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学者姓名：刘仁义
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Abstract ：
The publication of several high-quality genomes has contributed greatly to clarifying the evolution of citrus. However, due to their complex genetic backgrounds, the origins and evolution of many citrus species remain unclear. We assembled de novo the 294-Mbp chromosome-level genome of a more than 200-year-old primitive papeda (DYC002). Comparison between the two sets of homologous chromosomes of the haplotype-resolved genome revealed 1.2% intragenomic variations, including 1.75 million SNPs, 149,471 insertions and 154,215 deletions. Using this genome as a reference, we resequenced and performed population and phylogenetic analyses of 378 representative citrus accessions. Our study confirmed that the primary origin center of core Citrus species is in South China, particularly in the Himalaya-Hengduan Mountains. Papeda species are an ancient Citrus type compared with C. ichangensis. We found that the evolution of the Citrus genus followed two radiations through two routes (to East China and Southeast Asia) along river systems. Evidence for the origin and evolution of some individual citrus species was provided. Papeda probably played an important role in the origins of Australian finger lime, citrons, Honghe papeda and pummelos; Ichang papeda originated from Yuanjiang city of Yunnan Province, China, and C. mangshanensis has a close relationship with kumquat and Ichang papeda. Moreover, the Hunan and Guangdong Provinces of China are predicted to be the origin center of mandarin, sweet orange and sour orange. Additionally, our study revealed that fruit bitterness was significantly selected against during citrus domestication. Taken together, this study provides new insight into the origin and evolution of citrus species and may serve as a valuable genomic resource for citrus breeding and improvement.
Keyword ：
citrus citrus domestication domestication evolution evolution haplotype-resolved genome haplotype-resolved genome papeda papeda
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| GB/T 7714 | Wang, Fusheng , Wang, Shaohua , Wu, Yilei et al. Haplotype-resolved genome of a papeda provides insights into the geographical origin and evolution of Citrus [J]. | JOURNAL OF INTEGRATIVE PLANT BIOLOGY , 2025 , 67 (2) : 276-293 . |
| MLA | Wang, Fusheng et al. "Haplotype-resolved genome of a papeda provides insights into the geographical origin and evolution of Citrus" . | JOURNAL OF INTEGRATIVE PLANT BIOLOGY 67 . 2 (2025) : 276-293 . |
| APA | Wang, Fusheng , Wang, Shaohua , Wu, Yilei , Jiang, Dong , Yi, Qian , Zhang, Manman et al. Haplotype-resolved genome of a papeda provides insights into the geographical origin and evolution of Citrus . | JOURNAL OF INTEGRATIVE PLANT BIOLOGY , 2025 , 67 (2) , 276-293 . |
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Simple Summary Balclutha incisa is a widespread leafhopper found in the fields of rice and other crops, whose feeding habits and potential for pathogen transmission pose a threat to crop production. However, there is limited information about the viruses that B. incisa may carry. In this study, we used deep sequencing technology to examine the virome of B. incisa and reported the complete genomes of four novel viruses using rapid amplification of cDNA ends (RACE). Among these, B. incisa ollusvirus 1 (linear) and B. incisa ollusvirus 2 (circular) both exhibit the typical G-N-L genome structure characteristic of the order Jingchuvirales. Additionally, we identified two other viruses, B. incisa iflavirus 1 and B. incisa totivirus 1. Phylogenetic and sequence identity analyses suggest that these viruses represent new members of their respective families. Our study provides valuable insights into the virome of B. incisa and identifies four new viruses that may be potentially harmful to crops.Abstract Balclutha incisa (Cicadellidae: Deltocephalinae), a leafhopper prevalent in tropical and temperate regions, is notably abundant in grasses and rice. The virome of B. incisa was investigated using deep transcriptome sequencing, leading to the first identification of four viruses belonging to the families Aliusviridae, Iflaviridae, and Totiviridae in B. incisa. These viruses have been provisionally named B. incisa ollusvirus 1 (BiOV1), B. incisa ollusvirus 2 (BiOV2), B. incisa iflavirus 1 (BiIV1), and B. incisa totivirus 1 (BiTV1). The complete genome sequences of these viruses were obtained through rapid amplification of cDNA ends (RACE). BiOV1 has a linear genome of 15,125 nucleotides (nt), while BiOV2 possesses a circular genome of 14,853 nt. The BiIV1 genome, excluding the poly(A) tail, is 10,903 nt in length and encodes a single open reading frame (ORF) for a polyprotein consisting of 3194 amino acids (aa). The BiTV1 genome is 4357 nt long and contains two overlapping ORFs, with the viral RNA-dependent RNA polymerase (RdRp) translated via a -1 ribosomal frameshift. Phylogenetic and sequence identity analyses suggest that all these viruses are novel members of their respective families. This study significantly expands our understanding of the virome associated with B. incisa by reporting and characterizing these novel viruses.
