Xingtan Zhang
A5012608258- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Sugarcane Cultivation and Processing
- Plant Reproductive Biology
- Plant biochemistry and biosynthesis
- Biofuel production and bioconversion
- Genetic Mapping and Diversity in Plants and Animals
- Plant Molecular Biology Research
- Plant Gene Expression Analysis
- Plant and animal studies
- Plant Virus Research Studies
- Tea Polyphenols and Effects
- Financial Markets and Investment Strategies
- Plant Disease Resistance and Genetics
- Auction Theory and Applications
- Plant Pathogens and Fungal Diseases
- Genetic diversity and population structure
- Banana Cultivation and Research
- Plant nutrient uptake and metabolism
- Plant and Fungal Interactions Research
- Plant tissue culture and regeneration
- Plant and Fungal Species Descriptions
- Economic theories and models
- Papaya Research and Applications
- Plant Pathogenic Bacteria Studies
Agricultural Genomics Institute at Shenzhen
2020-2025
Chinese Academy of Agricultural Sciences
2020-2025
Chinese Academy of Tropical Agricultural Sciences
2025
Ministry of Agriculture and Rural Affairs
2022-2025
Huazhong Agricultural University
2025
Fujian Agriculture and Forestry University
2015-2024
University of Colorado Boulder
2016-2023
Guangxi University
2023
University of Nevada, Reno
2023
Fujian Normal University
2022
Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of spontaneum. Sequencing a haploid S. spontaneum, AP85-441, facilitated the assembly 32 pseudo-chromosomes comprising 8 homologous groups 4 members each, bearing 35,525 genes alleles defined. The reduction basic chromosome number 10 to in spontaneum was caused by fissions 2 ancestral chromosomes followed translocations chromosomes....
High oil and protein content make tetraploid peanut a leading food legume. Here we report high-quality genome sequence, comprising 2.54 Gb with 20 pseudomolecules 83,709 protein-coding gene models. We characterize functional groups implicated in seed size evolution, content, disease resistance symbiotic nitrogen fixation. The B subgenome has more genes general expression dominance, temporally associated long-terminal-repeat expansion the A that also raises questions about A-genome...
Abstract The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides independent line evidence, a combination multiple maps can improve the accuracy resulting chromosomal assemblies. We present ALLMAPS, method capable computing scaffold maximizes colinearity across collection maps. ALLMAPS robust against common errors, generates sequences are...
Abstract Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form so-called ANA-grade of angiosperms, which are extant representatives lineages that diverged earliest from lineage leading mesangiosperms 1–3 . Here we report 409-megabase genome sequence blue-petal water lily ( Nymphaea colorata ). Our phylogenomic analyses support Amborellales as successive sister all other angiosperms. The N. 19 transcriptomes reveal a Nymphaealean...
Abstract Tea is an important global beverage crop and largely clonally propagated. Despite previous studies on the species, its genetic evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of Oolong tea cultivar, Tieguanyin. Analysis allele-specific expression suggests potential mechanism in response to mutation load during long-term clonal propagation. Population genomic analysis using 190 Camellia accessions uncovered independent histories parallel...
Abstract Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar ‘Feizixiao’ was assembled into 15 pseudochromosomes, totaling ~470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total 13,517 allelic genes (42.4%) were differentially expressed diverse tissues. Analyses 72 resequenced lychee accessions revealed independent domestication events. extremely early maturing cultivars preferentially aligned to one haplotype domesticated...
Tea plants (Camellia sinensis) are commercially cultivated in >60 countries, and their fresh leaves processed into tea, which is the most widely consumed beverage world. Although several chromosome-level tea plant genomes have been published, they collapsed two haplotypes ignored a large number of allelic variations that may underlie important biological functions this species. Here, we present phased chromosome-scale assembly for an elite oolong cultivar, "Huangdan", well known its high...
Abstract Chrysanthemum ( morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum challenging due to its complex genetic background. Here, we report near-complete assembly annotation for C. comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative evolutionary analyses reveal whole-genome triplication (WGT) event shared by species approximately 6 million years ago (Mya) the...
Abstract The life cycle of genome builds spans interlocking pillars assembly, annotation, and comparative genomics to drive biological insights. While tools exist address each pillar separately, there is a growing need for integrate different project holistically. For example, approaches can provide quality control assembly or annotation; in turn, help identify artifacts that may complicate the interpretation comparisons. JCVI library versatile Python‐based offers suite excel across these...
Abstract To date, little is known about the evolution of fern genomes, with only two small genomes published from heterosporous Salviniales. Here we assembled genome Alsophila spinulosa , as flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation synteny, despite resulting an ancient whole-genome duplication over 100 million years ago, unprecedented in plants and probably speaks to uniqueness ferns. Our detailed investigations into stem anatomy lignin...
Abstract Sugarcane is a vital crop with significant economic and industrial value. However, the cultivated sugarcane’s ultra-complex genome still needs to be resolved due its high ploidy extensive recombination between two subgenomes. Here, we generate chromosomal-scale, haplotype-resolved assembly for hybrid sugarcane cultivar ZZ1. This contains 10.4 Gb genomic sequences 68,509 annotated genes defined alleles in sub-genomes distributed 99 original 15 recombined chromosomes. RNA-seq data...
ABSTRACT Background Sugarcane cultivars are polyploid interspecific hybrids of giant genomes, typically with 10–13 sets chromosomes from 2 Saccharum species. The ploidy, hybridity, and size the genome, estimated to have >10 Gb, pose a challenge for sequencing. Results Here we present gene space assembly SP80-3280, including 373,869 putative genes their potential regulatory regions. alignment single-copy in diploid grasses indicates that could resolve 2–6 (up 15) homo(eo)logs 99.1%...
The ripening of papaya is a physiological and metabolic process associated with accumulation carotenoids, alternation flesh color flavor, which depending on genotype external factors such as light hormone. Transcription regulating carotenoid biosynthesis have not been analyzed during fruit ripening. RNA-Seq experiments were implemented using different stages from two varieties. Cis-elements in lycopene β-cyclase genes (CpCYC-B CpLCY-B) identified, followed by genome-wide analysis to identify...
Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial solitary life-cycle phases, some social parasite species, they especially interesting models to understand evolution, behavior, ecology. Reports many species decline point pathogen transmission, habitat loss, pesticide usage, global climate change, as interconnected causes. These threats bumblebee diversity make our reliance on handful well-studied...
Abstract Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison genomes CB5, F153 MD2 elucidated genomic basis fiber production, color formation, sugar accumulation fruit maturation. also resequenced 89 genomes. Cultivars ‘Smooth Cayenne’ ‘Queen’ exhibited ancient recent admixture, while...
Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which well known for its high oil production. Here, we report high-quality genome assembly of typical semi-winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using combination single-molecule sequencing and chromosome conformation capture (Hi-C) techniques. Most the high-confidence sequences (93.1%) were anchored to individual chromosomes with total 19 centromeres identified, matching exact count B. napus. The repeat in...
Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% contigs into 50 pseudochromosomes. Comparative genomics enabled us disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative variants 16 wild crucian carp revealed origin identified genomic regions shaped by sweeps linked its domestication. Our...