Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations

Zhang, Ren-Gang; Shang, Hong-Yun; Jia, Kai-Hua; Ma, Yong-Peng

doi:10.1093/bib/bbad513

Cited by 3 publications

References 63 publications

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Unveiling allopolyploidization-driven genome duplications through progressive analysis of deep genome skimming data

Xie,

Lin,

Wang

et al. 2024

Preprint

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Whole-genome duplication (WGD) events are widespread across the Web of Life (WoL). Given the prevalence of WGDs in the polyploid Prunus (Rosaceae), this economically- and agriculturally-important angiosperm lineage provides an excellent model for exploring this mode of reticulation. We used the polyploid Prunus to demonstrate a progressive strategy for analyzing Deep Genome Skimming (DGS) data in the presence of WGDs. Phylogenomic discordance analyses indicated that allopolyploidization, rather than Incomplete Lineage Sorting (ILS), played a dominant role in the origin and dynamics of polyploid Prunus. This study underscores how a progressive strategy to identify WGD events at different depths in a phylogenetic tree reveals the nuances of evolutionary mechanisms driving allopolyploidization. We inferred that the continued uplift of the Himalayas from the Middle to Late Miocene drove the rapid diversification of the Eastern Asia endemic Maddenia clade, by facilitating frequent hybridization and allopolyploidization, specifically introgression between the Himalayas-Hengduan and the Central-Eastern China clades.

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Unveiling allopolyploidization-driven genome duplications through progressive analysis of deep genome skimming data

Xie,

Lin,

Wang

et al. 2024

Preprint

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Chromosome‐level genome assembly of a rare karst‐growing Rhododendron species provides insights into its evolution and environmental adaptation

Wen,

Cai,

Yang

et al. 2024

J of Systematics Evolution

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Rhododendron is a significant plant genus, with over 600 identified species in China. The subgenus Hymenanthes holds the largest number of Rhododendron germplasms and showcases strong environmental adaptability. However, there remains a lack of understanding regarding Rhododendron's evolution and environmental adaptations. Rhododendron bailiense Y.P.Ma, C.Q.Zhang & D.F.Chamb., an exceedingly rare species, thrives in the alkaline karst landforms of Guizhou, southwest China, different from the typical growing environment of other Rhododendron species. In this study, we present a chromosome‐level genome assembly of R. bailiense, revealing a genome size of 923.3 Mb, a contig N50 of 24.5 Mb, and a total of 47 567 predicted genes. An evolutionary analysis indicated that R. bailiense diverged from its ancestors prior to the other subgenus Hymenanthes rhododendrons, with the expanded and contracted genes being notably enriched in “stress response” and “growth,” respectively. Rhododendron bailiense is predominantly found on limestone soil in the mountains of Guizhou, with only two wild populations known. The genome of R. bailiense contained a high copy number of ankyrin repeat (ANK) and Ca2+‐ATPase (CAP) genes, primarily involved in Ca2+ transport, shedding light on how R. bailiense copes with karst high‐calcium stress. In contrast, the structures of the ANKs displayed unique characteristics, while the CAPs showed conservatism. The R. bailiense genome provides new insights into the adaptation and evolutionary history of Rhododendron plants in karst environments, potentially offering valuable information for adaptive breeding and ecological enhancement in such challenging settings.

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Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge—A Transcriptomics Perspective

Aufiero,

Fruggiero,

D’Angelo

et al. 2024

Genes

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Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.

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Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations

Cited by 3 publications

References 63 publications

Unveiling allopolyploidization-driven genome duplications through progressive analysis of deep genome skimming data

Unveiling allopolyploidization-driven genome duplications through progressive analysis of deep genome skimming data

Chromosome‐level genome assembly of a rare karst‐growing Rhododendron species provides insights into its evolution and environmental adaptation

Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge—A Transcriptomics Perspective

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