Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres

Liu, Zhao; Yue, Wei; Li, Dayong; Wang, Richard R.‐C.; Kong, Xiuying; Lü, Kun; Wang, Guixiang; Dong, Yushen; Jin, Weiwei; Zhang, Xueyong

doi:10.1007/s00412-008-0161-9

Cited by 111 publications

(129 citation statements)

References 55 publications

Supporting

Mentioning

124

Contrasting

Order By: Relevance

“…CRMs, a lineage of Ty3/gypsy retrotransposons, have been well characterized as centromeric retrotransposons in many species (20)(21)(22)(23)(24)(25), including G. hispidula and G. subglabra (15). Using phylogenetic analysis, we found that 55 U. gibba sequences are grouped within the subgroup A CRMs, which include the centromere-specific CRMs (SI Appendix, section 3.3.3).…”

Section: Significancementioning

confidence: 97%

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Lan

Renner

Ibarra-Laclette

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.

show abstract

Section: Significancementioning

confidence: 97%

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Lan

Renner

Ibarra-Laclette

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…The quality of RNA was checked on denaturing agarose gel, and possible DNA contamination was removed by treatment of total RNA with DNase (Ambion TURBO DNase; Invitrogen). Absence of DNA contamination was confirmed by PCR using primers specific for Bilby (Francki, 2001) or CRW2 repeats (Liu et al, 2008) (see Supplemental Table 1 online). cDNA was synthesized with 2.5 µg of DNase-treated total RNA using the RevertAid H Minus first-strand cDNA synthesis kit (Fermentas) according to the manufacturer's instructions.…”

Section: Methods Plant Materials and Plant Cultivationmentioning

confidence: 99%

“…Therefore, different parts of Ty3/Gypsy- type centromeric retrotransposons like the rye-specific element Bilby (Francki, 2001) and the sequences originally identified in wheat centromeric sequences 6C6-3/-4 (Zhang et al, 2004), 192-bp repeat (Ito et al, 2004), CCS1 (Aragón-Alcaide et al, 1996), and CRW2 (Liu et al, 2008), were in silico compared with 454-sequence reads (Martis et al, 2012) from flow-sorted As and Bs as well as from genomic DNA of 0B and +4B rye plants.…”

Section: The Composition Of Centromere Repeats Differs Between As and Bsmentioning

confidence: 99%

“…The cereal centromeric sequences Bilby (Francki, 2001), 6C6-3/-4 (Zhang et al, 2004), 192-bp repeat (Ito et al, 2004), CCS1 (Aragón-Alcaide et al, 1996), and CRW2 (Liu et al, 2008) were compared with rye B-derived sequence 454 reads (European Bioinformatics Institute-European Nucleotide Archive accession number ERP001061) by BLAST to identify similar B-located sequences for primer design (see Supplemental Table 1 online). In addition, their frequencies on A and B chromosomes were determined by PROFREP algorithm (Macas et al, 2007).…”

Section: Generation and Analysis Of Rye Centromeric Sequencesmentioning

confidence: 99%

See 1 more Smart Citation

Nondisjunction in Favor of a Chromosome: The Mechanism of Rye B Chromosome Drive during Pollen Mitosis

et al. 2012

View full text Add to dashboard Cite

B chromosomes (Bs) are supernumerary components of the genome and do not confer any advantages on the organisms that harbor them. The maintenance of Bs in natural populations is possible by their transmission at higher than Mendelian frequencies. Although drive is the key for understanding B chromosomes, the mechanism is largely unknown. We provide direct insights into the cellular mechanism of B chromosome drive in the male gametophyte of rye (Secale cereale). We found that nondisjunction of Bs is accompanied by centromere activity and is likely caused by extended cohesion of the B sister chromatids. The B centromere originated from an A centromere, which accumulated B-specific repeats and rearrangements. Because of unequal spindle formation at the first pollen mitosis, nondisjoined B chromatids preferentially become located toward the generative pole. The failure to resolve pericentromeric cohesion is under the control of the B-specific nondisjunction control region. Hence, a combination of nondisjunction and unequal spindle formation at first pollen mitosis results in the accumulation of Bs in the generative nucleus and therefore ensures their transmission at a higher than expected rate to the next generation.

