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Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish
BACKGROUND: Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation following genomic merging or doubling is primarily derived from plants and is...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030793/ https://www.ncbi.nlm.nih.gov/pubmed/29969984 http://dx.doi.org/10.1186/s12864-018-4883-7 |
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author | Li, Wuhui Liu, Junmei Tan, Hui Luo, Lingling Cui, Jialin Hu, Jie Wang, Shi Liu, Qingfeng Hu, Fangzhou Tang, Chenchen Ren, Li Yang, Conghui Zhao, Rurong Tao, Min Zhang, Chun Qin, Qinbo Liu, Shaojun |
author_facet | Li, Wuhui Liu, Junmei Tan, Hui Luo, Lingling Cui, Jialin Hu, Jie Wang, Shi Liu, Qingfeng Hu, Fangzhou Tang, Chenchen Ren, Li Yang, Conghui Zhao, Rurong Tao, Min Zhang, Chun Qin, Qinbo Liu, Shaojun |
author_sort | Li, Wuhui |
collection | PubMed |
description | BACKGROUND: Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation following genomic merging or doubling is primarily derived from plants and is sparse for vertebrates. RESULTS: We successfully obtained an F1 generation (including allodiploid hybrids and triploid hybrids) from female Megalobrama amblycephala Yih (BSB, 2n = 48) × male Xenocypri davidi Bleeker (YB, 2n = 48). The duplicated-gene expression patterns of the two types of hybrids were explored using RNA-Seq data. In total, 5.44 × 10(8) (69.32 GB) clean reads and 499,631 assembled unigenes were obtained from the testis transcriptomes. The sequence similarity analysis of 4265 orthologs revealed that the merged genomes were dominantly expressed in different ploidy hybrids. The differentially expressed genes in the two types of hybrids were asymmetric compared with those in both parents. Furthermore, the genome-wide expression level dominance (ELD) was biased toward the maternal BSB genome in both the allodiploid and triploid hybrids. In addition, the dosage-compensation mechanisms that reduced the triploid expression levels to the diploid state were determined in the triploid hybrids. CONCLUSIONS: Our results indicate that divergent genomes undergo strong interactions and domination in allopolyploid offspring. Genomic merger has a greater effect on the gene-expression patterns than genomic doubling. The various expression mechanisms (including maternal effect and dosage compensation) in different ploidy hybrids suggest that the initial genomic merger and doubling play important roles in polyploidy adaptation and evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4883-7) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6030793 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-60307932018-07-09 Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish Li, Wuhui Liu, Junmei Tan, Hui Luo, Lingling Cui, Jialin Hu, Jie Wang, Shi Liu, Qingfeng Hu, Fangzhou Tang, Chenchen Ren, Li Yang, Conghui Zhao, Rurong Tao, Min Zhang, Chun Qin, Qinbo Liu, Shaojun BMC Genomics Research Article BACKGROUND: Hybridization and polyploidization are regarded as the major driving forces in plant speciation, diversification, and ecological adaptation. Our knowledge regarding the mechanisms of duplicated-gene regulation following genomic merging or doubling is primarily derived from plants and is sparse for vertebrates. RESULTS: We successfully obtained an F1 generation (including allodiploid hybrids and triploid hybrids) from female Megalobrama amblycephala Yih (BSB, 2n = 48) × male Xenocypri davidi Bleeker (YB, 2n = 48). The duplicated-gene expression patterns of the two types of hybrids were explored using RNA-Seq data. In total, 5.44 × 10(8) (69.32 GB) clean reads and 499,631 assembled unigenes were obtained from the testis transcriptomes. The sequence similarity analysis of 4265 orthologs revealed that the merged genomes were dominantly expressed in different ploidy hybrids. The differentially expressed genes in the two types of hybrids were asymmetric compared with those in both parents. Furthermore, the genome-wide expression level dominance (ELD) was biased toward the maternal BSB genome in both the allodiploid and triploid hybrids. In addition, the dosage-compensation mechanisms that reduced the triploid expression levels to the diploid state were determined in the triploid hybrids. CONCLUSIONS: Our results indicate that divergent genomes undergo strong interactions and domination in allopolyploid offspring. Genomic merger has a greater effect on the gene-expression patterns than genomic doubling. The various expression mechanisms (including maternal effect and dosage compensation) in different ploidy hybrids suggest that the initial genomic merger and doubling play important roles in polyploidy adaptation and evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4883-7) contains supplementary material, which is available to authorized users. BioMed Central 2018-07-03 /pmc/articles/PMC6030793/ /pubmed/29969984 http://dx.doi.org/10.1186/s12864-018-4883-7 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Li, Wuhui Liu, Junmei Tan, Hui Luo, Lingling Cui, Jialin Hu, Jie Wang, Shi Liu, Qingfeng Hu, Fangzhou Tang, Chenchen Ren, Li Yang, Conghui Zhao, Rurong Tao, Min Zhang, Chun Qin, Qinbo Liu, Shaojun Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish |
title | Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish |
title_full | Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish |
title_fullStr | Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish |
title_full_unstemmed | Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish |
title_short | Asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish |
title_sort | asymmetric expression patterns reveal a strong maternal effect and dosage compensation in polyploid hybrid fish |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030793/ https://www.ncbi.nlm.nih.gov/pubmed/29969984 http://dx.doi.org/10.1186/s12864-018-4883-7 |
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