Cargando…
Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color
The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea br...
Autores principales: | , , , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9832866/ https://www.ncbi.nlm.nih.gov/pubmed/36643737 http://dx.doi.org/10.1093/hr/uhac241 |
_version_ | 1784868144386408448 |
---|---|
author | Nie, Shuai Zhao, Shi-Wei Shi, Tian-Le Zhao, Wei Zhang, Ren-Gang Tian, Xue-Chan Guo, Jing-Fang Yan, Xue-Mei Bao, Yu-Tao Li, Zhi-Chao Kong, Lei Ma, Hai-Yao Chen, Zhao-Yang Liu, Hui El-Kassaby, Yousry A Porth, Ilga Yang, Fu-Sheng Mao, Jian-Feng |
author_facet | Nie, Shuai Zhao, Shi-Wei Shi, Tian-Le Zhao, Wei Zhang, Ren-Gang Tian, Xue-Chan Guo, Jing-Fang Yan, Xue-Mei Bao, Yu-Tao Li, Zhi-Chao Kong, Lei Ma, Hai-Yao Chen, Zhao-Yang Liu, Hui El-Kassaby, Yousry A Porth, Ilga Yang, Fu-Sheng Mao, Jian-Feng |
author_sort | Nie, Shuai |
collection | PubMed |
description | The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding. |
format | Online Article Text |
id | pubmed-9832866 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-98328662023-01-12 Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color Nie, Shuai Zhao, Shi-Wei Shi, Tian-Le Zhao, Wei Zhang, Ren-Gang Tian, Xue-Chan Guo, Jing-Fang Yan, Xue-Mei Bao, Yu-Tao Li, Zhi-Chao Kong, Lei Ma, Hai-Yao Chen, Zhao-Yang Liu, Hui El-Kassaby, Yousry A Porth, Ilga Yang, Fu-Sheng Mao, Jian-Feng Hortic Res Article The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding. Oxford University Press 2022-10-26 /pmc/articles/PMC9832866/ /pubmed/36643737 http://dx.doi.org/10.1093/hr/uhac241 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Nanjing Agricultural University. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Article Nie, Shuai Zhao, Shi-Wei Shi, Tian-Le Zhao, Wei Zhang, Ren-Gang Tian, Xue-Chan Guo, Jing-Fang Yan, Xue-Mei Bao, Yu-Tao Li, Zhi-Chao Kong, Lei Ma, Hai-Yao Chen, Zhao-Yang Liu, Hui El-Kassaby, Yousry A Porth, Ilga Yang, Fu-Sheng Mao, Jian-Feng Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color |
title | Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color |
title_full | Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color |
title_fullStr | Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color |
title_full_unstemmed | Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color |
title_short | Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color |
title_sort | gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9832866/ https://www.ncbi.nlm.nih.gov/pubmed/36643737 http://dx.doi.org/10.1093/hr/uhac241 |
work_keys_str_mv | AT nieshuai gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT zhaoshiwei gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT shitianle gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT zhaowei gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT zhangrengang gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT tianxuechan gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT guojingfang gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT yanxuemei gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT baoyutao gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT lizhichao gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT konglei gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT mahaiyao gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT chenzhaoyang gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT liuhui gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT elkassabyyousrya gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT porthilga gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT yangfusheng gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor AT maojianfeng gaplessgenomeassemblyofazaleaandmultiomicsinvestigationintodivergencebetweentwospecieswithdistinctflowercolor |