show abstract

“…We assumed that intensive, ongoing intragenomic processes in this population could ultimately create the basis for parapatric speciation (Raskina et al 2004b). As has been repeatedly shown, the Daniela retrotransposon extensively amplified during the speciation of diploid ancestors of the A and D genomes of cultivated wheat (Liu et al 2008); therefore, it can be reasonably suggested that significant changes in the Daniela IRAP pattern may accompany the speciation process.…”

Section: Estimation Of the Level Of Irap Pattern Variabilitymentioning

confidence: 96%

Diversity of Long Terminal Repeat Retrotransposon Genome Distribution in Natural Populations of the Wild Diploid WheatAegilops speltoides

et al. 2012

View full text Add to dashboard Cite

The environment can have a decisive influence on the structure of the genome, changing it in a certain direction. Therefore, the genomic distribution of environmentally sensitive transposable elements may vary measurably across a species area. In the present research, we aimed to detect and evaluate the level of LTR retrotransposon intraspecific variability in Aegilops speltoides (2n = 2x = 14), a wild cross-pollinated relative of cultivated wheat. The interretrotransposon amplified polymorphism (IRAP) protocol was applied to detect and evaluate the level of retrotransposon intraspecific variability in Ae. speltoides and closely related species. IRAP analysis revealed significant diversity in TE distribution. Various genotypes from the 13 explored populations significantly differ with respect to the patterns of the four explored LTR retrotransposons (WIS2, Wilma, Daniela, and Fatima). This diversity points to a constant ongoing process of LTR retrotransposon fraction restructuring in populations of Ae. speltoides throughout the species' range and within single populations in time. Maximum changes were recorded in genotypes from small stressed populations. Principal component analysis showed that the dynamics of the Fatima element significantly differ from those of WIS2, Wilma, and Daniela. In terms of relationships between Sitopsis species, IRAP analysis revealed a grouping with Ae. sharonensis and Ae. longissima forming a separate unit, Ae. speltoides appearing as a dispersed group, and Ae. bicornis being in an intermediate position. IRAP display data revealed dynamic changes in LTR retrotransposon fractions in the genome of Ae. speltoides. The process is permanent and population specific, ultimately leading to the separation of small stressed populations from the main group. L ARGE cereal genomes are known to consist of an extraordinary number of transposable elements, in particular, LTR retrotransposons, which are highly dynamic (Bennetzen 1996;Wicker et al. 2003). Recent studies have shown that LTR retrotransposons are often found in different densities or copy numbers among individuals of the same species (Baucom et al. 2009;Belyayev et al. 2010), and "bursts" of transposable elements (TEs) in several species of angiosperms over time have been recorded (Vitte and Panaud 2003;Tsukahara et al. 2009;Belyayev et al. 2010). Although there are several known cases of temporal retroelement copy-number change, the important question of the level of current TE intraspecific variability across the area occupied by a particular species is still unclear, especially for a species whose area is declining or shifting under the influence of climate change. It is possible that populations with enhanced TE activity are more likely to survive as new forms, or even new species, during environmental fluctuations due to the production of an extended number of genomic variants for natural selection (Grant 1981;Raskina et al. 2004a;Belyayev et al. 2010). This is one of the key problems in understanding the mechanisms of sp...

show abstract

Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres

Cited by 111 publications

References 55 publications

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

Nondisjunction in Favor of a Chromosome: The Mechanism of Rye B Chromosome Drive during Pollen Mitosis

Diversity of Long Terminal Repeat Retrotransposon Genome Distribution in Natural Populations of the Wild Diploid WheatAegilops speltoides

Contact Info

Product

Resources

About