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Jiao N, Xu J, Wang Y, Li D, Chen F, Chen Y, Chen J. Genome-wide characterization of post-transcriptional processes related to wood formation in Dalbergia odorifera. BMC Genomics 2024; 25:372. [PMID: 38627613 PMCID: PMC11022335 DOI: 10.1186/s12864-024-10300-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvement in xylem development in Dalbergia odorifera, a valuable rosewood species with medicinal and commercial significance. We addressed this by conducting Isoform Sequencing (Iso-Seq) using PacBio's SMRT technology and combined it with RNA-seq analysis (RNA sequencing on Illumina platform) after collecting xylem samples from the transition zone and the sapwood of D. odorifera. RESULTS We identified 14,938 full-length transcripts, including 9,830 novel isoforms, which has updated the D. odorifera genome annotation. Our analysis has revealed that 4,164 genes undergo APA, whereas 3,084 genes encounter AS. We have also annotated 118 lncRNAs. Furthermore, RNA-seq analysis identified 170 differential alternative splicing (DAS) events, 344 genes with differential APA site usage (DE-APA), and 6 differentially expressed lncRNAs in the transition zone when compared to the sapwood. AS, APA, and lncRNAs are differentially regulated during xylem development. Differentially expressed APA genes were enriched for terpenoid and flavonoid metabolism, indicating their role in the heartwood formation. Additionally, DE-APA genes were associated with cell wall biosynthesis and terpenoid metabolism, implying an APA's role in wood formation. A DAS gene (involved in chalcone accumulation) with a significantly greater inclusion of the last exon in the transition zone than in the sapwood was identified. We also found that differentially expressed lncRNAs targeted the genes related to terpene synthesis. CONCLUSIONS This study enhances our understanding of the molecular regulatory mechanisms underlying wood formation in D. odorifera, and provides valuable genetic resources and insights for its molecular-assisted breeding.
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Affiliation(s)
- Nanbo Jiao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Jieru Xu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Yue Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China
| | - Dunxi Li
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Feifei Chen
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Yu Chen
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China
| | - Jinhui Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya, 572019, China.
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, 571100, China.
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Zhang T, Jia L, Niu Z, Li X, Men S, Jiang L, Ma M, Wang H, Tang X, Chen Q. Comparative transcriptomic analysis delineates adaptation strategies of Rana kukunoris toward cold stress on the Qinghai-Tibet Plateau. BMC Genomics 2024; 25:363. [PMID: 38609871 PMCID: PMC11015565 DOI: 10.1186/s12864-024-10248-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Cold hardiness is fundamental for amphibians to survive during the extremely cold winter on the Qinghai-Tibet plateau. Exploring the gene regulation mechanism of freezing-tolerant Rana kukunoris could help us to understand how the frogs survive in winter. RESULTS Transcriptome of liver and muscle of R. kukunoris collected in hibernation and spring were assisted by single molecule real-time (SMRT) sequencing technology. A total of 10,062 unigenes of R. kukunoris were obtained, and 9,924 coding sequences (CDS) were successfully annotated. Our examination of the mRNA response to whole body freezing and recover in the frogs revealed key genes concerning underlying antifreeze proteins and cryoprotectants (glucose and urea). Functional pathway analyses revealed differential regulated pathways of ribosome, energy supply, and protein metabolism which displayed a freeze-induced response and damage recover. Genes related to energy supply in the muscle of winter frogs were up-regulated compared with the muscle of spring frogs. The liver of hibernating frogs maintained modest levels of protein synthesis in the winter. In contrast, the liver underwent intensive high levels of protein synthesis and lipid catabolism to produce substantial quantity of fresh proteins and energy in spring. Differences between hibernation and spring were smaller than that between tissues, yet the physiological traits of hibernation were nevertheless passed down to active state in spring. CONCLUSIONS Based on our comparative transcriptomic analyses, we revealed the likely adaptive mechanisms of R. kukunoris. Ultimately, our study expands genetic resources for the freezing-tolerant frogs.
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Affiliation(s)
- Tao Zhang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lun Jia
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhiyi Niu
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xinying Li
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shengkang Men
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Lu Jiang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Miaojun Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Huihui Wang
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Xiaolong Tang
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China.
| | - Qiang Chen
- Department of Animal and Biomedical Sciences, School of Life Sciences, Lanzhou University, Lanzhou, China.
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Huang J, Xiong X, Zhang W, Chen X, Wei Y, Li H, Xie J, Wei Q, Zhou Q. Integrating miRNA and full-length transcriptome profiling to elucidate the mechanism of muscle growth in Muscovy ducks reveals key roles for miR-301a-3p/ANKRD1. BMC Genomics 2024; 25:340. [PMID: 38575872 PMCID: PMC10993543 DOI: 10.1186/s12864-024-10138-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/19/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND The popularity of Muscovy ducks is attributed not only to their conformation traits but also to their slightly higher content of breast and leg meat, as well as their stronger-tasting meat compared to that of typical domestic ducks. However, there is a lack of comprehensive systematic research on the development of breast muscle in Muscovy ducks. In addition, since the number of skeletal muscle myofibers is established during the embryonic period, this study conducted a full-length transcriptome sequencing and microRNA sequencing of the breast muscle. Muscovy ducks at four developmental stages, namely Embryonic Day 21 (E21), Embryonic Day 27 (E27), Hatching Day (D0), and Post-hatching Day 7 (D7), were used to isolate total RNA for analysis. RESULTS A total of 68,161 genes and 472 mature microRNAs were identified. In order to uncover deeper insights into the regulation of mRNA by miRNAs, we conducted an integration of the differentially expressed miRNAs (known as DEMs) with the differentially expressed genes (referred to as DEGs) across various developmental stages. This integration allowed us to make predictions regarding the interactions between miRNAs and mRNA. Through this analysis, we identified a total of 274 DEGs that may serve as potential targets for the 68 DEMs. In the predicted miRNA‒mRNA interaction networks, let-7b, miR-133a-3p, miR-301a-3p, and miR-338-3p were the hub miRNAs. In addition, multiple DEMs also showed predicted target relationships with the DEGs associated with skeletal system development. These identified DEGs and DEMs as well as their predicted interaction networks involved in the regulation of energy homeostasis and muscle development were most likely to play critical roles in facilitating the embryo-to-hatchling transition. A candidate miRNA, miR-301a-3p, exhibited increased expression during the differentiation of satellite cells and was downregulated in the breast muscle tissues of Muscovy ducks at E21 compared to E27. A dual-luciferase reporter assay suggested that the ANKRD1 gene, which encodes a transcription factor, is a direct target of miR-301a-3p. CONCLUSIONS miR-301a-3p suppressed the posttranscriptional activity of ANKRD1, which is an activator of satellite cell proliferation, as determined with gain- and loss-of-function experiments. miR-301a-3p functions as an inducer of myogenesis by targeting the ANKRD1 gene in Muscovy ducks. These results provide novel insights into the early developmental process of black Muscovy breast muscles and will improve understanding of the underlying molecular mechanisms.
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Affiliation(s)
- Jiangnan Huang
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Xiaolan Xiong
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Weihong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Xiaolian Chen
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Yue Wei
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Haiqin Li
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Jinfang Xie
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Qipeng Wei
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China.
| | - Quanyong Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China.
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Li C, Nong W, Boncan DAT, So WL, Yip HY, Swale T, Jia Q, Vicentin IG, Chung G, Bendena WG, Ngo JCK, Chan TF, Lam HM, Hui JHL. Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis. BMC Genomics 2024; 25:327. [PMID: 38565997 PMCID: PMC10985886 DOI: 10.1186/s12864-024-10232-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
Food security is important for the ever-growing global population. Soybean, Glycine max (L.) Merr., is cultivated worldwide providing a key source of food, protein and oil. Hence, it is imperative to maintain or to increase its yield under different conditions including challenges caused by abiotic and biotic stresses. In recent years, the soybean pod-sucking stinkbug Riptortus pedestris has emerged as an important agricultural insect pest in East, South and Southeast Asia. Here, we present a genomics resource for R. pedestris including its genome assembly, messenger RNA (mRNA) and microRNA (miRNA) transcriptomes at different developmental stages and from different organs. As insect hormone biosynthesis genes (genes involved in metamorphosis) and their regulators such as miRNAs are potential targets for pest control, we analyzed the sesquiterpenoid (juvenile) and ecdysteroid (molting) hormone biosynthesis pathway genes including their miRNAs and relevant neuropeptides. Temporal gene expression changes of these insect hormone biosynthesis pathways were observed at different developmental stages. Similarly, a diet-specific response in gene expression was also observed in both head and salivary glands. Furthermore, we observed that microRNAs (bantam, miR-14, miR-316, and miR-263) of R. pedestris fed with different types of soybeans were differentially expressed in the salivary glands indicating a diet-specific response. Interestingly, the opposite arms of miR-281 (-5p and -3p), a miRNA involved in regulating development, were predicted to target Hmgs genes of R. pedestris and soybean, respectively. These observations among others highlight stinkbug's responses as a function of its interaction with soybean. In brief, the results of this study not only present salient findings that could be of potential use in pest management and mitigation but also provide an invaluable resource for R. pedestris as an insect model to facilitate studies on plant-pest interactions.
