A5002532164- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Plant Reproductive Biology
- Plant Disease Resistance and Genetics
- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Photosynthetic Processes and Mechanisms
- Plant Gene Expression Analysis
- Plant biochemistry and biosynthesis
- Plant Molecular Biology Research
- Plant Pathogens and Resistance
- Plant Virus Research Studies
- Plant tissue culture and regeneration
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Environmental DNA in Biodiversity Studies
- Genetic Syndromes and Imprinting
- Plant nutrient uptake and metabolism
- Genome Rearrangement Algorithms
- Evolution and Genetic Dynamics
- Plant and animal studies
- Postharvest Quality and Shelf Life Management
- Genomic variations and chromosomal abnormalities
- Plant Pathogens and Fungal Diseases
- Oil Palm Production and Sustainability
- GABA and Rice Research
Huazhong Agricultural University
2012-2025
Shanghai Zhangjiang Laboratory
2023-2025
Max Planck Institute for Plant Breeding Research
2015-2024
Urologische Klinik München
2021-2022
Ludwig-Maximilians-Universität München
2021-2022
Yijun Ruan and colleagues report the draft genome of sweet orange, Citrus sinensis. Their data suggests orange originated from a cross between pummelo mandarin. Oranges are an important nutritional source for human health have immense economic value. Here we present comprehensive analysis (Citrus sinensis). The assembled sequence covers 87.3% estimated genome, which is relatively compact, as 20% composed repetitive elements. We predicted 29,445 protein-coding genes, half in heterozygous...
Genomic differences range from single nucleotide to complex structural variations. Current methods typically annotate sequence ranging SNPs large indels accurately but do not unravel the full complexity of rearrangements, including inversions, translocations, and duplications, where highly similar changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions then...
Abstract Despite hundreds of sequenced Arabidopsis genomes, very little is known about the degree genomic collinearity within single species, due to low number chromosome-level assemblies. Here, we report reference-quality assemblies seven thaliana accessions selected across its global range. Each genome reveals between 13–17 Mb rearranged, and 5–6 non-reference sequences introducing copy-number changes in ~5000 genes, including ~1900 genes. Quantifying genomes ~350 euchromatic regions,...
Early stages of a beneficial relationship Plants benefit from widespread symbiosis with arbuscular mycorrhizal fungi. This between plant and fungus aids plants in capturing mineral micronutrients the soil. Gutjahr et al. have now identified component an intracellular receptor, hydrolase DWARF 14 LIKE, required rice roots for initiating symbiosis. A similar receptor detects karrikins smoke that signal opportunity fireweed to grow after forest fire. Science , this issue p. 1521
Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. japonica Despite the fact that accounts for over 70% total production worldwide is genetically much more diverse, a high-quality reference genome has yet to be published. We conducted map-based sequencing lines, Zhenshan 97 (ZS97) Minghui 63 (MH63), which represent major varietal groups subspecies are parents an elite Chinese hybrid. The sequences were assembled into 237 181 (MH63) contigs, with accuracy...
Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because usually do not recover complement large-scale rearrangements, including transpositions inversions. Besides availability hundreds genomes diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: reference sequence. We have 117 Mb A. Landsberg...
Abstract Potato is the most widely produced tuber crop worldwide. However, reconstructing four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing 717 pollen genomes and Hi-C data. Unexpectedly, ~50% was identical-by-descent due to recent inbreeding, which contrasted by highly abundant structural...
Long-read sequencing can overcome the weaknesses of short reads in assembly eukaryotic genomes; however, at present additional scaffolding is needed to achieve chromosome-level assemblies. We generated Pacific Biosciences (PacBio) long-read data genomes three relatives model plant Arabidopsis thaliana and assembled all into only a few hundred contigs. To improve contiguities these assemblies, we BioNano Genomics optical mapping Dovetail chromosome conformation capture for genome scaffolding....
Generating chromosome-level, haplotype-resolved assemblies of heterozygous genomes remains challenging. To address this, we developed gamete binning, a method based on single-cell sequencing haploid gametes enabling separation the whole-genome reads into haplotype-specific sets. After assembling each haplotype, contigs are scaffolded to chromosome level using genetic map derived from gametes. We assemble two diploid apricot tree 445 individual pollen grains. The haplotype (N50: 25.5 and 25.8...