Keyword ：
Balclutha incisa Balclutha incisa iflavirus iflavirus novel viruses novel viruses ollusvirus ollusvirus totivirus totivirus
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| GB/T 7714 | Xiao, Jiajing , Yang, Guang , Liu, Renyi et al. Identification and Characterization of Four Novel Viruses in Balclutha incisa [J]. | INSECTS , 2024 , 15 (10) . |
| MLA | Xiao, Jiajing et al. "Identification and Characterization of Four Novel Viruses in Balclutha incisa" . | INSECTS 15 . 10 (2024) . |
| APA | Xiao, Jiajing , Yang, Guang , Liu, Renyi , Ge, Danfeng . Identification and Characterization of Four Novel Viruses in Balclutha incisa . | INSECTS , 2024 , 15 (10) . |
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Simple Summary: The homopteran insect, Pyrops candelaria (longan lanternfly), mainly harms longan trees, lychees, olives and other crops by absorbing the sap on the trunk. In this study, the reverse etiology method was used to find the pathogens carried by P. candelaria. Through RNA-seq, we found a new iflavirus in P. candelaria, which was first reported in P. candelaria, and we named it PyCaV (Pyrops candelaria associated virus). Identified by a pair of specific primers, it is worth noting that the presence of PyCaV can be identified in the head, chest and abdomen of P. candelaria, and that PyCaV infection rate of P. candelaria is affected by time and location. The above results provide new insights to reveal the role of P. candelaria as a potential vehicle for microbial pathogens and extend our understanding to iflavirus. Pyrops candelaria is one of the common pests of fruit trees, but the research on the pathogenic microorganisms it may carry is very limited. Therefore, it is essential to reveal the pathogenic microbes it carries and their potential hazards. This study found a new virus from the transcriptome of P. candelaria, which was first reported in P. candelaria and named PyCaV (Pyrops candelaria associated virus). RACE and bioinformatics assay revealed that the full length of PyCaV is 10,855 bp with the polyA tail, containing a single open-reading frame (ORF) encoding a polyprotein consisting of 3171 amino acid (aa). The virus has a typical iflavirus structure, including two rhv domains, an RNA helicase domain (HEL), a 3C cysteine protease domain (Pro), and an RNA-dependent RNA polymerase domain (RdRp). Further phylogenetic analysis revealed that this virus belongs to family Iflaviridae and sequence alignments analysis suggested PyCaV is a new member in an unassigned genus of family Iflaviridae. Further in-depth analysis of the virus infection showed that PyCaV is distributed throughout the whole P. candelaria, including its head, chest, and abdomen, but more PyCaV was identified in the chest. The distribution of PyCaV in different parts of P. candelaria was further explored, which showed that more PyCaV was detected in its piercing-sucking mouthparts and chest viscera. Statistical analysis showed that the PyCaV infection was affected by time and location.
Keyword ：
distribution distribution iflavirus iflavirus insect insect Pyrops candelaria Pyrops candelaria virus virus
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| GB/T 7714 | Lin, Hong , Song, Weitao , Ma, Dongmei et al. Screening and Characterization of a New Iflavirus Virus in the Fruit Tree Pest Pyrops candelaria [J]. | INSECTS , 2024 , 15 (8) . |
| MLA | Lin, Hong et al. "Screening and Characterization of a New Iflavirus Virus in the Fruit Tree Pest Pyrops candelaria" . | INSECTS 15 . 8 (2024) . |
| APA | Lin, Hong , Song, Weitao , Ma, Dongmei , Yang, Chi , Yao, Yanfang , Liu, Renyi et al. Screening and Characterization of a New Iflavirus Virus in the Fruit Tree Pest Pyrops candelaria . | INSECTS , 2024 , 15 (8) . |
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Leafhoppers are economically important pests and may serve as vectors for pathogenic viruses that cause substantial crop damage. In this study, using deep transcriptome sequencing, we identified three novel viruses within the order Mononegavirales, including two viruses belonging to the family Rhabdoviridae and one to the family Lispiviridae. The complete genome sequences were obtained via the rapid amplification of cDNA ends and tentatively named Recilia dorsalis rhabdovirus 1 (RdRV1, 14,251 nucleotides, nt), Nephotettix virescens rhabdovirus 1 (NvRV1, 13,726 nt), and Nephotettix virescens lispivirus 1 (NvLV1, 14,055 nt). The results of a phylogenetic analysis and sequence identity comparison suggest that RdRV1 and NvRV1 represent novel species within the family Rhabdoviridae, while NvLV1 is a new virus belonging to the family Lispiviridae. As negative-sense single-strand RNA viruses, RdRV1 and NvRV1 contain the conserved transcription termination signal and intergenic trinucleotides in the non-transcribed region. Intergenomic sequence and transcriptome profile analyses suggested that all these genes were co-transcriptionally expressed in these viral genomes, facilitated by specific intergenic trinucleotides and putative transcription initiation sequences.