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Affiliation(s)
- Chade Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | - Wenyan Nong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | - Delbert Almerick T Boncan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
| | - Wai Lok So
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | - Ho Yin Yip
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | | | - Qi Jia
- Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Ignacio G Vicentin
- Instituto Nacional de Tecnologia Agropecuaria, Avenida Rivadavia, Ciudad de Buenos, 1439, Argentina
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, 59626, Korea
| | - William G Bendena
- Department of Biology, Queen's University, 116 Barrie St, Kingston, ON K7L 3N6, Canada
| | - Jacky C K Ngo
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
| | - Ting Fung Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
- Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China.
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
- Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China.
| | - Jerome H L Hui
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China.
- Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China.
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Hao J, Liang Y, Ping J, Wang T, Su Y. Full-length transcriptome analysis of Ophioglossum vulgatum: effects of experimentally identified chloroplast gene clusters on expression and evolutionary patterns. PLANT MOLECULAR BIOLOGY 2024; 114:31. [PMID: 38509284 DOI: 10.1007/s11103-024-01423-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/24/2024] [Indexed: 03/22/2024]
Abstract
Genes with similar or related functions in chloroplasts are often arranged in close proximity, forming clusters on chromosomes. These clusters are transcribed coordinated to facilitate the expression of genes with specific function. Our previous study revealed a significant negative correlation between the chloroplast gene expression level of the rare medicinal fern Ophioglossum vulgatum and its evolutionary rates as well as selection pressure. Therefore, in this study, we employed a combination of SMRT and Illumina sequencing technology to analyze the full-length transcriptome sequencing of O. vulgatum for the first time. In particular, we experimentally identified gene clusters based on transcriptome data and investigated the effects of chloroplast gene clustering on expression and evolutionary patterns. The results revealed that the total sequenced data volume of the full-length transcriptome of O. vulgatum amounted to 71,950,652,163 bp, and 110 chloroplast genes received transcript coverage. Nine different types of gene clusters were experimentally identified in their transcripts. The chloroplast cluster genes may cause a decrease in non-synonymous substitution rate and selection pressure, as well as a reduction in transversion rate, transition rate, and their ratio. While expression levels of chloroplast cluster genes in leaf, sporangium, and stem would be relatively elevated. The Mann-Whitney U test indicated statistically significant in the selection pressure, sporangia and leaves groups (P < 0.05). We have contributed novel full-length transcriptome data resources for ferns, presenting new evidence on the effects of chloroplast gene clustering on expression land evolutionary patterns, and offering new theoretical support for transgenic research through gene clustering.
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Affiliation(s)
- Jing Hao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yingyi Liang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jingyao Ping
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen, 518057, China.
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Wu M, Zhang Y, Guo P, Liu H, Xia L, Wang M, Zeng C, Wang H, Shang F. Full-Length Transcriptome Sequencing and Comparative Transcriptomic Analyses Provide Comprehensive Insight into Molecular Mechanisms of Flavonoid Metabolites Biosynthesis in Styphnolobium japonicum. Genes (Basel) 2024; 15:329. [PMID: 38540388 PMCID: PMC10970609 DOI: 10.3390/genes15030329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 06/14/2024] Open
Abstract
Styphnolobium japonicum L. is a commonly consumed plant in China, known for its medicinal and nutritional benefits. This study focuses on the medicinal properties influenced by flavonoid metabolites, which vary during flower development. Utilizing full-length transcriptome sequencing on S. japonicum flowers, we observed changes in gene expression levels as the flowers progressed through growth stages. During stages S1 and S2, key genes related to flavonoid synthesis (PAL, 4CL, CHS, F3H, etc.) exhibited heightened expression. A weighted gene co-expression network analysis (WGCNA) identified regulatory genes (MYB, bHLH, WRKY) potentially involved in the regulatory network with flavonoid biosynthesis-related genes. Our findings propose a regulatory mechanism for flavonoid synthesis in S. japonicum flowers, elucidating the genetic underpinnings of this process. The identified candidate genes present opportunities for genetic enhancements in S. japonicum, offering insights into potential applications for improving its medicinal attributes.
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Affiliation(s)
- Miao Wu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Yu Zhang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
| | - Peng Guo
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
| | - Huiyuan Liu
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Linkui Xia
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Mengyuan Wang
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Chuqi Zeng
- College of Life Sciences and Engineering, Henan University of Urban Construction, Pingdingshan 467044, China; (M.W.)
| | - Hongwei Wang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
| | - Fude Shang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou 450002, China (H.W.)
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Fukuda A, Nakajima C, Suzuki Y, Usui M. Transferable linezolid resistance genes (optrA and poxtA) in enterococci derived from livestock compost at Japanese farms. J Glob Antimicrob Resist 2024; 36:336-344. [PMID: 38336229 DOI: 10.1016/j.jgar.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
OBJECTIVES Linezolid is a last-resort antimicrobial in human clinical settings to treat multidrug-resistant Gram-positive bacterial infections. Mobile linezolid resistance genes (optrA, poxtA, and cfr) have been detected in various sources worldwide. However, the presence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in Japan remains uncertain. Therefore, we clarified the existence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in farm environments in Japan. METHODS Enterococci isolates from faeces compost collected from 10 pig and 11 cattle farms in Japan in 2021 were tested for antimicrobial susceptibility and possession of mobile linezolid resistance genes. Whole-genome sequencing of optrA and/or poxtA genes positive-enterococci was performed. RESULTS Of 103 enterococci isolates, 12 from pig farm compost were not-susceptible (2 resistant and 10 intermediate) to linezolid. These 12 isolates carried mobile linezolid resistance genes on plasmids or chromosomes (5 optrA-positive Enterococcus faecalis, 6 poxtA-positive E. hirae or E. thailandicus, and 1 optrA- and poxtA-positive E. faecium). The genetic structures of optrA- and poxA-carrying plasmids were almost identical to those reported in other countries. These plasmids were capable of transferring among E. faecium and E. faecalis strains. The optrA- and poxtA-positive E. faecium belonged to ST324 (clade A2), a high-risk multidrug-resistant clone. The E. faecalis carrying optrA gene on its chromosome was identified as ST593. CONCLUSIONS Although linezolid is not used in livestock, linezolid-not-susceptible enterococci could be indirectly selected by frequently used antimicrobials, such as phenicols. Moreover, various enterococci species derived from livestock compost may serve as reservoirs of linezolid resistance genes carried on globally disseminated plasmids and multidrug-resistant high-risk clones.
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Affiliation(s)
- Akira Fukuda
- Department of Health and Environmental Sciences, Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; Division of Research Support, Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; Division of Research Support, Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
| | - Masaru Usui
- Department of Health and Environmental Sciences, Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan.
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Zervas A, Stougaard P, Thøgersen MS. Complete genome sequence of "Bacillaceae sp. strain IKA-2": a cold-active, amylase-producing bacterium from ikaite columns in SW Greenland. Microbiol Resour Announc 2024; 13:e0088723. [PMID: 38134028 PMCID: PMC10868235 DOI: 10.1128/mra.00887-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Bacillaceae sp. strain IKA-2 is a bacterium isolated from the permanently cold and alkaline ikaite columns in the Ikka Fjord in SW Greenland (61°12'05″N; 48°00'50″W). The bacterium grows well at 10°C in a substrate buffered to pH 10. It has a genome size of 4,424,890 bp and a guanine-cytosine (GC) content of 36.2%. The genome harbors genes involved in hydrolysis of long carbohydrates and in protection against cold shock.
