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Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

BACKGROUND: Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large a...

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Autores principales: Guo, Baocheng, Zou, Ming, Gan, Xiaoni, He, Shunping
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996927/
https://www.ncbi.nlm.nih.gov/pubmed/20569428
http://dx.doi.org/10.1186/1471-2164-11-396
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author Guo, Baocheng
Zou, Ming
Gan, Xiaoni
He, Shunping
author_facet Guo, Baocheng
Zou, Ming
Gan, Xiaoni
He, Shunping
author_sort Guo, Baocheng
collection PubMed
description BACKGROUND: Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. RESULTS: Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which is higher than that in the T. rubripes genome (6.89%) and that in the Te. nigroviridis genome (4.66%). In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced D. holocanthus genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in D. holocanthus genome increased to 10.6% compared with T. rubripes and increased to 9.19% compared with Te. nigroviridis. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in D. holocanthus genome is significantly longer than that in the smooth pufferfish genome (435 bp). CONCLUSION: Compared with the smooth pufferfish, D. holocanthus has a low gene density and repeat elements rich genome. Genome size variation between D. holocanthus and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non-homologous sequences. The length difference of intron is consistent with the genome size variation between D. holocanthus and the smooth pufferfish. Different transposable element accumulation is responsible for genome size variation between D. holocanthus and the smooth pufferfish.
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spelling pubmed-29969272010-12-07 Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing Guo, Baocheng Zou, Ming Gan, Xiaoni He, Shunping BMC Genomics Research Article BACKGROUND: Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. RESULTS: Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which is higher than that in the T. rubripes genome (6.89%) and that in the Te. nigroviridis genome (4.66%). In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced D. holocanthus genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in D. holocanthus genome increased to 10.6% compared with T. rubripes and increased to 9.19% compared with Te. nigroviridis. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in D. holocanthus genome is significantly longer than that in the smooth pufferfish genome (435 bp). CONCLUSION: Compared with the smooth pufferfish, D. holocanthus has a low gene density and repeat elements rich genome. Genome size variation between D. holocanthus and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non-homologous sequences. The length difference of intron is consistent with the genome size variation between D. holocanthus and the smooth pufferfish. Different transposable element accumulation is responsible for genome size variation between D. holocanthus and the smooth pufferfish. BioMed Central 2010-06-23 /pmc/articles/PMC2996927/ /pubmed/20569428 http://dx.doi.org/10.1186/1471-2164-11-396 Text en Copyright ©2010 Guo et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Guo, Baocheng
Zou, Ming
Gan, Xiaoni
He, Shunping
Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing
title Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing
title_full Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing
title_fullStr Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing
title_full_unstemmed Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing
title_short Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing
title_sort genome size evolution in pufferfish: an insight from bac clone-based diodon holocanthus genome sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996927/
https://www.ncbi.nlm.nih.gov/pubmed/20569428
http://dx.doi.org/10.1186/1471-2164-11-396
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