Molecular characterization and distribution of a 145-bp tandem repeat family in the genus <i>Populus</i>

This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.Key words: Satellite DNA, centromeric DNA, genome organization, phylogeny.

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Molecular characterization and functional study of a tandem-repeat Galectin-9 from Japanese flounder (Paralichthys olivaceus)

Fish & Shellfish Immunology ◽

10.1016/j.fsi.2021.02.013 ◽

2021 ◽

Vol 112 ◽

pp. 23-30

Author(s):

Mingming Yu ◽

Shun Zhou ◽

Yuanyuan Ding ◽

Huimin Guo ◽

Ying Li ◽

...

Keyword(s):

Molecular Characterization ◽

Tandem Repeat ◽

Paralichthys Olivaceus ◽

Japanese Flounder ◽

Functional Study

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Length of uninterrupted repeats determines instability at the unstable mouse expanded simple tandem repeat family MMS10 derived from independent SINE B1 elements

Mammalian Genome ◽

10.1007/s003350010251 ◽

2001 ◽

Vol 12 (2) ◽

pp. 104-111 ◽

Cited By ~ 14

Author(s):

Philippe R.J. Bois ◽

Laura Southgate ◽

Alec J. Jeffreys

Keyword(s):

Tandem Repeat ◽

Repeat Family ◽

Simple Tandem Repeat

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The pericentromeric heterochromatin of the grass Zingeria biebersteiniana (2n = 4) is composed of Zbcen1-type tandem repeats that are intermingled with accumulated dispersedly organized sequences

Genome ◽

10.1139/g01-092 ◽

2001 ◽

Vol 44 (6) ◽

pp. 955-961 ◽

Cited By ~ 19

Author(s):

Verity A Saunders ◽

Andreas Houben

Keyword(s):

In Situ Hybridization ◽

Tandem Repeat ◽

Tandem Repeats ◽

Repetitive Sequences ◽

Pericentromeric Region ◽

Pericentromeric Heterochromatin ◽

Repeat Family ◽

Dna Reassociation ◽

Copy Dna

DNA reassociation and hydroxyapatite chromatography were used to isolate high-copy DNA of the grass Zingeria biebersteiniana (2n = 4). In situ hybridization demonstrated that the DNA isolated was enriched for pericentromere-specific repetitive sequences. One abundant pericentromere-specific component is the differentially methylated tandem-repeat family Zbcen1. Other sequences isolated, Zb46 and Zb47A, are dispersed and display similarity to parts of the gypsy- and copia-like retrotransposable elements of other grasses. In situ hybridization with the copia-like sequence Zb47A resulted in dispersed labelling along the chromosome arms, with a significant signal accumulation in the pericentromeric region of all chromosomes. It is concluded that the pericentromeric heterochromatin of Z. biebersteiniana is composed of members of the Zbcen1 tandem repeat family and that these tandem arrays are intermingled with accumulated putative copia-like retrotransposon sequences. An observed Rabl interphase orientation suggests that the length of the chromosomes rather than the genome size is the determining factor of the Rabl phenomenon.Key Words: centromere, heterochromatin, tandemly repeated DNA, retrotransposon-like, DNA reassociation.

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