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Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum

BACKGROUND: Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. How...

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Autores principales: Xing, Longsheng, Wang, Meijia, He, Qiang, Zhang, Hongyu, Liang, Hanfei, Zhou, Qinghong, Liu, Yu, Liu, Ze, Wang, Yu, Du, Cailian, Xiao, Yao, Liu, Jianan, Li, Wei, Liu, Guixia, Du, Huilong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10362693/
https://www.ncbi.nlm.nih.gov/pubmed/37480118
http://dx.doi.org/10.1186/s12915-023-01643-w
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author Xing, Longsheng
Wang, Meijia
He, Qiang
Zhang, Hongyu
Liang, Hanfei
Zhou, Qinghong
Liu, Yu
Liu, Ze
Wang, Yu
Du, Cailian
Xiao, Yao
Liu, Jianan
Li, Wei
Liu, Guixia
Du, Huilong
author_facet Xing, Longsheng
Wang, Meijia
He, Qiang
Zhang, Hongyu
Liang, Hanfei
Zhou, Qinghong
Liu, Yu
Liu, Ze
Wang, Yu
Du, Cailian
Xiao, Yao
Liu, Jianan
Li, Wei
Liu, Guixia
Du, Huilong
author_sort Xing, Longsheng
collection PubMed
description BACKGROUND: Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation. RESULTS: Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum. CONCLUSIONS: Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-023-01643-w.
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spelling pubmed-103626932023-07-23 Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum Xing, Longsheng Wang, Meijia He, Qiang Zhang, Hongyu Liang, Hanfei Zhou, Qinghong Liu, Yu Liu, Ze Wang, Yu Du, Cailian Xiao, Yao Liu, Jianan Li, Wei Liu, Guixia Du, Huilong BMC Biol Research Article BACKGROUND: Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation. RESULTS: Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum. CONCLUSIONS: Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12915-023-01643-w. BioMed Central 2023-07-21 /pmc/articles/PMC10362693/ /pubmed/37480118 http://dx.doi.org/10.1186/s12915-023-01643-w Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Xing, Longsheng
Wang, Meijia
He, Qiang
Zhang, Hongyu
Liang, Hanfei
Zhou, Qinghong
Liu, Yu
Liu, Ze
Wang, Yu
Du, Cailian
Xiao, Yao
Liu, Jianan
Li, Wei
Liu, Guixia
Du, Huilong
Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum
title Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum
title_full Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum
title_fullStr Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum
title_full_unstemmed Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum
title_short Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum
title_sort differential subgenome expression underlies biomass accumulation in allotetraploid pennisetum giganteum
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10362693/
https://www.ncbi.nlm.nih.gov/pubmed/37480118
http://dx.doi.org/10.1186/s12915-023-01643-w
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