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Affiliation(s)
- A. Zervas
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - P. Stougaard
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - M. S. Thøgersen
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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Mackinnon AC, Chandrashekar DS, Suster DI. Molecular pathology as basis for timely cancer diagnosis and therapy. Virchows Arch 2024; 484:155-168. [PMID: 38012424 DOI: 10.1007/s00428-023-03707-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/16/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023]
Abstract
Precision and personalized therapeutics have witnessed significant advancements in technology, revolutionizing the capabilities of laboratories to generate vast amounts of genetic data. Coupled with computational resources for analysis and interpretation, and integrated with various other types of data, including genomic data, electronic medical health (EMH) data, and clinical knowledge, these advancements support optimized health decisions. Among these technologies, next-generation sequencing (NGS) stands out as a transformative tool in the field of cancer treatment, playing a crucial role in precision oncology. NGS-based workflows are employed across a range of applications, including gene panels, exome sequencing, and whole-genome sequencing, supporting comprehensive analysis of the entire cancer genome, including mutations, copy number variations, gene expression profiles, and epigenetic modifications. By utilizing the power of NGS, these workflows contribute to enhancing our understanding of disease mechanisms, diagnosis confirmation, identifying therapeutic targets, and guiding personalized treatment decisions. This manuscript explores the diverse applications of NGS in cancer treatment, highlighting its significance in guiding diagnosis and treatment decisions, identifying therapeutic targets, monitoring disease progression, and improving patient outcomes.
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Affiliation(s)
- A Craig Mackinnon
- Department of Pathology, University of Alabama at Birmingham, 619 19Th Street South, Birmingham, AL, 35249, USA.
| | | | - David I Suster
- Department of Pathology, Rutgers University New Jersey Medical School, 150 Bergen Street, Newark, NJ, 07103, USA.
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Rajput J, Chandra G, Jain C. Co-linear chaining on pangenome graphs. Algorithms Mol Biol 2024; 19:4. [PMID: 38279113 PMCID: PMC11288099 DOI: 10.1186/s13015-024-00250-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 01/28/2024] Open
Abstract
Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topology and cycles can be challenging. The seed-chain-extend based alignment algorithms use co-linear chaining as a standard technique to identify a good cluster of exact seed matches that can be combined to form an alignment. Recent works show how the co-linear chaining problem can be efficiently solved for acyclic pangenome graphs by exploiting their small width and how incorporating gap cost in the scoring function improves alignment accuracy. However, it remains open on how to effectively generalize these techniques for general pangenome graphs which contain cycles. Here we present the first practical formulation and an exact algorithm for co-linear chaining on cyclic pangenome graphs. We rigorously prove the correctness and computational complexity of the proposed algorithm. We evaluate the empirical performance of our algorithm by aligning simulated long reads from the human genome to a cyclic pangenome graph constructed from 95 publicly available haplotype-resolved human genome assemblies. While the existing heuristic-based algorithms are faster, the proposed algorithm provides a significant advantage in terms of accuracy. Implementation ( https://github.com/at-cg/PanAligner ).
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Affiliation(s)
- Jyotshna Rajput
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Ghanshyam Chandra
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Chirag Jain
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, 560012, Karnataka, India.
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Peng Y, Wang Z, Li M, Wang T, Su Y. Characterization and analysis of multi-organ full-length transcriptomes in Sphaeropteris brunoniana and Alsophila latebrosa highlight secondary metabolism and chloroplast RNA editing pattern of tree ferns. BMC PLANT BIOLOGY 2024; 24:73. [PMID: 38273309 PMCID: PMC10811885 DOI: 10.1186/s12870-024-04746-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024]
Abstract
BACKGROUND Sphaeropteris brunoniana and Alsophila latebrosa are both old relict and rare tree ferns, which have experienced the constant changes of climate and environment. However, little is known about their high-quality genetic information and related research on environmental adaptation mechanisms of them. In this study, combined with PacBio and Illumina platforms, transcriptomic analysis was conducted on the roots, rachis, and pinna of S. brunoniana and A. latebrosa to identify genes and pathways involved in environmental adaptation. Additionally, based on the transcriptomic data of tree ferns, chloroplast genes were mined to analyze their gene expression levels and RNA editing events. RESULTS In the study, we obtained 11,625, 14,391 and 10,099 unigenes of S. brunoniana root, rachis, and pinna, respectively. Similarly, a total of 13,028, 11,431 and 12,144 unigenes were obtained of A. latebrosa root, rachis, and pinna, respectively. According to the enrichment results of differentially expressed genes, a large number of differentially expressed genes were enriched in photosynthesis and secondary metabolic pathways of S. brunoniana and A. latebrosa. Based on gene annotation results and phenylpropanoid synthesis pathways, two lignin synthesis pathways (H-lignin and G-lignin) were characterized of S. brunoniana. Among secondary metabolic pathways of A. latebrosa, three types of WRKY transcription factors were identified. Additionally, based on transcriptome data obtained in this study, reported transcriptome data, and laboratory available transcriptome data, positive selection sites were identified from 18 chloroplast protein-coding genes of four tree ferns. Among them, RNA editing was found in positive selection sites of four tree ferns. RNA editing affected the protein secondary structure of the rbcL gene. Furthermore, the expression level of chloroplast genes indicated high expression of genes related to the chloroplast photosynthetic system in all four species. CONCLUSIONS Overall, this work provides a comprehensive transcriptome resource of S. brunoniana and A. latebrosa, laying the foundation for future tree fern research.
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Affiliation(s)
- Yang Peng
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhen Wang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Minghui Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ting Wang
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
- Research Institute of Sun Yat-Sen University in Shenzhen, Shenzhen, 518057, China.
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Jia M, Ni Y, Zhao H, Liu X, Yan W, Zhao X, Wang J, He B, Liu H. Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola. BMC PLANT BIOLOGY 2024; 24:64. [PMID: 38262910 PMCID: PMC10804834 DOI: 10.1186/s12870-024-04728-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Corynespora leaf spot is a common leaf disease occurring in sesame, and the disease causes leaf yellowing and even shedding, which affects the growth quality of sesame. At present, the mechanism of sesame resistance to this disease is still unclear. Understanding the resistance mechanism of sesame to Corynespora leaf spot is highly important for the control of infection. In this study, the leaves of the sesame resistant variety (R) and the sesame susceptible variety (S) were collected at 0-48 hpi for transcriptome sequencing, and used a combined third-generation long-read and next-generation short-read technology approach to identify some key genes and main pathways related to resistance. RESULTS The gene expression levels of the two sesame varieties were significantly different at 0, 6, 12, 24, 36 and 48 hpi, indicating that the up-regulation of differentially expressed genes in the R might enhanced the resistance. Moreover, combined with the phenotypic observations of sesame leaves inoculated at different time points, we found that 12 hpi was the key time point leading to the resistance difference between the two sesame varieties at the molecular level. The WGCNA identified two modules significantly associated with disease resistance, and screened out 10 key genes that were highly expressed in R but low expressed in S, which belonged to transcription factors (WRKY, AP2/ERF-ERF, and NAC types) and protein kinases (RLK-Pelle_DLSV, RLK-Pelle_SD-2b, and RLK-Pelle_WAK types). These genes could be the key response factors in the response of sesame to infection by Corynespora cassiicola. GO and KEGG enrichment analysis showed that specific modules could be enriched, which manifested as enrichment in biologically important pathways, such as plant signalling hormone transduction, plant-pathogen interaction, carbon metabolism, phenylpropanoid biosynthesis, glutathione metabolism, MAPK and other stress-related pathways. CONCLUSIONS This study provides an important resource of genes contributing to disease resistance and will deepen our understanding of the regulation of disease resistance, paving the way for further molecular breeding of sesame.
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Affiliation(s)
- Min Jia
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Yunxia Ni
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
| | - Hui Zhao
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Xintao Liu
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Wenqing Yan
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Xinbei Zhao
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Jing Wang
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Bipo He
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China
| | - Hongyan Liu
- Key Laboratory of IPM of Pests on Crop (Southern North China), Ministry of Agriculture, Key Laboratory of Crop Pest Control of Henan, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
- Key Laboratory of Specific Oilseed Crops Genomics of Henan Province, Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, China.