Keyword ：
deep sequencing deep sequencing leafhopper leafhopper Mononegavirales Mononegavirales
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| GB/T 7714 | Xiao, Jiajing , Nie, Binghua , Chen, Meng-En et al. Discovery and Genomic Analysis of Three Novel Viruses in the Order Mononegavirales in Leafhoppers [J]. | VIRUSES-BASEL , 2024 , 16 (8) . |
| MLA | Xiao, Jiajing et al. "Discovery and Genomic Analysis of Three Novel Viruses in the Order Mononegavirales in Leafhoppers" . | VIRUSES-BASEL 16 . 8 (2024) . |
| APA | Xiao, Jiajing , Nie, Binghua , Chen, Meng-En , Ge, Danfeng , Liu, Renyi . Discovery and Genomic Analysis of Three Novel Viruses in the Order Mononegavirales in Leafhoppers . | VIRUSES-BASEL , 2024 , 16 (8) . |
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Transposable elements (TEs) significantly contribute to the evolution and diversity of plant genomes. In this study, we explored the roles of TEs in the genomes of Citrus and Citrus-related genera by constructing a pan-genome TE library from 20 published genomes of Citrus and Citrus-related accessions. Our results revealed an increase in TE content and the number of TE types compared to the original annotations, as well as a decrease in the content of unclassified TEs. The average length of TEs per assembly was approximately 194.23 Mb, representing 41.76% (Murraya paniculata) to 64.76% (Citrus gilletiana) of the genomes, with a mean value of 56.95%. A significant positive correlation was found between genome size and both the number of TE types and TE content. Consistent with the difference in mean whole-genome size (39.83 Mb) between Citrus and Citrus-related genera, Citrus genomes contained an average of 34.36 Mb more TE sequences than Citrus-related genomes. Analysis of the estimated insertion time and half-life of long terminal repeat retrotransposons (LTR-RTs) suggested that TE removal was not the primary factor contributing to the differences among genomes. These findings collectively indicate that TEs are the primary determinants of genome size and play a major role in shaping genome structures. Principal coordinate analysis (PCoA) of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers revealed that the fragmented TEs were predominantly derived from ancestral genomes, while intact TEs were crucial in the recent evolutionary diversification of Citrus. Moreover, the presence or absence of intact TEs near the AdhE superfamily was closely associated with the bitterness trait in the Citrus species. Overall, this study enhances TE annotation in Citrus and Citrus-related genomes and provides valuable data for future genetic breeding and agronomic trait research in Citrus.
Keyword ：
bitterness bitterness Citrus Citrus genome evolution genome evolution pan-genome TE library pan-genome TE library transposable elements (TEs) transposable elements (TEs)
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| GB/T 7714 | Wu, Yilei , Wang, Fusheng , Lyu, Keliang et al. Comparative Analysis of Transposable Elements in the Genomes of Citrus and Citrus-Related Genera [J]. | PLANTS-BASEL , 2024 , 13 (17) . |
| MLA | Wu, Yilei et al. "Comparative Analysis of Transposable Elements in the Genomes of Citrus and Citrus-Related Genera" . | PLANTS-BASEL 13 . 17 (2024) . |
| APA | Wu, Yilei , Wang, Fusheng , Lyu, Keliang , Liu, Renyi . Comparative Analysis of Transposable Elements in the Genomes of Citrus and Citrus-Related Genera . | PLANTS-BASEL , 2024 , 13 (17) . |
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Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.
