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Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus)

Several whole genome duplication (WGD) events followed by rediploidization took place in the evolutionary history of vertebrates. Acipenserids represent a convenient model group for investigation of the consequences of WGD as their representatives underwent additional WGD events in different lineage...

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Autores principales: Andreyushkova, Daria A., Makunin, Alexey I., Beklemisheva, Violetta R., Romanenko, Svetlana A., Druzhkova, Anna S., Biltueva, Larisa S., Serdyukova, Natalya A., Graphodatsky, Alexander S., Trifonov, Vladimir A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704231/
https://www.ncbi.nlm.nih.gov/pubmed/29125582
http://dx.doi.org/10.3390/genes8110318
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author Andreyushkova, Daria A.
Makunin, Alexey I.
Beklemisheva, Violetta R.
Romanenko, Svetlana A.
Druzhkova, Anna S.
Biltueva, Larisa S.
Serdyukova, Natalya A.
Graphodatsky, Alexander S.
Trifonov, Vladimir A.
author_facet Andreyushkova, Daria A.
Makunin, Alexey I.
Beklemisheva, Violetta R.
Romanenko, Svetlana A.
Druzhkova, Anna S.
Biltueva, Larisa S.
Serdyukova, Natalya A.
Graphodatsky, Alexander S.
Trifonov, Vladimir A.
author_sort Andreyushkova, Daria A.
collection PubMed
description Several whole genome duplication (WGD) events followed by rediploidization took place in the evolutionary history of vertebrates. Acipenserids represent a convenient model group for investigation of the consequences of WGD as their representatives underwent additional WGD events in different lineages resulting in ploidy level variation between species, and these processes are still ongoing. Earlier, we obtained a set of sterlet (Acipenser ruthenus) chromosome-specific libraries by microdissection and revealed that they painted two or four pairs of whole sterlet chromosomes, as well as additional chromosomal regions, depending on rediploidization status and chromosomal rearrangements after genome duplication. In this study, we employed next generation sequencing to estimate the content of libraries derived from different paralogous chromosomes of sterlet. For this purpose, we aligned the obtained reads to the spotted gar (Lepisosteus oculatus) reference genome to reveal syntenic regions between these two species having diverged 360 Mya. We also showed that the approach is effective for synteny prediction at various evolutionary distances and allows one to clearly distinguish paralogous chromosomes in polyploid genomes. We postulated that after the acipenserid-specific WGD sterlet karyotype underwent multiple interchromosomal rearrangements, but different chromosomes were involved in this process unequally.
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spelling pubmed-57042312017-11-30 Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus) Andreyushkova, Daria A. Makunin, Alexey I. Beklemisheva, Violetta R. Romanenko, Svetlana A. Druzhkova, Anna S. Biltueva, Larisa S. Serdyukova, Natalya A. Graphodatsky, Alexander S. Trifonov, Vladimir A. Genes (Basel) Article Several whole genome duplication (WGD) events followed by rediploidization took place in the evolutionary history of vertebrates. Acipenserids represent a convenient model group for investigation of the consequences of WGD as their representatives underwent additional WGD events in different lineages resulting in ploidy level variation between species, and these processes are still ongoing. Earlier, we obtained a set of sterlet (Acipenser ruthenus) chromosome-specific libraries by microdissection and revealed that they painted two or four pairs of whole sterlet chromosomes, as well as additional chromosomal regions, depending on rediploidization status and chromosomal rearrangements after genome duplication. In this study, we employed next generation sequencing to estimate the content of libraries derived from different paralogous chromosomes of sterlet. For this purpose, we aligned the obtained reads to the spotted gar (Lepisosteus oculatus) reference genome to reveal syntenic regions between these two species having diverged 360 Mya. We also showed that the approach is effective for synteny prediction at various evolutionary distances and allows one to clearly distinguish paralogous chromosomes in polyploid genomes. We postulated that after the acipenserid-specific WGD sterlet karyotype underwent multiple interchromosomal rearrangements, but different chromosomes were involved in this process unequally. MDPI 2017-11-10 /pmc/articles/PMC5704231/ /pubmed/29125582 http://dx.doi.org/10.3390/genes8110318 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Andreyushkova, Daria A.
Makunin, Alexey I.
Beklemisheva, Violetta R.
Romanenko, Svetlana A.
Druzhkova, Anna S.
Biltueva, Larisa S.
Serdyukova, Natalya A.
Graphodatsky, Alexander S.
Trifonov, Vladimir A.
Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus)
title Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus)
title_full Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus)
title_fullStr Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus)
title_full_unstemmed Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus)
title_short Next Generation Sequencing of Chromosome-Specific Libraries Sheds Light on Genome Evolution in Paleotetraploid Sterlet (Acipenser ruthenus)
title_sort next generation sequencing of chromosome-specific libraries sheds light on genome evolution in paleotetraploid sterlet (acipenser ruthenus)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704231/
https://www.ncbi.nlm.nih.gov/pubmed/29125582
http://dx.doi.org/10.3390/genes8110318
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