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Liu C, Bian C, Gao Q, Gao Z, Huang Y, Wang L, Shi Q, Song L. Whole genome sequencing of a novel sea anemone (Actinostola sp.) from a deep-sea hydrothermal vent. Sci Data 2024; 11:102. [PMID: 38253640 PMCID: PMC10803348 DOI: 10.1038/s41597-024-02944-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Deep-sea hydrothermal vents are usually considered as extreme environments with high pressure, high temperature, scarce food, and chemical toxicity, while many local inhabitants have evolved special adaptive mechanisms for residence in this representative ecosystem. In this study, we constructed a high-quality genome assembly for a novel deep-sea anemone species (Actinostola sp.) that was resident at a depth of 2,971 m in an Edmond vent along the central Indian Ocean ridge, with a total size of 424.3 Mb and a scaffold N50 of 383 kb. The assembled genome contained 265 Mb of repetitive sequences and 20,812 protein-coding genes. Taken together, our reference genome provides a valuable genetic resource for exploring the evolution and adaptive clues of this deep-sea anemone.
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Affiliation(s)
- Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
| | - Chao Bian
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China
| | - Qiang Gao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, China
| | - Zijian Gao
- Shenzhen Key Lab of Marine Genomics, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, China.
| | - Qiong Shi
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518057, China.
- Shenzhen Key Lab of Marine Genomics, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, China.
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Sannino DR, Arroyo FA, Pepe-Ranney C, Chen W, Volland JM, Elisabeth NH, Angert ER. The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force. Proc Natl Acad Sci U S A 2023; 120:e2306160120. [PMID: 38109545 PMCID: PMC10756260 DOI: 10.1073/pnas.2306160120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.
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Affiliation(s)
| | | | - Charles Pepe-Ranney
- Soil & Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY14853
| | - Wenbo Chen
- Department of Microbiology, Cornell University, Ithaca, NY14853
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, CA94025
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Nathalie H. Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA94720
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An L, Pan Y, Yuan M, Wen Z, Qiao L, Wang W, Liu J, Li B, Liu W. Full-Length Transcriptome and Gene Expression Analysis of Different Ovis aries Adipose Tissues Reveals Transcript Variants Involved in Lipid Biosynthesis. Animals (Basel) 2023; 14:7. [PMID: 38200738 PMCID: PMC10777924 DOI: 10.3390/ani14010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/09/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Sheep have historically been bred globally as a vital food source. To explore the transcriptome of adipose tissue and investigate key genes regulating adipose metabolism in sheep, adipose tissue samples were obtained from F1 Dorper × Hu sheep. High-throughput sequencing libraries for second- and third-generation sequencing were constructed using extracted total RNA. Functional annotation of differentially expressed genes and isoforms facilitated the identification of key regulatory genes and isoforms associated with sheep fat metabolism. SMRT-seq generated 919,259 high-accuracy cDNA sequences after filtering. Full-length sequences were corrected using RNA-seq sequences, and 699,680 high-quality full-length non-chimeric (FLNC) reads were obtained. Upon evaluating the ratio of total lengths based on FLNC sequencing, it was determined that 36,909 out of 56,316 multiple-exon isoforms met the criteria for full-length status. This indicates the identification of 330,375 full-length FLNC transcripts among the 370,114 multiple-exon FLNC transcripts. By comparing the reference genomes, 60,276 loci and 111,302 isoforms were identified. In addition, 43,423 new genes and 44,563 new isoforms were identified. The results identified 185 (3198), 394 (3592), and 83 (3286) differentially expressed genes (transcripts) between tail and subcutaneous, tail and visceral, and subcutaneous and visceral adipose tissues, respectively. Functional annotation and pathway analysis revealed the following observations. (1) Among the differentially expressed genes (DEGs) of TF and SF tissues, the downregulation of ACADL, ACSL6, and NC_056060.1.2536 was observed in SF, while FFAR4 exhibited upregulation. (2) Among the DEGs of TF and VF tissues, expressions of ACADL, ACSL6, COL1A1, COL1A2, and SCD were downregulated in VF, with upregulation of FFAR4. (3) Among SF and VF expressions of COL1A1, COL1A2, and NC_056060.1.2536 were downregulated in VF. Specific differentially expressed genes (ACADL, ACSL6, COL1A1, COL1A2, FFAR4, NC_056060.1.2536, and SCD) and transcripts (NC_056066.1.1866.16 and NC_056066.1.1866.22) were identified as relevant to fat metabolism. These results provide a dataset for further verification of the regulatory pathway associated with fat metabolism in sheep.
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Affiliation(s)
- Lixia An
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
- School of Food & Environment, Jinzhong College of Information, Jinzhong 030801, China
| | - Yangyang Pan
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Mengjiao Yuan
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Zhonghao Wen
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Liying Qiao
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Weiwei Wang
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Jianhua Liu
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Baojun Li
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agricultural University, Jinzhong 030801, China; (L.A.); (Y.P.)
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Jaarsma AH, Zervas A, Sipes K, Campuzano Jiménez F, Smith AC, Svendsen LV, Thøgersen MS, Stougaard P, Benning LG, Tranter M, Anesio AM. The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome. Front Microbiol 2023; 14:1285791. [PMID: 38149278 PMCID: PMC10749974 DOI: 10.3389/fmicb.2023.1285791] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/24/2023] [Indexed: 12/28/2023] Open
Abstract
The Greenland Ice Sheet is a biome which is mainly microbially driven. Several different niches can be found within the glacial biome for those microbes able to withstand the harsh conditions, e.g., low temperatures, low nutrient conditions, high UV radiation in summer, and contrasting long and dark winters. Eukaryotic algae can form blooms during the summer on the ice surface, interacting with communities of bacteria, fungi, and viruses. Cryoconite holes and snow are also habitats with their own microbial community. Nevertheless, the microbiome of supraglacial habitats remains poorly studied, leading to a lack of representative genomes from these environments. Under-investigated extremophiles, like those living on the Greenland Ice Sheet, may provide an untapped reservoir of chemical diversity that is yet to be discovered. In this study, an inventory of the biosynthetic potential of these organisms is made, through cataloging the presence of biosynthetic gene clusters in their genomes. There were 133 high-quality metagenome-assembled genomes (MAGs) and 28 whole genomes of bacteria obtained from samples of the ice sheet surface, cryoconite, biofilm, and snow using culturing-dependent and -independent approaches. AntiSMASH and BiG-SCAPE were used to mine these genomes and subsequently analyze the resulting predicted gene clusters. Extensive sets of predicted Biosynthetic Gene Clusters (BGCs) were collected from the genome collection, with limited overlap between isolates and MAGs. Additionally, little overlap was found in the biosynthetic potential among different environments, suggesting specialization of organisms in specific habitats. The median number of BGCs per genome was significantly higher for the isolates compared to the MAGs. The most talented producers were found among Proteobacteria. We found evidence for the capacity of these microbes to produce antimicrobials, carotenoid pigments, siderophores, and osmoprotectants, indicating potential survival mechanisms to cope with extreme conditions. The majority of identified BGCs, including those in the most prevalent gene cluster families, have unknown functions, presenting a substantial potential for bioprospecting. This study underscores the diverse biosynthetic potential in Greenland Ice Sheet genomes, revealing insights into survival strategies and highlighting the need for further exploration and characterization of these untapped resources.
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Affiliation(s)
- Ate H. Jaarsma
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Katie Sipes
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | | | | | | | | | - Peter Stougaard
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Liane G. Benning
- German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, Germany
- Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Martyn Tranter
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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Li X, Wang X, Yu X, Yang C, Lin L, Huang Y. The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 2023; 24:751. [PMID: 38062370 PMCID: PMC10702090 DOI: 10.1186/s12864-023-09857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa. RESULTS The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs). CONCLUSIONS A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
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Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chao Yang
- Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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Yao T, Zhang Z, Li Q, Huang R, Hong Y, Li C, Zhang F, Huang Y, Fang Y, Cao Q, Jin X, Li C, Wang Z, Lin XJ, Li L, Wei W, Wang Z, Shen J. Long-Read Sequencing Reveals Alternative Splicing-Driven, Shared Immunogenic Neoepitopes Regardless of SF3B1 Status in Uveal Melanoma. Cancer Immunol Res 2023; 11:1671-1687. [PMID: 37756564 DOI: 10.1158/2326-6066.cir-23-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/13/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Tumor-specific neoepitopes are promising targets in cancer immunotherapy. However, the identification of functional tumor-specific neoepitopes remains challenging. In addition to the most common source, single-nucleotide variants (SNV), alternative splicing (AS) represents another rich source of neoepitopes and can be utilized in cancers with low SNVs such as uveal melanoma (UM). UM, the most prevalent adult ocular malignancy, has poor clinical outcomes due to a lack of effective therapies. Recent studies have revealed the promise of harnessing tumor neoepitopes to treat UM. Previous studies have focused on neoepitope targets associated with mutations in splicing factor 3b subunit 1 (SF3B1), a key splicing factor; however, little is known about the neoepitopes that are commonly shared by patients independent of SF3B1 status. To identify the AS-derived neoepitopes regardless of SF3B1 status, we herein used a comprehensive nanopore long-read-sequencing approach to elucidate the landscape of AS and novel isoforms in UM. We also performed high-resolution mass spectrometry to further validate the presence of neoepitope candidates and analyzed their structures using the AlphaFold2 algorithm. We experimentally evaluated the antitumor effects of these neoepitopes and found they induced robust immune responses by stimulating interferon (IFN)γ production and activating T cell-based UM tumor killing. These results provide novel insights into UM-specific neoepitopes independent of SF3B1 and lay the foundation for developing therapies by targeting these actionable neoepitopes.
