Dataset Information

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

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 with insertions of retrotransposons and plastidic DNA and the landscape of A. cepa and A. fistulosum centromeric regions possess insertions of plastidic DNA. Finally, we carried out detailed comparative satellitome analysis of A. cepa and A. fistulosum genomes and identified a new chromosome- and A. cepa-specific tandem repeat, TR2CL137, located in the centromeric region. Our results shed light on the Allium centromere organization and provide unique data for future application in Allium genome annotation.

SUBMITTER: Kirov I

PROVIDER: S-EPMC7644871 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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

Kirov Ilya I Odintsov Sergey S Omarov Murad M Gvaramiya Sofya S Merkulov Pavel P Dudnikov Maxim M Ermolaev Alexey A Van Laere Katrijn K Soloviev Alexander A Khrustaleva Ludmila L

Frontiers in plant science 20201023

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 ...[more]

PMID: 33193489

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Project description:BACKGROUND:The optimized illumination of plants using light-emitting diodes (LEDs) is beneficial to their photosynthetic performance, and in recent years, LEDs have been widely used in horticultural facilities. However, there are significant differences in the responses of different crops to different wavelengths of light. Thus, the influence of artificial light on photosynthesis requires further investigation to provide theoretical guidelines for the light environments used in industrial crop production. In this study, we tested the effects of different LEDs (white, W; blue, B; green, G; yellow, Y; and red, R) with the same photon flux density (300??mol/m2·s) on the growth, development, photosynthesis, chlorophyll fluorescence characteristics, leaf structure, and chloroplast ultrastructure of Welsh onion (Allium fistulosum L.) plants. RESULTS:Plants in the W and B treatments had significantly higher height, leaf area, and fresh weight than those in the other treatments. The photosynthetic pigment content and net photosynthetic rate (Pn) in the W treatment were significantly higher than those in the monochromatic light treatments, the transpiration rate (E) and stomatal conductance (Gs) were the highest in the B treatment, and the intercellular CO2 concentration (Ci) was the highest in the Y treatment. The non-photochemical quenching coefficient (NPQ) was the highest in the Y treatment, but the other chlorophyll fluorescence characteristics differed among treatments in the following order: W?>?B?>?R?>?G?>?Y. This includes the maximum photochemical efficiency of photosystem II (PSII) under dark adaptation (Fv/Fm), maximum photochemical efficiency of PSII under light adaptation (Fv'/Fm'), photochemical quenching coefficient (qP), actual photochemical efficiency (?PSII), and apparent electron transport rate (ETR). Finally, the leaf structure and chloroplast ultrastructure showed the most complete development in the B treatment. CONCLUSIONS:White and blue light significantly improved the photosynthetic efficiency of Welsh onions, whereas yellow light reduced the photosynthetic efficiency.

Dataset Information

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

Publications

Functional <i>Allium fistulosum</i> Centromeres Comprise Arrays of a Long Satellite Repeat, Insertions of Retrotransposons and Chloroplast DNA.

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