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学者姓名：张亮生
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Abstract ：
Invertebrate species are a natural reservoir of viral genetic diversity, and invertebrate pests are widely distributed in crop fields. However, information on viruses infecting invertebrate pests of crops is limited. In this report, we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields. We identified 296 new RNA viruses and 13 known RNA viruses. These viruses clustered within 31 families, with many highly divergent viruses constituting potentially new families and genera. Of the identified viruses, 13 RNA viruses clustered within the Fiersviridae family of bacteriophages, and 48 RNA viruses clustered within families and genera of mycoviruses. We detected known rice viruses in novel invertebrate hosts at high abundances. Furthermore, some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus species. Forty-five potential insect pathogenic RNA viruses were detected in invertebrate species. Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity. Cross-species transmission of RNA viruses was detected between invertebrate hosts. Newly identified viral genomes showed extensive variation for invertebrate viral families or genera. Together, the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species, the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.
Keyword ：
invertebrate species invertebrate species metatranscriptome metatranscriptome viral diversity viral diversity viral genomes viral genomes viral transmission viral transmission
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| GB/T 7714 | Wang, Haoran , Chao, Shufen , Yan, Qing et al. Genetic diversity of RNA viruses infecting invertebrate pests of rice [J]. | SCIENCE CHINA-LIFE SCIENCES , 2023 , 67 (1) : 175-187 . |
| MLA | Wang, Haoran et al. "Genetic diversity of RNA viruses infecting invertebrate pests of rice" . | SCIENCE CHINA-LIFE SCIENCES 67 . 1 (2023) : 175-187 . |
| APA | Wang, Haoran , Chao, Shufen , Yan, Qing , Zhang, Shu , Chen, Guoqing , Mao, Chonghui et al. Genetic diversity of RNA viruses infecting invertebrate pests of rice . | SCIENCE CHINA-LIFE SCIENCES , 2023 , 67 (1) , 175-187 . |
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Clarifying the evolutionary processes underlying species diversification and adaptation is a key focus of evolutionary biology. Begonia (Begoniaceae) is one of the most species-rich angiosperm genera with c. 2000 species, most of which are shade-adapted. Here, we present chromosome-scale genome assemblies for four species of Begonia (B. loranthoides, B. masoniana, B. darthvaderiana and B. peltatifolia), and whole genome shotgun data for an additional 74 Begonia representatives to investigate lineage evolution and shade adaptation of the genus. The four genome assemblies range in size from 331.75 Mb (B. peltatifolia) to 799.83 Mb (B. masoniana), and harbor 22 059-23 444 protein-coding genes. Synteny analysis revealed a lineage-specific whole-genome duplication (WGD) that occurred just before the diversification of Begonia. Functional enrichment of gene families retained after WGD highlights the significance of modified carbohydrate metabolism and photosynthesis possibly linked to shade adaptation in the genus, which is further supported by expansions of gene families involved in light perception and harvesting. Phylogenomic reconstructions and genomics studies indicate that genomic introgression has also played a role in the evolution of Begonia. Overall, this study provides valuable genomic resources for Begonia and suggests potential drivers underlying the diversity and adaptive evolution of this mega-diverse clade.
Keyword ：
Begonia Begonia evolution evolution genomes genomes introgression introgression shade adaptation shade adaptation whole-genome duplication whole-genome duplication
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| GB/T 7714 | Li, Lingfei , Chen, Xiaoli , Fang, Dongming et al. Genomes shed light on the evolution of Begonia, a mega-diverse genus [J]. | NEW PHYTOLOGIST , 2022 , 234 (1) : 295-310 . |
| MLA | Li, Lingfei et al. "Genomes shed light on the evolution of Begonia, a mega-diverse genus" . | NEW PHYTOLOGIST 234 . 1 (2022) : 295-310 . |
| APA | Li, Lingfei , Chen, Xiaoli , Fang, Dongming , Dong, Shanshan , Guo, Xing , Li, Na et al. Genomes shed light on the evolution of Begonia, a mega-diverse genus . | NEW PHYTOLOGIST , 2022 , 234 (1) , 295-310 . |
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Unlike the flower of the model monocot rice, which has diverged greatly from the ancestral monocot flower, the pineapple (Ananas comosus) flower is more typical of monocot flowers. Here, we identified 43 pineapple genes containing MADS-box domains, including 11 type I and 32 type II genes. RNA-seq expression data generated from five pineapple floral organs (sepals, petals, stamens, pistils, and ovules) and quantitative real-time PCR revealed tissue-specific expression patterns for some genes. We found that AcAGL6 and AcFUL1 were mainly expressed in sepals and petals, suggesting their involvement in the regulation of these floral organs. A pineapple 'ABCDE' model was proposed based on the phylogenetic analysis and expression patterns of MADS-box genes. Unlike rice and orchid with frequent species-specific gene duplication and subsequent expression divergence, the composition and expression of the ABCDE genes were conserved in pineapple. We also found that AcSEP1/3, AcAG, AcAGL11a/b/c, and AcFUL1 were highly expressed at different stages of fruit development and have similar expression profiles, implicating these genes' role in fruit development and ripening processes. We propose that the pineapple flower can be used as a model for studying the ancestral form of monocot flowers to investigate their development and evolutionary history.
