Jie Qiu

Jie Qiu
Shanghai Normal University | SHNU

PhD

About

73
Publications
18,822
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Publications

Publications (73)
Article
Full-text available
De-domestication is a unique evolutionary process by which domesticated crops are converted into 'wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four rep...
Article
Full-text available
Barnyardgrass (Echinochloa crus-galli) is a pernicious weed in agricultural fields worldwide. The molecular mechanisms underlying its success in the absence of human intervention are presently unknown. Here we report a draft genome sequence of the hexaploid species E. crus-galli, i.e., a 1.27 Gb assembly representing 90.7% of the predicted genome s...
Article
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Background: Worldwide feralization of crop species into agricultural weeds threatens global food security. Weedy rice is a feral form of rice that infests paddies worldwide and aggressively outcompetes cultivated varieties. Despite increasing attention in recent years, a comprehensive understanding of the origins of weedy crop relatives and how a...
Article
Full-text available
Extensive allelic variation in agronomically important genes serves as the basis of rice breeding. Here, we present a comprehensive map of rice quantitative trait nucleotides (QTNs) and inferred QTN effects based on eight genome-wide association study cohorts. Population genetic analyses revealed that domestication, local adaptation and heterosis a...
Article
Full-text available
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology...
Article
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Nitrate allocation in Arabidopsis (Arabidopsis thaliana) represents an important mechanism for mediating plant environmental adaptation. However, whether this mechanism occurs or has any physiological/agronomic importance in the ammoniphilic plant rice (Oriza sativa L.) remains unknown. Here, we address this question through functional characteriza...
Article
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As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and...
Article
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Deleterious mutations can reduce the fitness of crop varieties, which limits the plant breeding efficacy. While crop deleterious mutations have been extensively examined, most studies focused on one specific crop with different analyzing methods, which hinders unveiling shared genomic characteristics of deleterious mutations across diverse crops. H...
Article
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Chinese wild rice ( Zizania latifolia ; family: Gramineae) is a valuable medicinal homologous grain in East and Southeast Asia. Here, using Nanopore sequencing and Hi-C scaffolding, we generated a 547.38 Mb chromosome-level genome assembly comprising 332 contigs and 164 scaffolds (contig N50 = 4.48 Mb; scaffold N50 = 32.79 Mb). The genome harbors 3...
Article
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Rye (Secale cereale) is an important crop with multi-usages and a valuable genetic resource for wheat breeding. However, due to its complex genome and outcrossing nature, the origin of cultivated rye remains elusive. Geneticist N. I. Vavilov proposed that cultivated rye was domesticated from weedy rye, rather than directly from wild species like ot...
Article
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Background Common walnut ( Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored. Results We report a comprehensive walnut genomic variation...
Article
Full-text available
Many important crops (e.g., tuber, root and tree crops) have the cross-pollination nature. In these crops, no inbred lines are available for genetic study and breeding due to self-incompatibility, clonal propagation way or long generation time, which makes the identifications of agronomically important genes difficult, particularly in crops with co...
Article
Full-text available
The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields, especially in rice paddies. Its evolutionary history is similar to that of bread wheat, arising through polyploidization after hybridization between a tetraploid and a diploid species. Here we generated and analyzed high quality genome sequences of dip...
Article
Chimonanthus salicifolius , a member of the Calycanthaceae of magnoliids, is one of the most famous medicinal plants in Eastern China. Here, we report a chromosome‐level genome assembly of C . salicifolius , comprising 820.1 Mb of genomic sequence with a contig N50 of 2.3 Mb and containing 36,651 annotated protein‐coding genes. Phylogenetic analyse...
Article
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Momilactones are bioactive diterpenoids that contribute to plant defense against pathogens and allelopathic interactions between plants. Both cultivated and wild grass species of Oryza and Echinochloa crus-galli (barnyard grass) produce momilactones using a biosynthetic gene cluster (BGC) in their genomes. The bryophyte Calohypnum plumiforme (forme...
Article
Alkaligrass (Puccinellia tenuiflora) is a monocotyledonous halophytic forage grass widely distributed in Northern China. It belongs to the Gramineae family and shares a close phylogenetic relationship with the cereal crops, wheat and barley. Here, we present a high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, Pac...
Article
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The common walnut Juglans regia and its related species in the genus Juglans are important economic trees, which have been widely grown for nut and wood productions in many counties. In the Juglans genus, there are ~21 diploid species all with 2n=32 chromosomes, which can be divided into four major sections based on phylogenetic analyses and fruit...
Article
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Main conclusion The study performed genome-wide identification, characterization and evolution analysis of gene clusters for phytoalexin terpenoid biosynthesis in tobacco, and specifically illustrated ones for capsidiol, an efficient defensive specialized metabolite. Abstract Terpenoid phytoalexins play an important role in plant self-defense agai...
Article
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Vavilovian mimicry is an evolutionary process by which weeds evolve to resemble domesticated crop plants and is thought to be the result of unintentional selection by humans. Unravelling its molecular mechanisms will extend our knowledge of mimicry and contribute to our understanding of the origin and evolution of agricultural weeds, an important...
Article
Full-text available
Rice (Oryza sativa L.) is one of the most important crops worldwide. Its relatives, including phylogenetically related species of rice and paddy weeds with a similar ecological niche, can provide crucial genetic resources (such as resistance to biotic and abiotic stresses and high photosynthetic efficiency) for rice research. Although many rice gen...