Seedlessness is a most valuable trait in fruit crops for fresh consumption and processing. The mutations essential meiosis genes are known to confer sterility seed abortion plants. However, defects have rarely been reported crops. Here, we found caused seedless citrus bud sport cultivar, with massive unpaired univalents during diakinesis, indicating disruption crossover formation. A non-functional CrMER3A-103 bp allele 103-bp deletion the gene body, together other CrMER3a T exon, were...
Graph pangenome references can address single-reference bias, thereby enhancing the accuracy of variant genotyping and empowering downstream applications in population genetics quan-titative genetics. However, existing pangenome-based methods struggle with large or complex graphs, particularly polyploid genomes. Here, we introduce Varigraph, an algorithm that leverages comparison unique repetitive k-mers between sites short reads for both small variants. Varigraph outperforms current...
Sweet orange is cultivated worldwide but suffers from various devastating diseases because of its monogenetic background. The elucidation the origin a crop facilitates domestication new crops that may better cope with challenges. Here we collected and sequenced 226 citrus accessions assembled telomere-to-telomere phased diploid genomes sweet sour orange. On basis high-resolution haplotype-resolved genome analysis, inferred originated × mandarin cross confirmed this model using artificial...
P. serrula is widely distributed in Yunnan, Xizang, and Sichuan, usually grows at high altitudes between 2,600 3,900 meters above sea level. In this study, we obtained a high-quality chromosome-level assembly genome of using Illumina sequencing, Oxford Nanopore ultra-long Hi-C technology. The was 284.5 Mb length, with scaffold N50 32.4 91.9% the anchored onto 8 pseudochromosomes. BUSCO completeness value 98.5% demonstrated completed genome, total 35,151 protein-coding genes 47,340...
Abstract Innovations in DNA sequencing technologies have greatly boosted population-level genomic studies plants, facilitating the identification of key genetic variations for investigating population diversity and accelerating molecular breeding crops. Conventional methods analysis typically rely on small variants, such as SNPs indels, use single linear reference genomes, which introduces biases reduces performance highly divergent regions. By integrating level sequences, pangenomes,...
Abstract Background Although sequencing technologies have boosted the measurement of genomic diversity plant crops, it remains challenging to accurately genotype millions genetic variants, especially structural variations, with only short reads. In recent years, many graph-based variation genotyping methods been developed address this issue and tested for human genomes. However, their performance in genomes largely elusive. Furthermore, pipelines integrating advantages current might be...
Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit flow. When different copies of a duplicated are pseudofunctionalized in genotypes, incompatibilities can arise their hybrid offspring. such cases have been reported after manual crosses, it remains unclear whether occur nature how affect natural populations. Here, we identified four duplicated-gene based including one previously not within an artificial Arabidopsis...
Abstract Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and placenta mammals—tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes are implicated imprinting establishment, direct investigations impact de novo TE transposition on genomic remain scarce. In this study, we explored effects chemically induced Copia element...
Heterozyosity is an important feature of many plant genomes, and related to heterosis. Sweet orange, a highly heterozygous species, thought have originated from inter-species hybrid between pummelo mandarin. To investigate the heterozygosity sweet orange genome examine how this affects gene expression, we characterized Valencia for single nucleotide variations (SNVs), small insertions deletions (InDels) structural (SVs), determined their functional effects on protein-coding genes non-coding...
Abstract Tree peony belongs to one of the Saxifragales families, Paeoniaceae. It is most famous ornamental plants, and also a promising woody oil plant. Although two Paeoniaceae genomes have been released, their assembly qualities are still be improved. Additionally, more from wild peonies needed accelerate genomic-assisted breeding. Here we assemble high-quality chromosome-scale 10.3-Gb genome Tibetan tree peony, Paeonia ludlowii, which features substantial sequence divergence, including...
Abstract Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long‐term resilience of populations. Thus, we investigated within between pristine sites fossil floodplain compared to restored by hay transfer 1997 2014. RAD‐seq genotyping revealed that stenoecious species Arabis nemorensis co‐occurring with individuals that, based on ploidy, ITS‐sequencing morphology, probably belong close relative sagittata ,...