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Wei X, Xu D, Liu Z, Liu Q, Zhuo Z. SMRT Sequencing Technology Was Used to Construct the Batocera horsfieldi (Hope) Transcriptome and Reveal Its Features. Insects 2023; 14:625. [PMID: 37504630 PMCID: PMC10380457 DOI: 10.3390/insects14070625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023]
Abstract
Batocera horsfieldi (Hope) (Coleoptera: Cerambycidae) is an important forest pest in China that mainly infests timber and economic forests. This pest primarily causes plant tissue to necrotize, rot, and eventually die by feeding on the woody parts of tree trunks. To gain a deeper understanding of the genetic mechanism of B. horsfieldi, this study employed single-molecule real-time sequencing (SMRT) and Illumina RNA-seq technologies to conduct full-length transcriptome sequencing of the insect. Total RNA extracted from male and female adults was mixed and subjected to SMRT sequencing, generating a complete transcriptome. Transcriptome analysis, prediction of long non-coding RNA (lncRNA), coding sequences (CDs), analysis of simple sequence repeats (SSR), prediction of transcription factors, and functional annotation of transcripts were performed in this study. The collective 20,356,793 subreads (38.26 G, clean reads) were generated, including 432,091 circular consensus sequences and 395,851 full-length non-chimera reads. The full-length non-chimera reads (FLNC) were clustered and redundancies were removed, resulting in 39,912 consensus reads. SSR and ANGEL software v3.0 were used for predicting SSR and CDs. In addition, four tools were used for annotating 6058 lncRNAs, identifying 636 transcription factors. Furthermore, a total of 84,650 transcripts were functionally annotated in seven different databases. This is the first time that the full-length transcriptome of B. horsfieldi has been obtained using SMRT sequencing. This provides an important foundation for investigating the gene regulation underlying the interaction between B. horsfieldi and its host plants through gene editing in the future and provides a scientific basis for the prevention and control of B. horsfieldi.
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Affiliation(s)
- Xinju Wei
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Danping Xu
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Zhiqian Liu
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Quanwei Liu
- College of Life Science, China West Normal University, Nanchong 637002, China
| | - Zhihang Zhuo
- College of Life Science, China West Normal University, Nanchong 637002, China
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Du Y, Gu Z, Li Z, Yuan Z, Zhao Y, Zheng X, Bo X, Chen H, Wang C. Dynamic Interplay between Structural Variations and 3D Genome Organization in Pancreatic Cancer. Adv Sci (Weinh) 2022; 9:e2200818. [PMID: 35570408 PMCID: PMC9218654 DOI: 10.1002/advs.202200818] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/04/2022] [Indexed: 06/05/2023]
Abstract
Structural variations (SVs) are the greatest source of variations in the genome and can lead to oncogenesis. However, the identification and interpretation of SVs in human cancer remain technologically challenging. Here, long-read sequencing is first employed to depict the signatures of structural variations in carcinogenesis of human pancreatic ductal epithelium. Then widespread reprogramming of the 3D chromatin architecture is revealed by an in situ Hi-C technique. Integrative analyses indicate that the distribution pattern of SVs among the 3D genome is highly cell-type specific and the bulk remodeling effects of SVs in the chromatin organization partly depend on intercellular genomic heterogeneity. Meanwhile, contact domains tend to minimize these disrupting effects of SVs within local adjacent genomic regions to maintain overall stability. Notably, complex genomic rearrangements involving two key driver genes CDKN2A and SMAD4 are identified, and their influence on the expression of oncogenes MIR31HG, MYO5B, etc., are further elucidated from both a linear view and 3D perspective. Overall, this work provides a genome-wide resource and highlights the impact, complexity, and dynamicity of the interplay between structural variations and high-order chromatin organization, which expands the current understanding of the pathogenesis of SVs in human cancer.