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Affiliation(s)
- Tengteng Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Zhe Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Huang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanhong Hong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Lingang Laboratory, Shanghai, China
| | - Chen Li
- High Performance Computing Center, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Zhang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingying Huang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Lingang Laboratory, Shanghai, China
| | - Yan Fang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qin Cao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoliang Jin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS Shanghai Institute of Nutrition and Health, Shanghai, China
| | - Xinhua James Lin
- High Performance Computing Center, Shanghai Jiao Tong University, Shanghai, China
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Lingang Laboratory, Shanghai, China
| | - Zhaoyang Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
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Kang X, Xu J, Luo X, Schönhuth A. Hybrid-hybrid correction of errors in long reads with HERO. Genome Biol 2023; 24:275. [PMID: 38041098 PMCID: PMC10690975 DOI: 10.1186/s13059-023-03112-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023] Open
Abstract
Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in polyploid and mixed samples. We suggest HERO, as the first "hybrid-hybrid" approach, to make use of both de Bruijn graphs and overlap graphs for optimal catering to the particular strengths of NGS and TGS reads. Extensive benchmarking experiments demonstrate that HERO improves indel and mismatch error rates by on average 65% (27[Formula: see text]95%) and 20% (4[Formula: see text]61%). Using HERO prior to genome assembly significantly improves the assemblies in the majority of the relevant categories.
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Affiliation(s)
- Xiongbin Kang
- College of Biology, Hunan University, Changsha, China
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Jialu Xu
- College of Biology, Hunan University, Changsha, China
| | - Xiao Luo
- College of Biology, Hunan University, Changsha, China.
| | - Alexander Schönhuth
- Genome Data Science, Faculty of Technology, Bielefeld University, Bielefeld, Germany.
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Wang M, Yu W, Yang J, Hou Z, Li C, Niu Z, Zhang B, Xue Q, Liu W, Ding X. Mitochondrial genome comparison and phylogenetic analysis of Dendrobium (Orchidaceae) based on whole mitogenomes. BMC PLANT BIOLOGY 2023; 23:586. [PMID: 37993773 PMCID: PMC10666434 DOI: 10.1186/s12870-023-04618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
BACKGROUND Mitochondrial genomes are essential for deciphering the unique evolutionary history of seed plants. However, the rules of their extreme variation in genomic size, multi-chromosomal structure, and foreign sequences remain unresolved in most plant lineages, which further hindered the application of mitogenomes in phylogenetic analyses. RESULTS Here, we took Dendrobium (Orchidaceae) which shows the great divergence of morphology and difficulty in species taxonomy as the study focus. We first de novo assembled two complete mitogenomes of Dendrobium wilsonii and Dendrobium henanense that were 763,005 bp and 807,551 bp long with multichromosomal structures. To understand the evolution of Dendrobium mitogenomes, we compared them with those of four other orchid species. The results showed great variations of repetitive and chloroplast-derived sequences in Dendrobium mitogenomes. Moreover, the intergenic content of Dendrobium mitogenomes has undergone expansion during evolution. We also newly sequenced mitogenomes of 26 Dendrobium species and reconstructed phylogenetic relationships of Dendrobium based on genomic mitochondrial and plastid data. The results indicated that the existence of chloroplast-derived sequences made the mitochondrial phylogeny display partial characteristics of the plastid phylogeny. Additionally, the mitochondrial phylogeny provided new insights into the phylogenetic relationships of Dendrobium species. CONCLUSIONS Our study revealed the evolution of Dendrobium mitogenomes and the potential of mitogenomes in deciphering phylogenetic relationships at low taxonomic levels.
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Grants
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- 32070353 National Natural Science Foundation of China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- LYKJ[2021]12 Forestry independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
- CX (22) 3147 Agricultural independent innovation project of Jiangsu Province, China
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Affiliation(s)
- Mengting Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Cixi, China
| | - Wenhui Yu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jiapeng Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenyu Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chao Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhitao Niu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Benhou Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qingyun Xue
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wei Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoyu Ding
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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Catapano PL, Falcinelli M, Damiani C, Cappelli A, Koukouli D, Rossi P, Ricci I, Napolioni V, Favia G. De novo genome assembly of the invasive mosquito species Aedes japonicus and Aedes koreicus. Parasit Vectors 2023; 16:427. [PMID: 37986088 PMCID: PMC10658958 DOI: 10.1186/s13071-023-06048-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Recently, two invasive Aedes mosquito species, Ae. japonicus and Ae. koreicus, are circulating in several European countries posing potential health risks to humans and animals. Vector control is the main option to prevent mosquito-borne diseases, and an accurate genome sequence of these mosquitoes is essential to better understand their biology and to develop effective control strategies. METHODS A de novo genome assembly of Ae. japonicus (Ajap1) and Ae. koreicus (Akor1) has been produced based on a hybrid approach that combines Oxford Nanopore long-read and Illumina short-read data. Their quality was ascertained using various metrics. Masking of repetitive elements, gene prediction and functional annotation was performed. RESULTS Sequence analysis revealed a very high presence of repetitive DNA and, among others, thermal adaptation genes and insecticide-resistance genes. Through the RNA-seq analysis of larvae and adults of Ae. koreicus and Ae. japonicus exposed to different temperatures, we also identified genes showing a differential temperature-dependent activation. CONCLUSIONS The assembly of Akor1 and Ajap1 genomes constitutes the first updated collective knowledge of the genomes of both mosquito species, providing the possibility of understanding key mechanisms of their biology such as the ability to adapt to harsh climates and to develop insecticide-resistance mechanisms.
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Affiliation(s)
- Paolo L Catapano
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Monica Falcinelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Claudia Damiani
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Alessia Cappelli
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Despoina Koukouli
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Paolo Rossi
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Irene Ricci
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Valerio Napolioni
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Guido Favia
- School of Biosciences and Veterinary Medicine, University of Camerino, CIRM Italian Malaria Network, Via Gentile III da Varano, 62032, Camerino, Italy.
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Liu Z, Huang Y, Chen H, Liu C, Wang M, Bian C, Wang L, Song L. Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat. BMC Genomics 2023; 24:679. [PMID: 37950158 PMCID: PMC10638732 DOI: 10.1186/s12864-023-09760-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/22/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The deep-sea snail Phymorhynchus buccinoides belongs to the genus Phymorhynchus (Neogastropoda: Raphitomidae), and it is a dominant specie in the cold seep habitat. As the environment of the cold seep is characterized by darkness, hypoxia and high concentrations of toxic substances such as hydrogen sulfide (H2S), exploration of the diverse fauna living around cold seeps will help to uncover the adaptive mechanisms to this unique habitat. In the present study, a chromosome-level genome of P. buccinoides was constructed and a series of genomic and transcriptomic analyses were conducted to explore its molecular adaptation mechanisms to the cold seep environments. RESULTS The assembled genome size of the P. buccinoides was approximately 2.1 Gb, which is larger than most of the reported snail genomes, possibly due to the high proportion of repetitive elements. About 92.0% of the assembled base pairs of contigs were anchored to 34 pseudo-chromosomes with a scaffold N50 size of 60.0 Mb. Compared with relative specie in the shallow water, the glutamate regulative and related genes were expanded in P. buccinoides, which contributes to the acclimation to hypoxia and coldness. Besides, the relatively high mRNA expression levels of the olfactory/chemosensory genes in osphradium indicate that P. buccinoides might have evolved a highly developed and sensitive olfactory organ for its orientation and predation. Moreover, the genome and transcriptome analyses demonstrate that P. buccinoides has evolved a sulfite-tolerance mechanism by performing H2S detoxification. Many genes involved in H2S detoxification were highly expressed in ctenidium and hepatopancreas, suggesting that these tissues might be critical for H2S detoxification and sulfite tolerance. CONCLUSIONS In summary, our report of this chromosome-level deep-sea snail genome provides a comprehensive genomic basis for the understanding of the adaptation strategy of P. buccinoides to the extreme environment at the deep-sea cold seeps.
