology · 2007Article
- Characterization of terminal-repeat retrotransposon in miniature (TRIM) in Brassica relatives.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2007Article
- Arabidopsis carboxyl-terminal domain phosphatase-like isoforms share common catalytic and interaction domains but have distinct in planta functions.Plant physiology · 2006Article
- Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa.The Plant cell · 2006Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We sequenced a continuous 326-kb DNA stretch of a microscopically defined centromeric region of tomato chromosome 12. A total of 84% of the sequence (270 kb) was composed of a nested complex of repeat sequences including 27 retrotransposons, two transposable elements, three MITEs, two terminal repeat retrotransposons in miniature (TRIMs), ten unclassified repeats and three chloroplast DNA insertions. The retrotransposons were grouped into three families of Ty3-Gypsy type long terminal repeat (LTR) retrotransposons (PCRT1-PCRT3) and one LINE-like retrotransposon (PCRT4). High-resolution fluorescence in situ hybridization analyses on pachytene complements revealed that PCRT1a occurs on the pericentromere heterochromatin blocks. PCRT1 was the prevalent retrotransposon family occupying more than 60% of the 326-kb sequence with 19 members grouped into eight subfamilies (PCRT1a-PCRT1h) based on LTR sequence. The PCRT1a subfamily is a rapidly amplified element occupying tens of megabases. The other PCRT1 subfamilies (PCRT1b-PCRT1h) were highly degenerated and interrupted by insertions of other elements. The PCRT1 family shows identity with a previously identified tomato-specific repeat TGR2 and a CENP-B like sequence. A second previously described genomic repeat, TGR3, was identified as a part of the LTR sequence of an Athila-like PCRT2 element of which four copies were found in the 326-kb stretch. A large block of trinucleotide microsatellite (CAA)n occupies the centromere and large portions of the flanking pericentromere heterochromatin blocks of chromosome 12 and most of the other chromosomes. Five putative genes in the remaining 14% of the centromere region were identified, of which one is similar to a transcription regulator (ToCPL1) and a candidate jointless-2 gene.
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