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Affiliation(s)
- Yongxing Du
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Zongting Gu
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Zongze Li
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Zan Yuan
- Annoroad Gene Technology Co. LtdBeijing100176P. R. China
| | - Yue Zhao
- Annoroad Gene Technology Co. LtdBeijing100176P. R. China
| | - Xiaohao Zheng
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xiaochen Bo
- Department of BiotechnologyInstitute of Health Service and Transfusion MedicineBeijing100850P. R. China
| | - Hebing Chen
- Department of BiotechnologyInstitute of Health Service and Transfusion MedicineBeijing100850P. R. China
| | - Chengfeng Wang
- Department of Pancreatic and Gastric SurgeryNational Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
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Liu Q, Guo S, Zheng X, Shen X, Zhang T, Liao B, He W, Hu H, Cheng R, Xu J. Licorice Germplasm Resources Identification Using DNA Barcodes Inner-Variants. Plants (Basel) 2021; 10:plants10102036. [PMID: 34685843 PMCID: PMC8541099 DOI: 10.3390/plants10102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Based on the gradual transformation from wild growth to artificial cultivation, the accurate authentication of licorice seeds contributes to the first committed step of its quality control and is pivotal to ensure the clinical efficacy of licorice. However, it is still challenging to obtain genetically stable licorice germplasm resources due to the multi-source, multi-heterozygous, polyploid, and hybrid characteristics of licorice seeds. Here, a new method for determining the heterozygosity of licorice seed mixture, based on the various sites, and finding the composition characteristics of licorice seed is preliminarily designed and proposed. Namely, high-throughput full-length multiple DNA barcodes(HFMD), based on ITS multi-copy variation exist, the full-length amplicons of ITS2, psbA-trnH and ITS are directly sequenced by rDNA through the next-generation sequence(NGS) and single-molecule real-time (SMRT) technologies. By comparing the three sequencing methods, our results proved that SMRT sequencing successfully identified the complete gradients of complex mixed samples with the best performance. Meanwhile, HFMD is a brilliant and feasible method for evaluating the heterozygosity of licorice seeds. It shows a perfect interpretation of DNA barcoding and can be applied in multi-base multi-heterozygous and polyploid species.
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Affiliation(s)
- Qianwen Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Shuai Guo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (S.G.); (W.H.)
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China;
| | - Xiaofeng Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China;
| | - Tianyi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Wenrui He
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (S.G.); (W.H.)
| | - Haoyu Hu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Ruiyang Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
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Lu S, Yang J, Dai X, Xie F, He J, Dong Z, Mao J, Liu G, Chang Z, Zhao R, Wan W, Zhang R, Li Y, Wang W, Li X. Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation DNA sequencing and Hi-C analysis. Gigascience 2019; 8:giz128. [PMID: 31682256 PMCID: PMC6827417 DOI: 10.1093/gigascience/giz128] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/18/2019] [Accepted: 10/04/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Papilio bianor Cramer, 1777 (commonly known as the Chinese peacock butterfly) (Insecta, Lepidoptera, Papilionidae) is a widely distributed swallowtail butterfly with a wide number of geographic populations ranging from the southeast of Russia to China, Japan, India, Vietnam, Myanmar, and Thailand. Its wing color consists of both pigmentary colored scales (black, reddish) and structural colored scales (iridescent blue or green dust). A high-quality reference genome of P. bianor is an important foundation for investigating iridescent color evolution, phylogeography, and the evolution of swallowtail butterflies. FINDINGS We obtained a chromosome-level de novo genome assembly of the highly heterozygous P. bianor using long Pacific Biosciences sequencing reads and high-throughput chromosome conformation capture technology. The final assembly is 421.52 Mb on 30 chromosomes (29 autosomes and 1 Z sex chromosome) with 13.12 Mb scaffold N50. In total, 15,375 protein-coding genes and 233.09 Mb of repetitive sequences were identified. Phylogenetic analyses indicated that P. bianor separated from a common ancestor of swallowtails ∼23.69-36.04 million years ago. Demographic history suggested that the population expansion of this species from the last interglacial period to the last glacial maximum possibly resulted from its decreased natural enemies and its adaptation to climate change during the glacial period. CONCLUSIONS We present a high-quality chromosome-level reference genome of P. bianor using long-read single-molecule sequencing and Hi-C-based chromatin interaction maps. Our results lay the foundation for exploring the genetic basis of special biological features of P. bianor and also provide a useful data source for comparative genomics and phylogenomics among butterflies and moths.