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Affiliation(s)
- Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yuting Huang
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Chen
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Minxiao Wang
- Center of Deep Sea Research, and CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Bian
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China.
- Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
- Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
- Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
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73
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Han T, Liao X, Guo Z, Chen JY, He C, Lu Z. Comparative transcriptome analysis reveals deep molecular landscapes in stony coral Montipora clade. Front Genet 2023; 14:1297483. [PMID: 38028626 PMCID: PMC10662330 DOI: 10.3389/fgene.2023.1297483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Coral reefs, among the most invaluable ecosystems in the world, face escalating threats from climate change and anthropogenic activities. To decipher the genetic underpinnings of coral adaptation and resilience, we undertook comprehensive transcriptome profiling of two emblematic coral species, Montipora foliosa and Montipora capricornis, leveraging PacBio Iso-Seq technology. These species were strategically selected for their ecological significance and their taxonomic proximity within the Anthozoa class. Methods: Our study encompassed the generation of pristine transcriptomes, followed by thorough functional annotation via diverse databases. Subsequently, we quantified transcript abundance and scrutinized gene expression patterns, revealing notable distinctions between the two species. Results: Intriguingly, shared orthologous genes were identified across a spectrum of coral species, highlighting a substantial genetic conservation within scleractinian corals. Importantly, a subset of genes, integral to biomineralization processes, emerged as exclusive to scleractinian corals, shedding light on their intricate evolutionary history. Furthermore, we discerned pronounced upregulation of genes linked to immunity, stress response, and oxidative-reduction processes in M. foliosa relative to M. capricornis. These findings hint at the presence of more robust mechanisms in M. foliosa for maintaining internal equilibrium and effectively navigating external challenges, underpinning its potential ecological advantage. Beyond elucidating genetic adaptation in corals, our research underscores the urgency of preserving genetic diversity within coral populations. Discussion: These insights hold promise for informed conservation strategies aimed at safeguarding these imperiled ecosystems, bearing ecological and economic significance. In synthesis, our study seamlessly integrates genomic inquiry with ecological relevance, bridging the gap between molecular insights and the imperative to conserve coral reefs in the face of mounting threats.
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Affiliation(s)
- Tingyu Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Liao
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, China
| | - Zhuojun Guo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - J.-Y. Chen
- Nanjing Institute of Geology and Paleontology, Nanjing, China
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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Bramsiepe J, Krabberød AK, Bjerkan KN, Alling RM, Johannessen IM, Hornslien KS, Miller JR, Brysting AK, Grini PE. Structural evidence for MADS-box type I family expansion seen in new assemblies of Arabidopsis arenosa and A. lyrata. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:942-961. [PMID: 37517071 DOI: 10.1111/tpj.16401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/24/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023]
Abstract
Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The three species differ by genome-wide polymorphisms and morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based on the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors is specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for its high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de-novo assembled and annotated chromosome-level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS-box type I gene family in Arabidopsis to predict orthologs, copy number, and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression in the endosperm of A. arenosa and A. lyrata ssp. petraea, suggesting a genetic cause for the endosperm-based hybridization barrier between A. arenosa and A. lyrata ssp. petraea.
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Affiliation(s)
- Jonathan Bramsiepe
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Anders K Krabberød
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Katrine N Bjerkan
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Renate M Alling
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Ida M Johannessen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Karina S Hornslien
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Jason R Miller
- College of STEM, Shepherd University, Shepherdstown, West Virginia, 25443-5000, USA
| | - Anne K Brysting
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
- CEES, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
| | - Paul E Grini
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, 0316, Oslo, Norway
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Chandra G, Jain C. Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs. J Comput Biol 2023; 30:1182-1197. [PMID: 37902967 DOI: 10.1089/cmb.2023.0186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023] Open
Abstract
A pangenome graph can serve as a better reference for genomic studies because it allows a compact representation of multiple genomes within a species. Aligning sequences to a graph is critical for pangenome-based resequencing. The seed-chain-extend heuristic works by finding short exact matches between a sequence and a graph. In this heuristic, colinear chaining helps identify a good cluster of exact matches that can be combined to form an alignment. Colinear chaining algorithms have been extensively studied for aligning two sequences with various gap costs, including linear, concave, and convex cost functions. However, extending these algorithms for sequence-to-graph alignment presents significant challenges. Recently, Makinen et al. introduced a sparse dynamic programming framework that exploits the small path cover property of acyclic pangenome graphs, enabling efficient chaining. However, this framework does not consider gap costs, limiting its practical effectiveness. We address this limitation by developing novel problem formulations and provably good chaining algorithms that support a variety of gap cost functions. These functions are carefully designed to enable fast chaining algorithms whose time requirements are parameterized in terms of the size of the minimum path cover. Through an empirical evaluation, we demonstrate the superior performance of our algorithm compared with existing aligners. When mapping simulated long reads to a pangenome graph comprising 95 human haplotypes, we achieved 98.7% precision while leaving <2% of reads unmapped.
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Affiliation(s)
- Ghanshyam Chandra
- Department of Computational and Data Sciences, Indian Institute of Science Bengaluru, India
| | - Chirag Jain
- Department of Computational and Data Sciences, Indian Institute of Science Bengaluru, India
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Pourmohammadi R, Abouei J, Anpalagan A. Error analysis of the PacBio sequencing CCS reads. Int J Biostat 2023; 19:439-453. [PMID: 37155831 DOI: 10.1515/ijb-2021-0091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/07/2022] [Indexed: 05/10/2023]
Abstract
Third generation sequencing technologies such as Pacific Biosciences and Oxford Nanopore provide faster, cost-effective and simpler assembly process generating longer reads than the ones in the next generation sequencing. However, the error rates of these long reads are higher than those of the short reads, resulting in an error correcting process before the assembly such as using the Circular Consensus Sequencing (CCS) reads in PacBio sequencing machines. In this paper, we propose a probabilistic model for the error occurrence along the CCS reads. We obtain the error probability of any arbitrary nucleotide as well as the base calling Phred quality score of the nucleotides along the CCS reads in terms of the number of sub-reads. Furthermore, we derive the error rate distribution of the reads in relation to the pass number. It follows the binomial distribution which can be approximated by the normal distribution for long reads. Finally, we evaluate our proposed model by comparing it with three real PacBio datasets, namely, Lambda, and E. coli genomes, and Alzheimer's disease targeted experiment.
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Affiliation(s)
- Reza Pourmohammadi
- WINEL Research Laboratory at the Department of Electrical Engineering, Yazd University, Yazd, Iran
| | - Jamshid Abouei
- WINEL Research Laboratory at the Department of Electrical Engineering, Yazd University, Yazd, Iran
| | - Alagan Anpalagan
- Department of Electrical, Computer and Biomedical Engineering, Ryerson University, Toronto, Canada
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77
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Guo L, Chen T, Chu X, Sun K, Yu F, Que F, Ahmad Z, Wei Q, Ramakrishnan M. Anatomical and Transcriptome Analyses of Moso Bamboo Culm Neck Growth: Unveiling Key Insights. PLANTS (BASEL, SWITZERLAND) 2023; 12:3478. [PMID: 37836218 PMCID: PMC10574802 DOI: 10.3390/plants12193478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/24/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
The Moso bamboo culm neck, connected with the rhizome and the shoot bud, is an important hub for connecting and transporting the aboveground and belowground systems of bamboo for the shoot bud development and rapid growth. Our previous study revealed that the culm neck generally undergoes six different developmental stages (CNS1-CNS6), according to the primary thickening growth of the underground shoot bud. However, the molecular mechanism of the culm neck development remains unknown. The present study focused on the developmental process of the CNS3-CNS5 stages, representing the early, middle, and late elongation stages, respectively. These stages are densely packed with vascular tissues and consist of epidermis, hypodermis, cortex, and ground tissue. Unlike the hollow structure of the culms, the culm necks are solid structures. As the culm neck continues to grow, the lignin deposition increases noticeably, contributing to its progressive strengthening. For the transcriptome analysis, a total of 161,160 transcripts with an average length of 2373 were obtained from these stages using both PacBio and Illumina sequencing. A total of 92.2% of the reads mapped to the Moso bamboo reference genome. Further analysis identified a total of 5524 novel genes and revealed a dynamic transcriptome. Secondary-metabolism- and transport-related genes were upregulated particularly with the growth of the culm neck. Further analysis revealed the molecular processes of lignin accumulation in the culm neck, which include differentially expressed genes (DEGs) related to cell wall loosening and remodeling and secondary metabolism. Moreover, the upregulations of transcription factors such as MYBH and RSM in the MYB family play crucial roles during critical transitions in the culm neck development, such as changes in the angle between the rhizome and the culm neck. Our new findings provide essential insights into the cellular roadmaps, transcriptional networks, and key genes involved in the culm neck development.