Article
Full-text available
Allelopathy is a central process in crop-weed interactions and is mediated by the release of allelochemicals that result in adverse growth effects on one or the other plant in the interaction. The genomic mechanism for the biosynthesis of many critical allelochemicals is unknown but may involve the clustering of non-homologous biosynthetic genes in...
Article
Full-text available
Allelopathy is a central process in crop–weed interactions and is mediated by the release of allelochemicals that result in adverse growth effects on one or the other plant in the interaction. The genomic mechanism for the biosynthesis of many critical allelochemicals is unknown but may involve the clustering of non-homologous biosynthetic genes in...
Article
In recent years, the application of Whole Genome Sequencing (WGS) on plants has generated sufficient data for the identification of trait-associated genomic loci or genes. A high-throughput genome-assisted QTL-seq strategy, combined with bulked-segregant analysis and WGS of two bulked populations from a segregating progeny with opposite phenotypic...
Article
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Brassica napus (AACC, 2n=38) is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic groups, such as European and Asian rapeseed, and the impacts of historical large‐scale introgression events on this young tetraploid. In this study, we r...
Data
Figure S1 The female and male tree of red bayberry used for sequencing and assembly. Figure S2 The distribution of 17‐mer depth of the female and male Illumina PE reads. Figure S3 The red bayberry genetic haploblock (HB) map constructed using RAD tag sequencing technology Figure S4 Genome wide Heatmap of the recombination frequencies for 406 hap...
Data
Table S3 The alignment results of two parents and their 95 progenies. Table S7 Classification of red bayberry repeat sequences. Table S11 Comparison of red bayberry transcription factors with other species in number observed per transcription factor class. Table S14 GO cluster/analysis for genes in M. rubra unique families. Table S15 Plant mate...
Article
Full-text available
Rice (Oryza sativa L.) is one of the most important crops worldwide. Its relatives, including phylogenetically related species of rice and paddy weeds with a similar ecological niche, can provide crucial genetic resources (such as resistance to biotic and abiotic stresses and high photosynthetic efficiency) for rice research. Although many rice gen...
Article
Drought resistance is required in rice breeding to address the challenge of frequent droughts. However, the evolution of rice drought resistance is not fully understood. We investigated the genetic differentiation between upland and lowland rice domesticated in agro-ecosystems of contrasting water-soil conditions by high-throughput SNPs. We estimat...
Article
Agronomically critical weeds that have evolved alongside crop species are characterized by rapid adaptation and invasiveness, which can result in an enormous reduction in annual crop yield worldwide. We discuss here recent genome-based research studies on agricultural weeds and crop–weed interactions that reveal several major evolutionary innovatio...
Preprint
Full-text available
Brassica napus (AACC, 2n=38), is an important oilseed crop grown worldwide. However, little is known about the population evolution of this species, the genomic difference between its major genetic clusters, such as European and Asian rapeseed, and impacts of historical large-sale introgression events in this young tetraploid. In this study, we rep...
Article
Full-text available
Maternal effects can substantially affect ecological and evolutionary processes in natural populations. However, as they often are environmentally induced, establishing their genetic basis is challenging. One important, but largely neglected, source of maternal effects are egg coats (i.e., the maternally derived extracellular matrix that surrounds...
Data
Supplemental information 2. Correlation between unigenes and acid tolerance.
Data
Supplemental information 3. SNPs differentiation between S and T populations.
Article
Full-text available
Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high‐quality genome for both a female and a male individual of red bayberry. The genome size was 313‐Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32,493 predicted genes. By whole genome comparison be...
Data
Functionally characterized genes in divergent genomic regions (Z(FST) ≥ 3) between weedy and cultivated rice.
Data
Genomic windows with high Z-transformed FST values (≥ 3) of weedy rice versus cultivated rice populations.
Data
Allele frequency differentiation (AFD) of standing and new SNPs for japonica and indica weedy rice, respectively.
Data
Non-synonymous SNPs with high allele frequency difference (>0.7) between weedy rice and cultivated rice
Data
Supplementary Figures and Supplementary Tables
Data
Genotyping and Tajima's D of OsEXPA3 by Sanger method.
Data
Demographic model parameters inferred for Chinese weedy rice.
Data
Genes with high positive Tajima's D values in the Mb-scale regions of chromosome 5 of Jiangsu weedy rice.
Data
GO enrichment terms for putative novel genes of weedy rice relative to cultivated rice.
Article
Full-text available
Variegated ‘Marble Queen’ (Epipremnum aureum) plant has white (VMW) and green (VMG) sectors within the same leaf. The white sector cells containing undifferentiated chloroplasts are viable, but the underlying mechanism for their survival and whether these white cells would use any metabolites as signal molecules to communicate with the nucleus for...
Article
Full-text available
Epipremnum aureum is an extremely popular houseplant belonging to the Araceae family of angiosperms, but it does not flower either in the wild or under cultivation. We uncovered the potential causes of its shy-flowering nature by building the transcriptome using next-generation sequencing and identifying floral-related genes that are differentially...
Article
Full-text available
The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenc...
Article
Full-text available
The interaction between non-coding endogenous target mimicry (eTM) and its corresponding miRNA is a newly discovered regulatory mechanism and plays pivotal roles in various biological processes in plants. Tobacco (Nicotiana tabacum) is a model plant for studying secondary metabolite alkaloids, of which nicotine accounts for ~90%. In this work, we i...
Article
Full-text available
Despite the importance of host-microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. The vegetable crop "Jiaobai" with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) appr...