Contribution of the satellitome to the exceptionally large genome of dinoflagellates : The case of the harmful alga Alexandrium minutum
Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved..
Dinoflagellates are known to possess an exceptionally large genome organized in permanently condensed chromosomes. Focusing on the contribution of satellite DNA (satDNA) to the whole DNA content of genomes and its potential role in the architecture of the chromosomes, we present the characterization of the satellitome of Alexandriun minutum strain VGO577. To achieve this, we analyzed Illumina reads using graph-based clustering and performed complementary bioinformatic analyses. In this way, we discovered 180 satDNAs occupying 17.38 % of the genome. The 12 most abundant satDNAs represent the half of the satellitome but no satDNA is overrepresented, with the most abundant contributing ∼1.56 % of the genome. The largest repeat unit is 517 bp long but more than the half of the satDNAs (101) have repeat units shorter than 20 bp. We used FISH to map a selected set of 26 satDNAs. Although some satDNAs generate discrete hybridization signals at specific chromosomal locations (hybridization sites, HS), our cytological analysis showed that most satDNAs are dispersed throughout the genome, probably forming short arrays. Two satDNAs co-localize with the 45S rDNA. With the exception of telomeric DNA, no other satDNA yields HS on all chromosomes. In addition, we analyzed nine satDNAs yielding HS in VGO577 in four other A. minutum strains. Polymorphism at the intraspecific level was found for the presence/absence and/or abundance of some satDNAs, suggesting the amplification/deletion of these satDNAs following geographic separation or during culture maintenance of the strains. We also discuss how these results contribute to the understanding of chromosome architecture and evolution of dinoflagellate genomes.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2023 |
|---|---|
| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:130 |
|---|---|
| Enthalten in: |
Harmful algae - 130(2023) vom: 07. Dez., Seite 102543 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Cuadrado, Ángeles [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Alexandrium |
|---|
| Anmerkungen: |
Date Completed 16.12.2023 Date Revised 16.12.2023 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1016/j.hal.2023.102543 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM365527106 |
|---|
| LEADER | 01000caa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM365527106 | ||
| 003 | DE-627 | ||
| 005 | 20231227133838.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2023 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1016/j.hal.2023.102543 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1231.xml |
| 035 | |a (DE-627)NLM365527106 | ||
| 035 | |a (NLM)38061820 | ||
| 035 | |a (PII)S1568-9883(23)00168-3 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Cuadrado, Ángeles |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Contribution of the satellitome to the exceptionally large genome of dinoflagellates |b The case of the harmful alga Alexandrium minutum |
| 264 | 1 | |c 2023 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 16.12.2023 | ||
| 500 | |a Date Revised 16.12.2023 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved. | ||
| 520 | |a Dinoflagellates are known to possess an exceptionally large genome organized in permanently condensed chromosomes. Focusing on the contribution of satellite DNA (satDNA) to the whole DNA content of genomes and its potential role in the architecture of the chromosomes, we present the characterization of the satellitome of Alexandriun minutum strain VGO577. To achieve this, we analyzed Illumina reads using graph-based clustering and performed complementary bioinformatic analyses. In this way, we discovered 180 satDNAs occupying 17.38 % of the genome. The 12 most abundant satDNAs represent the half of the satellitome but no satDNA is overrepresented, with the most abundant contributing ∼1.56 % of the genome. The largest repeat unit is 517 bp long but more than the half of the satDNAs (101) have repeat units shorter than 20 bp. We used FISH to map a selected set of 26 satDNAs. Although some satDNAs generate discrete hybridization signals at specific chromosomal locations (hybridization sites, HS), our cytological analysis showed that most satDNAs are dispersed throughout the genome, probably forming short arrays. Two satDNAs co-localize with the 45S rDNA. With the exception of telomeric DNA, no other satDNA yields HS on all chromosomes. In addition, we analyzed nine satDNAs yielding HS in VGO577 in four other A. minutum strains. Polymorphism at the intraspecific level was found for the presence/absence and/or abundance of some satDNAs, suggesting the amplification/deletion of these satDNAs following geographic separation or during culture maintenance of the strains. We also discuss how these results contribute to the understanding of chromosome architecture and evolution of dinoflagellate genomes | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Alexandrium | |
| 650 | 4 | |a FISH | |
| 650 | 4 | |a RepeatExplorer | |
| 650 | 4 | |a Repetitive DNA | |
| 650 | 4 | |a Satellite DNA | |
| 650 | 4 | |a Satellitome | |
| 650 | 7 | |a DNA, Satellite |2 NLM | |
| 650 | 7 | |a DNA, Ribosomal |2 NLM | |
| 700 | 1 | |a Montiel, Eugenia E |e verfasserin |4 aut | |
| 700 | 1 | |a Mora, Pablo |e verfasserin |4 aut | |
| 700 | 1 | |a Figueroa, Rosa I |e verfasserin |4 aut | |
| 700 | 1 | |a Lorite, Pedro |e verfasserin |4 aut | |
| 700 | 1 | |a de Bustos, Alfredo |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Harmful algae |d 2004 |g 130(2023) vom: 07. Dez., Seite 102543 |w (DE-627)NLM179163892 |x 1878-1470 |7 nnns |
| 773 | 1 | 8 | |g volume:130 |g year:2023 |g day:07 |g month:12 |g pages:102543 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1016/j.hal.2023.102543 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 130 |j 2023 |b 07 |c 12 |h 102543 | ||