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Affiliation(s)
- Lin Guo
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Tianguo Chen
- Changzhou Agricultural Technology Extension Center, Changzhou 213000, China
| | - Xue Chu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Kai Sun
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Fen Yu
- Changzhou Agricultural Technology Extension Center, Changzhou 213000, China
| | - Feng Que
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Zishan Ahmad
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Wei
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang 330045, China
| | - Muthusamy Ramakrishnan
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
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Wu C, Li L, Wang Y, Wei S, Zhu J. Morphological, functional, compositional and transcriptional constraints shape the distinct venom profiles of the assassin bug Sycanus croceovittatus. Int J Biol Macromol 2023; 250:126162. [PMID: 37558034 DOI: 10.1016/j.ijbiomac.2023.126162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023]
Abstract
Predatory bugs employ a salivary venom apparatus to generate complex venoms for capturing and digesting prey. The venom apparatus consists of different glands for the production of distinct venom sets, but the underlying mechanisms behind this process remain poorly understood. Here we present a comprehensive analysis of the morphological, functional, compositional and transcriptional characteristics of venoms derived from posterior main gland (PMG), anterior main gland (AMG), and accessory gland (AG) of the assassin bug Sycanus croceovittatus. Structural observations revealed the intricate constructions of the venom apparatus, enabling the production and storage of three distinct venom sets in anatomically varied glands and allowing them to be modulated in a context-dependent manner upon utilization. There were remarkable differences in the biological activities exhibited by PMG, AMG, and AG venoms. Proteotranscriptomic analysis demonstrated that these venoms displayed compositional heterogeneity at both the quantity and variety levels of proteins. Transcriptional profiles of the identified venom proteins revealed gland-specific or biased expression patterns. These findings indicate that the divergence in venom profiles among different glands arises from morphological, functional, compositional and transcriptional constraints on the venom apparatus, reflecting remarkable morphogenesis and regulatory gene networks responsible for the compartmentalized production of venom proteins in different glands.
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Affiliation(s)
- Chaoyan Wu
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Lu Li
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Yuqin Wang
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Shujun Wei
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China; Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jiaying Zhu
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China; Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China.
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79
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Yan X, Chen X, Li Y, Li Y, Wang F, Zhang J, Ning G, Bao M. The Abundant and Unique Transcripts and Alternative Splicing of the Artificially Autododecaploid London Plane ( Platanus × acerifolia). Int J Mol Sci 2023; 24:14486. [PMID: 37833935 PMCID: PMC10572260 DOI: 10.3390/ijms241914486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Transcription and alternative splicing (AS) are now appreciated in plants, but few studies have examined the effects of changing ploidy on transcription and AS. In this study, we showed that artificially autododecaploid plants of London plane (Platanus × acerifolia (Aiton) Willd) had few flowers relative to their hexaploid progenitors. Transcriptome analysis based on full-length Oxford Nanopore Technologies (ONTs) and next-generation sequencing (NGS) revealed that the increased ploidy level in P. × acerifolia led to more transcribed isoforms, accompanied by an increase in the number of isoforms per gene. The functional enrichment of genes indicated that novel genes transcribed specifically in the dodecaploids may have been highly correlated with the ability to maintain genome stability. The dodecaploids showed a higher number of genes with upregulated differentially expressed genes (DEGs) compared with the hexaploid counterpart. The genome duplication of P. × acerifolia resulted mainly in the DEGs involved in basic biological pathways. It was noted that there was a greater abundance of alternative splicing (AS) events and AS genes in the dodecaploids compared with the hexaploids in P. × acerifolia. In addition, a significant difference between the structure and expression of AS events between the hexaploids and dodecaploids of Platanus was found. Of note, some DEGs and differentially spliced genes (DSGs) related to floral transition and flower development were consistent with the few flower traits in the dodecaploids of P. × acerifolia. Collectively, our findings explored the difference in transcription and AS regulation between the hexaploids and dodecaploids of P. × acerifolia and gained new insight into the molecular mechanisms underlying the few-flower phenotype of P. × acerifolia. These results contribute to uncovering the regulatory role of transcription and AS in polyploids and breeding few-flower germplasms.
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Affiliation(s)
| | | | | | | | | | | | | | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (X.Y.); (J.Z.)
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80
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Lin Z, Qin Y, Chen H, Shi D, Zhong M, An T, Chen L, Wang Y, Lin F, Li G, Ji ZL. TransIntegrator: capture nearly full protein-coding transcript variants via integrating Illumina and PacBio transcriptomes. Brief Bioinform 2023; 24:bbad334. [PMID: 37779246 DOI: 10.1093/bib/bbad334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Genes have the ability to produce transcript variants that perform specific cellular functions. However, accurately detecting all transcript variants remains a long-standing challenge, especially when working with poorly annotated genomes or without a known genome. To address this issue, we have developed a new computational method, TransIntegrator, which enables transcriptome-wide detection of novel transcript variants. For this, we determined 10 Illumina sequencing transcriptomes and a PacBio full-length transcriptome for consecutive embryo development stages of amphioxus, a species of great evolutionary importance. Based on the transcriptomes, we employed TransIntegrator to create a comprehensive transcript variant library, namely iTranscriptome. The resulting iTrancriptome contained 91 915 distinct transcript variants, with an average of 2.4 variants per gene. This substantially improved current amphioxus genome annotation by expanding the number of genes from 21 954 to 38 777. Further analysis manifested that the gene expansion was largely ascribed to integration of multiple Illumina datasets instead of involving the PacBio data. Moreover, we demonstrated an example application of TransIntegrator, via generating iTrancriptome, in aiding accurate transcriptome assembly, which significantly outperformed other hybrid methods such as IDP-denovo and Trinity. For user convenience, we have deposited the source codes of TransIntegrator on GitHub as well as a conda package in Anaconda. In summary, this study proposes an affordable but efficient method for reliable transcriptomic research in most species.
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Affiliation(s)
- Zhe Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, 361102, Xiamen, China
| | - Yangmei Qin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Hao Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Dan Shi
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Mindong Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Te An
- School of Informatics, Xiamen University, 361005, Xiamen, China
| | - Linshan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Yiquan Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Fan Lin
- National Institute for Data Science in Health and Medicine, Xiamen University, 361102, Xiamen, China
- School of Informatics, Xiamen University, 361005, Xiamen, China
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
| | - Zhi-Liang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China
- National Institute for Data Science in Health and Medicine, Xiamen University, 361102, Xiamen, China
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81
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Liufu Y, Xi F, Wu L, Zhang Z, Wang H, Wang H, Zhang J, Wang B, Kou W, Gao J, Zhao L, Zhang H, Gu L. Inhibition of DNA and RNA methylation disturbs root development of moso bamboo. TREE PHYSIOLOGY 2023; 43:1653-1674. [PMID: 37294626 DOI: 10.1093/treephys/tpad074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/25/2023] [Accepted: 06/03/2023] [Indexed: 06/11/2023]
Abstract
DNA methylation (5mC) and N6-methyladenosine (m6A) are two important epigenetics regulators, which have a profound impact on plant growth development. Phyllostachys edulis (P. edulis) is one of the fastest spreading plants due to its well-developed root system. However, the association between 5mC and m6A has seldom been reported in P. edulis. In particular, the connection between m6A and several post-transcriptional regulators remains uncharacterized in P. edulis. Here, our morphological and electron microscope observations showed the phenotype of increased lateral root under RNA methylation inhibitor (DZnepA) and DNA methylation inhibitor (5-azaC) treatment. RNA epitranscriptome based on Nanopore direct RNA sequencing revealed that DZnepA treatment exhibits significantly decreased m6A level in the 3'-untranslated region (3'-UTR), which was accompanied by increased gene expression, full-length ratio, higher proximal poly(A) site usage and shorter poly(A) tail length. DNA methylation levels of CG and CHG were reduced in both coding sequencing and transposable element upon 5-azaC treatment. Cell wall synthesis was impaired under methylation inhibition. In particular, differentially expressed genes showed a high percentage of overlap between DZnepA and 5-azaC treatment, which suggested a potential correlation between two methylations. This study provides preliminary information for a better understanding of the link between m6A and 5mC in root development of moso bamboo.