Keyword ：
cultivated strawberry cultivated strawberry Fragaria Fragaria genome evolution genome evolution long terminal repeat retrotransposons (LTR-RTs) long terminal repeat retrotransposons (LTR-RTs) transposable elements (TEs) transposable elements (TEs)
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| GB/T 7714 | Lyu, Keliang , Xiao, Jiajing , Lyu, Shiheng et al. Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2023 , 24 (23) . |
| MLA | Lyu, Keliang et al. "Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 24 . 23 (2023) . |
| APA | Lyu, Keliang , Xiao, Jiajing , Lyu, Shiheng , Liu, Renyi . Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2023 , 24 (23) . |
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Konjac glucomannan (KGM) is a naturally occurring macromolecular polysaccharide that exhibits remarkable film-forming and gel-forming properties, and a high degree of biocompatibility and biodegradability. The helical structure of KGM is maintained by the acetyl group, which plays a crucial role in preserving its structural integrity. Various degradation methods, including the topological structure, can enhance the stability of KGM and improve its biological activity. Recent research has focused on modifying KGM to enhance its properties, utilizing multi-scale simulation, mechanical experiments, and biosensor research. This review presents a comprehensive overview of the structure and properties of KGM, recent advancements in non-alkali thermally irreversible gel research, and its applications in biomedical materials and related areas of research. Additionally, this review outlines prospects for future KGM research, providing valuable research ideas for follow-up experiments.
Keyword ：
gelation gelation konjac glucomannan konjac glucomannan medical biology medical biology property property structure structure
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| GB/T 7714 | Sun, Yilan , Xu, Xiaowei , Zhang, Qinhua et al. Review of Konjac Glucomannan Structure, Properties, Gelation Mechanism, and Application in Medical Biology [J]. | POLYMERS , 2023 , 15 (8) . |
| MLA | Sun, Yilan et al. "Review of Konjac Glucomannan Structure, Properties, Gelation Mechanism, and Application in Medical Biology" . | POLYMERS 15 . 8 (2023) . |
| APA | Sun, Yilan , Xu, Xiaowei , Zhang, Qinhua , Zhang, Di , Xie, Xiaoyu , Zhou, Hanlin et al. Review of Konjac Glucomannan Structure, Properties, Gelation Mechanism, and Application in Medical Biology . | POLYMERS , 2023 , 15 (8) . |
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Konjac glucomannan (KGM) is a natural polysaccharide extracted from konjac tubers that has a topological structure composed of glucose and mannose. KGM can be used as a gel carrier to load active molecules in food preservation. The three-dimensional gel network structure based on KGM provides good protection for the loaded active molecules and allows for sustained release, thus enhancing the antioxidant and antimicrobial activities of these molecules. KGM loaded with various active molecules has been used in aquatic foods preservation, with great potential for different food preservation applications. This review summarizes recent advances in KGM, including: (i) structural characterization, (ii) the formation mechanism, (iii) preparation methods, (iv) functional properties and (v) the preservation of aquatic food.
Keyword ：
aquatic food aquatic food food preservation food preservation gel formation gel formation konjac glucomannan konjac glucomannan
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| GB/T 7714 | Sun, Yilan , Xu, Xiaowei , Wu, Zhenzhen et al. Structure, Merits, Gel Formation, Gel Preparation and Functions of Konjac Glucomannan and Its Application in Aquatic Food Preservation [J]. | FOODS , 2023 , 12 (6) . |
| MLA | Sun, Yilan et al. "Structure, Merits, Gel Formation, Gel Preparation and Functions of Konjac Glucomannan and Its Application in Aquatic Food Preservation" . | FOODS 12 . 6 (2023) . |
| APA | Sun, Yilan , Xu, Xiaowei , Wu, Zhenzhen , Zhou, Hanlin , Xie, Xiaoyu , Zhang, Qinhua et al. Structure, Merits, Gel Formation, Gel Preparation and Functions of Konjac Glucomannan and Its Application in Aquatic Food Preservation . | FOODS , 2023 , 12 (6) . |
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The aster leafhopper Macrosteles fascifrons is a common insect pest that feeds on rice and other plants and may serve as a vector to transmit various viruses. Here, we discovered a novel virus from M. fascifrons using metagenomic sequencing. We obtained its complete genome sequence by contig assembly and rapid amplification of cDNA ends, and verified the genome sequence by Sanger sequencing of overlapping segments. Based on homology search and phylogenetic analysis, the new virus belongs to the family Iflaviridae and it is tentatively named "Macrosteles fascifrons iflavirus 1 " (MfIV1). Excluding the poly(A) tail, the MfIV1 genome is 10,581 nucleotides in length and it is predicted to encode a polyprotein of 3119 amino acids long, which is likely further processed to several polypeptides with conserved domains, including two rhinovirus like (rhv-like) capsid domains, a cricket paralysis virus (CRPV) capsid domain, a helicase domain, and an RNA-dependent RNA polymerase (RdRp) domain. BLAST searches show that the highest amino acid sequence identity between the capsid proteins of MfIV1 and those of other reported iflaviruses is 60.22%, indicating that MfIV1 is a new member in the family Iflaviridae.
