Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids

Published on May 13, 2021in National Science Review17.275
· DOI :10.1093/NSR/NWAA277
Ying Wu12
Estimated H-index: 12
(WSU: Washington State University),
Fan Lin7
Estimated H-index: 7
+ 14 AuthorsBao Liu57
Estimated H-index: 57
(Ministry of Education)
Sources
Abstract
References89
Newest
#1Annaliese S. Mason (University of Giessen)H-Index: 30
#2Jonathan F. Wendel (Iowa State University)H-Index: 105
Polyploidy is a major force in plant evolution and speciation. In newly formed allopolyploids, pairing between related chromosomes from different subgenomes (homoeologous chromosomes) during meiosis is common. The initial stages of allopolyploid formation are characterized by a spectrum of saltational genomic and regulatory alterations that are responsible for evolutionary novelty. Here we highlight the possible effects and roles of recombination between homoeologous chromosomes during the early...
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#1Yohei Koide (Hokkaido University)H-Index: 9
#2Daichi Kuniyoshi (Hokkaido University)H-Index: 2
Last. Yuji Kishima (Hokkaido University)H-Index: 19
view all 3 authors...
Ploidy manipulation is an efficient technique for the development of novel phenotypes in plant breeding. However, in rice (Oryza sativa L.), severe seed sterility has been considered a barrier preventing cultivation of autotetraploids since the 1930s. Recently, a series of studies identified two fertile autotetraploids, identified herein as the PMeS (Polyploid Meiosis Stability) and Neo-Tetraploid lines. Here, we summarize their characteristics, focusing on the recovery of seed fertility, and di...
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#1Jonathan P. Spoelhof (UF: University of Florida)H-Index: 3
#2Rachel M. Keeffe (UF: University of Florida)H-Index: 4
Last. Stuart F. McDaniel (UF: University of Florida)H-Index: 10
view all 3 authors...
: A broad difference in the frequencies of plant and animal polyploidy (whole-genome duplication, WGD) has been recognized since the early 20th century (e.g., Gates, 1924; Dobzhansky, 1937; Stebbins, 1950), and is generally supported by numerous studies of plant and animal karyotypes, genome sizes, and phylogenies (Otto & Whitton, 2000; Gregory & Mable, 2005).
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#1Zhibin Zhang (Weizmann Institute of Science)H-Index: 9
#2Xiaowan Gou (Jiangsu Normal University)H-Index: 7
Last. Avraham A. Levy (Weizmann Institute of Science)H-Index: 55
view all 11 authors...
Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence anal...
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#1Jing Luo (Yunnan University)H-Index: 14
#2Jing Chai (KIZ: Kunming Institute of Zoology)H-Index: 6
Last. Shengnan Li (Hunan Normal University)H-Index: 4
view all 39 authors...
A persistent enigma is the rarity of polyploidy in animals, compared to its prevalence in plants. Although animal polyploids are thought to experience deleterious genomic chaos during initial polyploidization and subsequent rediploidization processes, this hypothesis has not been tested. We provide an improved reference-quality de novo genome for allotetraploid goldfish whose origin dates to ~15 million years ago. Comprehensive analyses identify changes in subgenomic evolution from asymmetrical ...
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#1Zoé Joly-Lopez (NYU: New York University)H-Index: 11
#2Adrian E. Platts (NYU: New York University)H-Index: 20
Last. Michael D. Purugganan (NYU: New York University)H-Index: 74
view all 8 authors...
The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibil...
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#1Xiaoyu Liu (YZU: Yangzhou University)H-Index: 2
#2Shang Sun (YZU: Yangzhou University)H-Index: 1
Last. Zhiyun Gong (YZU: Yangzhou University)H-Index: 15
view all 12 authors...
: Fluorescence in situ hybridization using probes based on oligonucleotides (oligo-FISH) is a useful tool for chromosome identification and karyotype analysis. Here we developed two oligo-FISH probes that allow the identification of each of the 12 pairs of chromosomes in rice (Oryza sativa). These two probes comprised 25 717 (green) and 25 215 (red) oligos (45 nucleotides), respectively, and generated 26 distinct FISH signals that can be used as a barcode to uniquely label each of the 12 pairs o...
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#1Anthony E. Baniaga (UA: University of Arizona)H-Index: 5
#2Hannah E. Marx (UM: University of Michigan)H-Index: 9
Last. Michael S. Barker (UA: University of Arizona)H-Index: 36
view all 4 authors...
Polyploid speciation entails substantial and rapid postzygotic reproductive isolation of nascent species that are initially sympatric with one or both parents. Despite strong postzygotic isolation, ecological niche differentiation has long been thought to be important for polyploid success. Using biogeographic data from across vascular plants, we tested whether the climatic niches of polyploid species are more differentiated than their diploid relatives and if the climatic niches of polyploid sp...
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#1Xiao Liu (SJTU: Shanghai Jiao Tong University)H-Index: 2
#2Weichen Song (SJTU: Shanghai Jiao Tong University)H-Index: 4
Last. Xianting Ding (SJTU: Shanghai Jiao Tong University)H-Index: 20
view all 7 authors...
With the expanding applications of mass cytometry in medical research, a wide variety of clustering methods, both semi-supervised and unsupervised, have been developed for data analysis. Selecting the optimal clustering method can accelerate the identification of meaningful cell populations. To address this issue, we compared three classes of performance measures, “precision” as external evaluation, “coherence” as internal evaluation, and stability, of nine methods based on six independent bench...
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#1Anna Runemark (Lund University)H-Index: 15
#2Mario Vallejo-Marín (University of Stirling)H-Index: 29
Last. Joana I. Meier (University of Cambridge)H-Index: 16
view all 3 authors...
Interspecific hybridization is the process where closely related species mate and produce offspring with admixed genomes. The genomic revolution has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive and reproduce, enabling the transfer of adaptive variants across the species boundary, and even result in the formation of novel evolutionary lineages. ...
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Cited By6
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#1Robin Burns (Austrian Academy of Sciences)H-Index: 3
#2Terezie Mandáková (Central European Institute of Technology)H-Index: 28
Last. Magnus Nordborg (Austrian Academy of Sciences)H-Index: 74
view all 8 authors...
Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of ‘genome shock’, such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemente...
Source
#1Yue Sun (Northeast Normal University)H-Index: 5
#2Ying Wu (Northeast Normal University)H-Index: 12
Last. Bao Liu (Northeast Normal University)H-Index: 57
view all 13 authors...
Whether merger of two divergent genomes by hybridization at the homoploid level or coupled with WGD (allopolyploidy) can bestow plants better tolerance to stress conditions remains understudied. In this study, two diploid rice (Oryza sativa L.) subspecies, japonica, and indica, their reciprocal F1 hybrids and segmental allotetraploids were compared for phenotypic performance and gene expression under normal and nitrogen (N)-deficient conditions. We found that F1 hybrids and tetraploids showed hi...
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#1Xiue Wang (NAU: Nanjing Agricultural University)H-Index: 24
Source
#1Joel Sharbrough (New Mexico Institute of Mining and Technology)H-Index: 9
#2Justin L. Conover (Iowa State University)H-Index: 9
Last. Daniel B. Sloan (CSU: Colorado State University)H-Index: 39
view all 7 authors...
Whole-genome duplications (WGDs), in which the number of nuclear genome copies is elevated as a result of autopolyploidy or allopolyploidy, are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes upon cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend upon successful interaction between the 3000+ nuclear-en...
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