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| GB/T 7714 | Hu, Juan , Chang, Xiaojun , Zhang, Ying et al. The pineapple MADS-box gene family and the evolution of early monocot flower [J]. | SCIENTIFIC REPORTS , 2021 , 11 (1) . |
| MLA | Hu, Juan et al. "The pineapple MADS-box gene family and the evolution of early monocot flower" . | SCIENTIFIC REPORTS 11 . 1 (2021) . |
| APA | Hu, Juan , Chang, Xiaojun , Zhang, Ying , Yu, Xianxian , Qin, Yuan , Sun, Yun et al. The pineapple MADS-box gene family and the evolution of early monocot flower . | SCIENTIFIC REPORTS , 2021 , 11 (1) . |
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Azalea belongs to Rhododendron, which is one of the largest genera of flowering plants and is well known for the diversity and beauty in its more than 1000 woody species. Rhododendron contains two distinct groups: the most high-altitude and a few low-altitude species; however, the former group is difficult to be domesticated for urban landscaping, and their evolution and adaptation are little known. Rhododendron ovatum has broad adaptation in low-altitude regions but possesses evergreen characteristics like high-altitude species, and it has floral fragrance that is deficient in most cultivars. Here we report the chromosome-level genome assembly of R. ovatum, which has a total length of 549 Mb with scaffold N50 of 41 Mb and contains 41 264 predicted genes. Genomic micro-evolutionary analysis of R. ovatum in comparison with two high-altitude Rhododendron species indicated that the expansion genes in R. ovatum were significantly enriched in defence responses, which may account for its adaptability in low altitudes. The R. ovatum genome contains much more terpene synthase genes (TPSs) compared with the species that lost floral fragrance. The subfamily b members of TPS are involved in the synthesis of sesquiterpenes as well as monoterpenes and play a major role in flora scent biosynthesis and defence responses. Tandem duplication is the primary force driving expansion of defence-responsive genes for extensive adaptability to the low-altitude environments. The R. ovatum genome provides insights into low-altitude adaptation and gain or loss of floral fragrance for Rhododendron species, which are valuable for alpine plant domestication and floral scent breeding.
Keyword ：
adaptability adaptability altitude altitude Azalea Azalea defence response defence response floral scent floral scent Rhododendron ovatum Rhododendron ovatum tandem duplication tandem duplication terpene synthase (TPS) terpene synthase (TPS)
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| GB/T 7714 | Wang, Xiuyun , Gao, Yuan , Wu, Xiaopei et al. High-quality evergreen azalea genome reveals tandem duplication-facilitated low-altitude adaptability and floral scent evolution [J]. | PLANT BIOTECHNOLOGY JOURNAL , 2021 , 19 (12) : 2544-2560 . |
| MLA | Wang, Xiuyun et al. "High-quality evergreen azalea genome reveals tandem duplication-facilitated low-altitude adaptability and floral scent evolution" . | PLANT BIOTECHNOLOGY JOURNAL 19 . 12 (2021) : 2544-2560 . |
| APA | Wang, Xiuyun , Gao, Yuan , Wu, Xiaopei , Wen, Xiaohui , Li, Danqing , Zhou, Hong et al. High-quality evergreen azalea genome reveals tandem duplication-facilitated low-altitude adaptability and floral scent evolution . | PLANT BIOTECHNOLOGY JOURNAL , 2021 , 19 (12) , 2544-2560 . |
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The early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon-sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different data sets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon-usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony-informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provide additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.
Keyword ：
early angiosperm radiation early angiosperm radiation incongruence incongruence mitochondrial genome mitochondrial genome phylogenomics phylogenomics systematic error systematic error
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| GB/T 7714 | Xue, Jia-Yu , Dong, Shan-Shan , Wang, Ming-Qiang et al. Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants [J]. | JOURNAL OF SYSTEMATICS AND EVOLUTION , 2021 , 60 (4) : 773-788 . |
| MLA | Xue, Jia-Yu et al. "Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants" . | JOURNAL OF SYSTEMATICS AND EVOLUTION 60 . 4 (2021) : 773-788 . |
| APA | Xue, Jia-Yu , Dong, Shan-Shan , Wang, Ming-Qiang , Song, Tian-Qiang , Zhou, Guang-Can , Li, Zhen et al. Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants . | JOURNAL OF SYSTEMATICS AND EVOLUTION , 2021 , 60 (4) , 773-788 . |
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| GB/T 7714 | Zhang, Liangsheng , Shen, Fu-ming , Chen, Fei et al. Origin and Evolution of the 2019 Novel Coronavirus [J]. | CLINICAL INFECTIOUS DISEASES , 2020 , 71 (15) : 882-883 . |
| MLA | Zhang, Liangsheng et al. "Origin and Evolution of the 2019 Novel Coronavirus" . | CLINICAL INFECTIOUS DISEASES 71 . 15 (2020) : 882-883 . |
| APA | Zhang, Liangsheng , Shen, Fu-ming , Chen, Fei , Lin, Zhenguo . Origin and Evolution of the 2019 Novel Coronavirus . | CLINICAL INFECTIOUS DISEASES , 2020 , 71 (15) , 882-883 . |
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| GB/T 7714 | Tang, Haibao , Zhang, Liangsheng , Chen, Fei et al. Nymphaea colorata (Blue-Petal Water Lily) [J]. | TRENDS IN GENETICS , 2020 , 36 (9) : 718-719 . |
| MLA | Tang, Haibao et al. "Nymphaea colorata (Blue-Petal Water Lily)" . | TRENDS IN GENETICS 36 . 9 (2020) : 718-719 . |
| APA | Tang, Haibao , Zhang, Liangsheng , Chen, Fei , Zhang, Xingtan , Chen, Feng , Ma, Hong et al. Nymphaea colorata (Blue-Petal Water Lily) . | TRENDS IN GENETICS , 2020 , 36 (9) , 718-719 . |
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The R2R3-MYB transcription factors play critical roles in various processes in embryophytes (land plants). Here, we identified genes encoding R2R3-MYB proteins from rhodophytes, glaucophytes, Chromista, chlorophytes, charophytes, and embryophytes. We classified the R2R3-MYB genes into three subgroups (I, II, and III) based on their evolutionary history and gene structure. The subgroup I is the most ancient group that includes members from all plant lineages. The subgroup II was formed before the divergence of charophytes and embryophytes. The subgroup III genes form a monophyletic group and only comprise members from land plants with conserved exon-intron structure. Each subgroup was further divided into multiple clades. The subgroup I can be divided into I-A, I-B, I-C, and I-D. The I-A, I-B, and I-C are the most basal clades that have originated before the divergence of Archaeplastida. The I-D with the II and III subgroups form a monophyletic group, containing only green plants. The II and III subgroups form another monophyletic group with Streptophyta only. Once on land, the subgroup III genes have experienced two rounds of major expansions. The first round occurred before the origin of land plants, and the second round occurred after the divergence of land plants. Due to significant gene expansion, the subgroup III genes have become the predominant group of R2R3-MYBs in land plants. The highly unbalanced pattern of birth and death evolution of R2R3-MYB genes indicates their important roles in the successful adaptation and massive radiation of land plants to occupy a multitude of terrestrial environments.
Keyword ：
charophytes charophytes chlorophytes chlorophytes embryophytes embryophytes land plant adaptation land plant adaptation
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| GB/T 7714 | Chang, Xiaojun , Xie, Shupeng , Wei, Lanlan et al. Origins and Stepwise Expansion of R2R3-MYB Transcription Factors for the Terrestrial Adaptation of Plants [J]. | FRONTIERS IN PLANT SCIENCE , 2020 , 11 . |
| MLA | Chang, Xiaojun et al. "Origins and Stepwise Expansion of R2R3-MYB Transcription Factors for the Terrestrial Adaptation of Plants" . | FRONTIERS IN PLANT SCIENCE 11 (2020) . |
| APA | Chang, Xiaojun , Xie, Shupeng , Wei, Lanlan , Lu, Zhaolian , Chen, Zhong-Hua , Chen, Fei et al. Origins and Stepwise Expansion of R2R3-MYB Transcription Factors for the Terrestrial Adaptation of Plants . | FRONTIERS IN PLANT SCIENCE , 2020 , 11 . |
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Alternative splicing is an essential post-transcriptional regulatory mechanism that can impact mRNA stability and protein diversity of eukaryotic genomes. Although numerous forms of stress-responsive alternative splicing have been identified in model plants, a large-scale study of alternative splicing dynamics under abiotic stress conditions in cassava has not been conducted. Here, we report the parallel employment of isoform-Seq, ssRNA-Seq, and Degradome-Seq to investigate the diversity, abundance, and fate of alternatively spliced isoforms in response to cold and drought stress. We identified 38 164 alternative splicing events, among which 3292 and 1025 events were significantly regulated by cold and drought stress, respectively. Intron retention was the most abundant subtype of alternative splicing. Global analysis of splicing regulators revealed that the number of their alternatively spliced isoforms and the corresponding abundance were specifically modulated by cold stress. We found that 58.5% of cold-regulated alternative splicing events introduced a premature termination codon into the transcripts, and 77.6% of differential alternative splicing events were detected by Degradome-Seq. Our data reveal that cold intensely affects both quantitative and qualitative aspects of gene expression via alternative splicing pathways, and advances our understanding of the high complexity and specificity of gene regulation in response to abiotic stresses.
Keyword ：
Alternative splicing Alternative splicing cassava cassava cold stress cold stress drought stress drought stress RNA-Seq RNA-Seq splicing factor splicing factor
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| GB/T 7714 | Li, Shuxia , Yu, Xiang , Cheng, Zhihao et al. Large-scale analysis of the cassava transcriptome reveals the impact of cold stress on alternative splicing [J]. | JOURNAL OF EXPERIMENTAL BOTANY , 2020 , 71 (1) : 422-434 . |
| MLA | Li, Shuxia et al. "Large-scale analysis of the cassava transcriptome reveals the impact of cold stress on alternative splicing" . | JOURNAL OF EXPERIMENTAL BOTANY 71 . 1 (2020) : 422-434 . |
| APA | Li, Shuxia , Yu, Xiang , Cheng, Zhihao , Zeng, Changying , Li, Wenbin , Zhang, Liangsheng et al. Large-scale analysis of the cassava transcriptome reveals the impact of cold stress on alternative splicing . | JOURNAL OF EXPERIMENTAL BOTANY , 2020 , 71 (1) , 422-434 . |
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Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high-quality genome assembly of a typical semi-winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single-molecule sequencing and chromosome conformation capture (Hi-C) techniques. Most of the high-confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR-RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide-binding leucine-rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head-to-head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi-winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits.
Keyword ：
Brassica napus Brassica napus disease resistance disease resistance long‐ long‐ read sequencing read sequencing selective sweep selective sweep subgenome evolution subgenome evolution
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| GB/T 7714 | Chen, Xuequn , Tong, Chaobo , Zhang, Xingtan et al. A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance [J]. | PLANT BIOTECHNOLOGY JOURNAL , 2020 , 19 (3) : 615-630 . |
| MLA | Chen, Xuequn et al. "A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance" . | PLANT BIOTECHNOLOGY JOURNAL 19 . 3 (2020) : 615-630 . |
| APA | Chen, Xuequn , Tong, Chaobo , Zhang, Xingtan , Song, Aixia , Hu, Ming , Dong, Wei et al. A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance . | PLANT BIOTECHNOLOGY JOURNAL , 2020 , 19 (3) , 615-630 . |
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