Keyword ：
Genome sequencing Genome sequencing Iflavirus Iflavirus Leafhopper Leafhopper Phylogenetic analysis Phylogenetic analysis
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| GB/T 7714 | Xiao, Jiajing , Zhu, Kai , Ma, Rui et al. Full genome sequence of a novel iflavirus from the aster leafhopper Macrosteles fascifrons [J]. | VIRUS GENES , 2022 , 59 (2) : 338-342 . |
| MLA | Xiao, Jiajing et al. "Full genome sequence of a novel iflavirus from the aster leafhopper Macrosteles fascifrons" . | VIRUS GENES 59 . 2 (2022) : 338-342 . |
| APA | Xiao, Jiajing , Zhu, Kai , Ma, Rui , Zhang, Chunmin , Lv, Keliang , Ge, Danfeng et al. Full genome sequence of a novel iflavirus from the aster leafhopper Macrosteles fascifrons . | VIRUS GENES , 2022 , 59 (2) , 338-342 . |
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Specialized metabolites not only play important roles in biotic and abiotic stress adaptation of tea plants (Camellia sinensis (L.) O. Kuntze) but also contribute to the unique flavor of tea, the most important nonalcoholic beverage. However, the molecular networks and major genes that regulate specialized metabolites in tea plants are not well understood. Here, we constructed a population-level pan-transcriptome of the tea plant leaf using second-leaf transcriptome data from 134 accessions to investigate global expression differences in the population, expression presence or absence variations (ePAVs), and differentially expressed genes (DEGs) between pure Camellia sinensis var. assamica (CSA) and pure Camellia sinensis var. sinensis (CSS) accessions. Next, we used a genome-wide association study, a quantitative trait transcript study, and a transcriptome-wide association study to integrate genotypes, accumulation levels of specialized metabolites, and expression levels of pan-transcriptome genes to identify candidate regulatory genes for flavor-related metabolites and to construct a regulatory network for specialized metabolites in tea plants. The pan-transcriptome contains 30 482 expressed genes, 4940 and 5506 of which were newly annotated from a de novo transcriptome assembly without a reference and a genome reference-based assembly, respectively. DEGs and ePAVs indicated that CSA and CSS were clearly differentiated at the population transcriptome level, and they were closely related to abiotic tolerance and secondary metabolite synthesis phenotypes of CSA and CSS based on gene annotations. The regulatory network contained 212 specialized metabolites, 3843 candidate genes, and 3407 eQTLs, highlighting many pleiotropic candidate genes, candidate gene-rich eQTLs, and potential regulators of specialized metabolites. These included important transcription factors in the AP2/ERF-ERF, MYB, WD40, and bHLH families. CsTGY14G0001296, an ortholog of AtANS, appeared to be directly related to variation in proanthocyanins in the tea plant population, and the CsTGY11G0002074 gene encoding F3'5'H was found to contribute to the biased distribution of catechins between pure CSAs and pure CSSs. Together, these results provide a new understanding of the metabolite diversity in tea plants and offer new insights for more effective breeding of better-flavored tea varieties.
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| GB/T 7714 | Kong, Weilong , Jiang, Mengwei , Wang, Yibin et al. Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis [J]. | HORTICULTURE RESEARCH , 2022 , 9 . |
| MLA | Kong, Weilong et al. "Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis" . | HORTICULTURE RESEARCH 9 (2022) . |
| APA | Kong, Weilong , Jiang, Mengwei , Wang, Yibin , Chen, Shuai , Zhang, Shengcheng , Lei, Wenlong et al. Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis . | HORTICULTURE RESEARCH , 2022 , 9 . |
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