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Affiliation(s)
- Sihan Lu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Jie Yang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road,Yangling, Shaanxi 712100, China
| | - Feiang Xie
- School of Marine Science and Technology, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Changzhi Island, Zhoushan, Zhejiang 316022, China
| | - Jinwu He
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
| | - Zhiwei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Junlai Mao
- School of Marine Science and Technology, Zhejiang Ocean University, No.1 Haida South Road, Lincheng Changzhi Island, Zhoushan, Zhejiang 316022, China
| | - Guichun Liu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Zhou Chang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Wenting Wan
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
| | - Ru Zhang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
| | - Yuan Li
- Nextomics Biosciences Institute, No.666 Gaoxin Road, Wuhan, Hubei 430000, China
| | - Wen Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, No.1 Dongxiang Road, Chang'an District, Xi'an, Shaanxi 710129, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No.32 Jiaochang Raod, Kunming, Yunnan 650223, China
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Massonnet M, Morales‐Cruz A, Figueroa‐Balderas R, Lawrence DP, Baumgartner K, Cantu D. Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum. Mol Plant Pathol 2018; 19:21-34. [PMID: 27608421 PMCID: PMC6637977 DOI: 10.1111/mpp.12491] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 05/24/2023]
Abstract
The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability to colonize woody tissue, combined with the secretion of phytotoxic compounds, is thought to underlie its pathogenicity and virulence. Here, we describe the repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem. We assembled and annotated a highly contiguous genome using single-molecule real-time DNA sequencing. Transcriptome profiling by RNA sequencing determined the genome-wide patterns of expression of virulence factors both in vitro (potato dextrose agar or medium amended with grape wood as substrate) and in planta. Pairwise statistical testing of differential expression, followed by co-expression network analysis, revealed that physically clustered genes coding for putative virulence functions were induced depending on the substrate or stage of plant infection. Co-expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also in those associated with cell wall degradation, suggesting that dynamic co-regulation of transcriptional networks contributes to multiple aspects of N. parvum virulence. In most of the co-expressed clusters, all genes shared at least a common motif in their promoter region, indicative of co-regulation by the same transcription factor. Co-expression analysis also identified chromatin regulators with correlated expression with inducible clusters of virulence factors, suggesting a complex, multi-layered regulation of the virulence repertoire of N. parvum.
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Affiliation(s)
- Mélanie Massonnet
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | - Abraham Morales‐Cruz
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | | | - Daniel P. Lawrence
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Kendra Baumgartner
- US Department of Agriculture ‐ Agricultural Research ServiceCrops Pathology and Genetics Research UnitDavisCA95616USA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
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Wöhrmann T, Huettel B, Wagner N, Weising K. Microsatellites from Fosterella christophii (Bromeliaceae) by de novo transcriptome sequencing on the Pacific Biosciences RS platform. Appl Plant Sci 2016; 4:apps1500084. [PMID: 26819858 PMCID: PMC4716777 DOI: 10.3732/apps.1500084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 09/24/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed in Fosterella christophii (Bromeliaceae) to investigate the genetic diversity and population structure within the F. micrantha group, comprising F. christophii, F. micrantha, and F. villosula. METHODS AND RESULTS Full-length cDNAs were isolated from F. christophii and sequenced on a Pacific Biosciences RS platform. A total of 1590 high-quality consensus isoforms were assembled into 971 unigenes containing 421 perfect microsatellites. Thirty primer sets were designed, of which 13 revealed a high level of polymorphism in three populations of F. christophii, with four to nine alleles per locus. Each of these 13 loci cross-amplified in the closely related species F. micrantha and F. villosula, with one to six and one to 11 alleles per locus, respectively. CONCLUSIONS The new markers are promising tools to study the population genetics of F. christophii and to discover species boundaries within the F. micrantha group.
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Affiliation(s)
- Tina Wöhrmann
- Systematics and Morphology of Plants, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Bruno Huettel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Natascha Wagner
- Systematics and Morphology of Plants, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Kurt Weising
- Systematics and Morphology of Plants, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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