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Article
| Open Access
Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Subgenome dominance is widely observed in allopolyploid species, but the molecular mechanisms remain unclear. Here, the authors generate genome-wide map of accessible chromatin regions (ACRs) in allo-octoploid cultivated strawberry and reveal that dynamics of the ACRs play an important role in its subgenome dominance.
- Chao Fang
- , Ning Jiang
- & Jiming Jiang
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Article
| Open Access
Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility
Self-incompatibility in diploid Arabidopsis relatives is determined by a dominance relationship that is epigenetically regulated. Using transgenic methods, this study demonstrates that the dominance relationship between subgenomes of the allopolyploid species Arabidopsis kamchatica underlies it’s self-compatibility.
- Chow-Lih Yew
- , Takashi Tsuchimatsu
- & Kentaro K. Shimizu
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Article
| Open Access
Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat
The direct impacts of transposable element dynamics on polyploid regulation and developmental specificity remain unclear. Here, the authors show that a large proportion of enhancer-like elements (ELEs) are mainly originated from RLG_famc7.3 specifically expanded in subgenome A, producing active nascent transcripts and influencing wheat spike development.
- Yilin Xie
- , Songbei Ying
- & Yijing Zhang
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Article
| Open Access
Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization
The occurrence and consequences of polyploidization in clonally reproducing animals is unclear. Here, the authors generate 4 polyploid Meloidogyne genomes, identifying a telomeric element, resolving genome structures and extensive chromosome fusion events, and revealing origin patterns.
- Dadong Dai
- , Chuanshuai Xie
- & Ming Sun
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Article
| Open Access
Nacα protects the larval fat body from cell death by maintaining cellular proteostasis in Drosophila
Protein homeostasis is crucial for maintaining cellular homeostasis. Here, the authors show that proteotoxic stress caused by Nacalpha mutants specifically and progressively induces cell death in the apoptosis-resistant Drosophila larval fat body.
- Takayuki Yamada
- , Yuto Yoshinari
- & Takashi Nishimura
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Article
| Open Access
Independent rediploidization masks shared whole genome duplication in the sturgeon-paddlefish ancestor
Whole genome duplication can generate new genes and support survival through mass extinctions. Here, the authors show that paddlefish and sturgeon shared a genome duplication event 200 million years ago that was previously unrecognised due to the mixed signals from independent rediploidisation.
- Anthony K. Redmond
- , Dearbhaile Casey
- & Aoife McLysaght
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Article
| Open Access
Unlocking the functional potential of polyploid yeasts
Domesticated industrial yeast strains are sterile, which hampers to breed strains with novel properties. Here, the authors employ the genetics paradigm return-to-growth to induce genome wide recombination in two sterile polyploid industrial yeasts and identify clones with superior biotechnological traits.
- Simone Mozzachiodi
- , Kristoffer Krogerus
- & Gianni Liti
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Article
| Open Access
Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution
Early vertebrate genomes were shaped by multiple whole-genome duplication (WGD) events of debated timings. Here the authors’ reconstruction of ancestral genomes using the probabilistic macrosynteny model supports a WGD shared by all vertebrates and a gnathostome-specific WGD, and reveals evidence of a cyclostome-specific genome triplication.
- Yoichiro Nakatani
- , Prashant Shingate
- & Byrappa Venkatesh
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Article
| Open Access
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
Existing plant pan-genomic studies usually report considerable intraspecific whole gene presence-absence variation. Here, the authors use pan-genomic approach to reveal gradual polyploid genome evolution by analyzing of Brachypodium hybridum and its diploid progenitors.
- Sean P. Gordon
- , Bruno Contreras-Moreira
- & John P. Vogel
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Article
| Open Access
Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation
Why transposable elements (TEs) accumulate in polyploids and the evolutionary implications remain unclear. Here, the authors show that following whole genome duplication, relaxed purifying selection is the main driver of TE over-accumulation, which provides variants for rapid local adaptation.
- Pierre Baduel
- , Leandro Quadrana
- & Vincent Colot
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Article
| Open Access
Interspecific introgression mediates adaptation to whole genome duplication
Whole genome duplication (WGD) presents new challenges to the establishment of optimal allelic combinations and to the meiotic machinery. Here, the authors show that adaptive gene flow from Arabidopsis arenosa could rescue the nascent A. lyrata from extinction following WGD.
- Sarah Marburger
- , Patrick Monnahan
- & Levi Yant
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Article
| Open Access
Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce
Genome assembly for many plant species can be challenging due to large size and high repeat content. Here, the authors usein vitroproximity ligation to assemble the genome of lettuce, revealing a family-specific triplication event and providing a comprehensive reference genome for a member of the Compositae.
- Sebastian Reyes-Chin-Wo
- , Zhiwen Wang
- & Richard W. Michelmore
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RUNX1-induced silencing of non-muscle myosin heavy chain IIB contributes to megakaryocyte polyploidization
Megakaryocytes undergo polyploidization prior to forming platelets but this process is poorly characterised. In this study, non-muscle myosin IIB heavy chain, that localizes to the contractile ring during mitosis, is shown to be silenced prior to polyploidization in a RUNX1-dependent manner.
- Larissa Lordier
- , Dominique Bluteau
- & Yunhua Chang
Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages