Functional Allium fistulosum Centromeres Comprise Arrays of a Long Satellite Repeat, Insertions of Retrotransposons and Chloroplast DNA

Frontiers in Plant Science
Ilya V KirovLudmila I Khrustaleva

Abstract

The centromere is a unique part of the chromosome combining a conserved function with an extreme variability in its DNA sequence. Most of our knowledge about the functional centromere organization is obtained from species with small and medium genome/chromosome sizes while the progress in plants with big genomes and large chromosomes is lagging behind. Here, we studied the genomic organization of the functional centromere in Allium fistulosum and A. cepa, both species with a large genome (13 Gb and 16 Gb/1C, 2n = 2x = 16) and large-sized chromosomes. Using low-depth DNA sequencing for these two species and previously obtained CENH3 immunoprecipitation data we identified two long (1.2 Kb) and high-copy repeats, AfCen1K and AcCen1K. FISH experiments showed that AfCen1K is located in all centromeres of A. fistulosum chromosomes while no AcCen1K FISH signals were identified on A. cepa chromosomes. Our molecular cytogenetic and bioinformatics survey demonstrated that these repeats are partially similar but differ in chromosomal location, sequence structure and genomic organization. In addition, we could conclude that the repeats are transcribed and their RNAs are not polyadenylated. We also observed that these repeats are associated...Continue Reading

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Citations

May 19, 2021·BMC Plant Biology·Alberto VangelistiTommaso Giordani

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Datasets Mentioned

BETA
AB735741
AB735740
MT374062
MT374061
KM088013.1
SRR1312066
PRJNA649851

Methods Mentioned

BETA
ChIP
PCR
RNAseq
HTseq
electrophoresis

Software Mentioned

TBLASTN
ggplot2
Hisat2
golang
DRAWID
AxioVision
outfmt
TAREAN
BLASTn
R

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