A5101942034- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- Plant biochemistry and biosynthesis
- Peanut Plant Research Studies
- Photosynthetic Processes and Mechanisms
- Plant tissue culture and regeneration
- Plant Molecular Biology Research
- Legume Nitrogen Fixing Symbiosis
- Fern and Epiphyte Biology
- Plant Disease Resistance and Genetics
- CRISPR and Genetic Engineering
- Plant Diversity and Evolution
- Plant Reproductive Biology
- Plant-Microbe Interactions and Immunity
- Advances in Cucurbitaceae Research
- Lipid metabolism and biosynthesis
- Wheat and Barley Genetics and Pathology
- Plant nutrient uptake and metabolism
- Phytochemical compounds biological activities
- Soybean genetics and cultivation
- Identification and Quantification in Food
North China University of Science and Technology
2016-2022
Mainly due to their economic importance, genomes of 10 legumes, including soybean (Glycine max), wild peanut (Arachis duranensis and Arachis ipaensis), barrel medic (Medicago truncatula), have been sequenced. However, a family-level comparative genomics analysis has unavailable. With grape (Vitis vinifera) selected legume as outgroups, we managed perform hierarchical event-related alignment these deconvoluted layers homologous regions produced by ancestral polyploidizations or speciations....
Cucurbitaceae plants are of considerable biological and economic importance, genomes cucumber, watermelon, melon have been sequenced. However, a comparative genomics exploration their genome structures evolution has not available. Here, we aimed at performing hierarchical inference genomic homology resulted from recursive paleopolyploidizations. Unexpectedly, found that, shortly after core-eudicot-common hexaploidy, cucurbit-common tetraploidization (CCT) occurred, overlooked by previous...
Cold stress profoundly affects plant growth and development is a key factor affecting the geographic distribution evolution of plants. Plants have evolved adaptive mechanisms to cope with cold stress. Here, through genomic analysis Arabidopsis, three Brassica species 17 other representative species, we found that both cold-related genes (CRGs) their collinearity were preferentially retained after polyploidization followed by genome instability, while genome-wide gene sets exhibited variety...
The genome of kiwifruit (Actinidia chinensis) was sequenced previously, the first in Actinidiaceae family. It shown to have been affected by polyploidization events, nature which has elusive. Here, we performed a reanalysis and found clear evidence 2 tetraploidization with one occurring ∼50-57 million years ago (Mya) other ∼18-20 Mya. Two subgenomes produced each event under balanced fractionation. Moreover, genes were revealed express way between duplicated copies chromosomes. Besides,...
Polyploidy has contributed to the divergence and domestication of plants; however, estimation relative roles that different types polyploidy have played during evolution been difficult. Unbalanced balanced gene removal was previously related allopolyploidies autopolyploidies, respectively. Here, infer polyploidies evaluate their evolutionary effects, we devised a statistic, Polyploidy-index or P-index, characterize degree between subgenomes polyploidy, find whether there unbalanced from...
As a model plant to study perennial trees in the Salicaceae family, genome of poplar was sequenced, revealing recurrent paleo-polyploidizations during its evolution. A comparative and hierarchical alignment well-selected reference would help understand structure gene family Here, by adopting relatively simpler grape as reference, inferring intra- inter-genomic colinearity, we produced united two genomes, hierarchically distinguished layers paralogous orthologous genes, related recursive...
Abstract Lycophytes and seed plants constitute the typical vascular plants. have been thought to no paleo-polyploidization although event is known be critical for fast expansion of Here, genomic analyses including homologous gene dot plot analysis detected multiple events, with one occurring approximately 13–15 million years ago (MYA) another about 125–142 MYA, during evolution genome Selaginella moellendorffii, a model lycophyte. In addition, comparative reconstructed ancestral genomes...
Rice is one of the most researched model plant, and has a genome structure resembling that grass common ancestor after tetraploidization ∼100 million years ago. There been standing controversy whether there had five or seven basic chromosomes, before tetraploidization, which were tackled but could not be well solved for lacking sequenced assembled outgroup plant to have conservative structure. Recently, availability pineapple genome, subjected grass-common provides precious opportunity solve...
Abstract Background Duplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes Asian cultivated rice Oryza sativa ssp. indica (XI) japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing conversion events their impact on genome evolution. Results Using comparative genomics phylogenetic analyses, we evaluated...
Grass genomes are complicated structures as they share a common tetraploidization, and particular have been further affected by extra polyploidizations. These events the following genomic re-patternings resulted in complex, interweaving gene homology both within genome, between genomes. Accurately deciphering structure of these plant would help us better understand their compositional functional evolution at multiple scales. Here, we build on our previous research performing hierarchical...
Owing to their nutritional and commercial values, the genomes of several citrus plants have been sequenced, genome one close relative in Rutaceae family, atalantia (Atalantia buxifolia), has also sequenced. Here, we show a family-level comparative analysis genomes. By using grape as outgroup checking cross-genome gene collinearity, systematically performed hierarchical event-related alignment genomes, produced list defining homologous regions based on ancestral polyploidization or...
Chinese mahogany (Toona sinensis) is of considerable medical and economic importance, its genome has been deciphered. However, the process underlying polyploidy unclear, chromosomal evolutionary trajectory poorly understood. Here, by reanalysing T. sinensis genome, we found evidence a tetraploidization event (T. special tetraploidization, TST) that occurred approximately 15–17 million years ago (MYA) after core eudicot-common hexaploidization (ECH or gamma) event. We characterized synonymous...
The peanut (Arachis hypogaea L.) is the leading oil and food crop among legume family. Extensive duplicate gene pairs generated from recursive polyploidizations with high sequence similarity could result conversion, caused by illegitimate DNA recombination. Here, through synteny-based comparisons of two diploid three tetraploid genomes, we identified duplicated genes common tetraploidy (LCT) recent allo-tetraploidy (PRT) within genomes. In each genome (or subgenomes), inferred that 6.8-13.1%...
Abstract Seed plants and lycophytes constitute the extant vascular plants. As a model lycophyte, Selaginalla moellendroffii was deciphered its genome, previously proposed to have avoided polyploidies, as key events contributing origination fast expansion of seed Here, using gold-standard streamline recently deconvolute complex genomes, we reanalyzed S. genome. To our surprise, found clear evidence multiple paleo-polyploidies, with one being recent (~ 13-15 millions years ago or Mya), another...
Abstract Extensive sequence similarity between duplicated gene pairs produced by paleo-polyploidization may result from illegitimate recombination homologous chromosomes. The genomes of Asian cultivated rice Xian/ indica (XI) and Geng/ japonica (GJ) have recently been updated, providing new opportunities for investigating on-going conversion events. Using comparative genomics phylogenetic analyses, we evaluated rates genes polyploidization 100 million years ago (mya) in GJ XI. At least...
Abstract BackgroundPolyploidization creates duplicated sets of genomes in a plant. Dominance by subgenome is often observed polyploid species. Here, we studied the genomic regions soybean, which was affected tetraploidization 13 million years ago.ResultsBy referring to eudicot relatives, detailed that genes are retained balanced manner among homoeologs. Moreover, found colinearity extant genome expressed at balance. Notably, DNA methylation patterns shared similar levels three different...