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Affiliation(s)
- Yuxiang Liufu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Feihu Xi
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin Wu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Zeyu Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Huihui Wang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Huiyuan Wang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Jun Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Baijie Wang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Wenjing Kou
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
| | - Jian Gao
- Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Liangzhen Zhao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao Zhang
- Key Laboratory of Bamboo and Rattan Science and Technology, State Forestry Administration, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province 350002, China
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82
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Xue JY, Fan HY, Zeng Z, Zhou YH, Hu SY, Li SX, Cheng YJ, Meng XR, Chen F, Shao ZQ, Van de Peer Y. Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato. HORTICULTURE RESEARCH 2023; 10:uhad147. [PMID: 37691964 PMCID: PMC10483172 DOI: 10.1093/hr/uhad147] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/15/2023] [Indexed: 09/12/2023]
Abstract
MicroTom has a short growth cycle and high transformation efficiency, and is a prospective model plant for studying organ development, metabolism, and plant-microbe interactions. Here, with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments, we constructed multiple gene co-expression networks, which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth, e.g. arbuscular mycorrhizal symbiosis and fruit development. Additionally, non-coding RNAs, including miRNAs, lncRNAs, and circRNAs were also identified, together with their potential targets. Interacting networks between different types of non-coding RNAs (miRNA-lncRNA), and non-coding RNAs and genes (miRNA-mRNA and lncRNA-mRNA) were constructed as well. Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit. Lastly, we established a database (http://eplant.njau.edu.cn/microTomBase/) with genomic and transcriptomic data, as well as details of gene co-expression and interacting networks on MicroTom, and this database should be of great value to those who want to adopt MicroTom as a model plant for research.
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Affiliation(s)
- Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai-Yun Fan
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Zeng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yu-Han Zhou
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuai-Ya Hu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Sai-Xi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ying-Juan Cheng
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiang-Ru Meng
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Chen
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Haikou 570228, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Biotechnology and Bioinformatics, VIB-UGent Center for Plant Systems Biology, Ghent University, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
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83
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Tian M, Jin B, Chen L, Ma R, Ma Q, Li X, Chen T, Guo J, Ge H, Zhao X, Lai C, Tang J, Cui G, Huang L. Functional diversity of diterpene synthases in Aconitum plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107968. [PMID: 37619270 DOI: 10.1016/j.plaphy.2023.107968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/30/2023] [Accepted: 08/06/2023] [Indexed: 08/26/2023]
Abstract
Members of the Aconitum genus within the Ranunculaceae family are known to accumulate a broad array of medicinal and toxic diterpenoid alkaloids (DAs). Historically, ent-copalyl diphosphate (ent-CPP) was considered the sole precursor in DAs biosynthesis. However, the recent discovery of ent-8,13-CPP synthase in A. gymnandrum Maxim., which participates in ent-atiserene biosynthesis, raises the question of whether this gene is conserved throughout the Aconitum genus. In this study, RNA sequencing and PacBio Iso-sequencing were employed to identify diterpene synthases (diTPSs) in four additional Aconitum species with distinct DA compositions. In vitro and in vivo analyses functionally characterized a diverse array of 10 class II and 9 class I diTPSs. In addition to the identification of seven class II diTPSs as ent-CPP synthases, three other synthases generating ent-8,13-CPP, 8,13-CPP, and 8α-hydroxy-CPP were also discovered. Four class I kaurene synthases-like (KSLs) were observed to react with ent-CPP to yield ent-kaurene. Three KSLs not only reacted with ent-CPP but also ent-8,13-CPP to produce ent-atiserene. AsiKSL2-1 was found to react with 8α-hydroxy-CPP to produce Z-abienol and AsiKSL2-2 exhibited no activity with any of the four intermediates. This research delineates the known diterpene biosynthesis pathways in six Aconitum species and explores the highly divergent diterpene synthases within the genus, which are consistent with their phylogeny and may be responsible for the differential distribution of diterpenoid alkaloids in root and aerial parts. These findings contribute valuable insights into the diversification of diterpene biosynthesis and establish a solid foundation for future investigation into DA biosynthetic pathways in Aconitum.
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Affiliation(s)
- Mei Tian
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baolong Jin
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Lingli Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China; Institute of Traditional Chinese Medicine, Anhui Food and Drug Inspection and Research Institute, Hefei, 230051, China
| | - Rui Ma
- School of Pharmacy, Henan University of Chinese Medicine, Henan, 450046, China
| | - Qing Ma
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaolin Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Tong Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Juan Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Hui Ge
- Gansu University of Traditional Chinese Medicine, Gansu, 730000, China
| | - Xin Zhao
- Gansu University of Traditional Chinese Medicine, Gansu, 730000, China
| | - Changjiangsheng Lai
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jinfu Tang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Guanghong Cui
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Luqi Huang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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84
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Duan Q, Luo Q, Tang Q, Deng L, Zhang R, Li Y. Comprehensive transcripts analysis based on single-molecule real-time sequencing and Illumina sequencing provides insights into the mining of Toll-like receptor family in Schizothorax lissolabiatus. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108963. [PMID: 37481099 DOI: 10.1016/j.fsi.2023.108963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
Schizothorax lissolabiatus is an economically important cold-water fish species in southwestern China. Because of water pollution and habitat destruction, the number of wild populations has dramatically decreased. In this study, we used PacBio single-molecule real-time (SMRT) sequencing and Illumina sequencing to generate the first full-length transcriptome and transcriptome, respectively. A total of 19 310 polished consensus reads (PC) were obtained, with an average length of 1379 bp and an N50 length of 1485 bp. Meanwhile, 12 253 transcripts were successfully annotated as known homologous genes. The pathway annotation indicated that the enrichment and expression of most genes were mainly related to membrane, signal transduction and binding, and immune response. Furthermore, we identified 16 Toll-like receptors (TLRs) by mining the data from the transcripts. Phylogeny analysis showed that S. lissolabiatus TLR genes (slTLRs) supported the classification of TLRs into six families as in other vertebrates. Selection pressure analyses showed that 16 slTLRs revealed purification selection at the overall evolutionary selection. Further, positive selection signals were still detected in eight slTLRs, and most of the positive selection sites were located in the leucine-rich repeat region (LRR domain) associated with the recognition of pathogenic microorganisms, indicating that the function of these slTLR genes may be affected. Tissue specific expression analysis showed all slTLRs are present in kidney, spleen and liver but the relative expression varied among tissues. In conclusion, this study not only provided a valuable resource of transcripts for further research on S. lissolabiatus, but also contributed to improve the current understanding of the evolutionary history of immune-related genes and the TLR gene family in S. lissolabiatus.
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Affiliation(s)
- Qian Duan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Qi Luo
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Qian Tang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Lei Deng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China
| | - Renyi Zhang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
| | - Yanping Li
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, China.
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85
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Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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86
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Sukumaran S, Sebastian W, Gopalakrishnan A, Mathew OK, Vysakh VG, Rohit P, Jena JK. The sequence and de novo assembly of the genome of the Indian oil sardine, Sardinella longiceps. Sci Data 2023; 10:565. [PMID: 37626109 PMCID: PMC10457283 DOI: 10.1038/s41597-023-02481-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The Indian oil sardine, Sardinella longiceps, is a widely distributed and commercially important small pelagic fish of the Northern Indian Ocean. The genome of the Indian oil sardine has been characterized using Illumina and Nanopore platforms. The assembly is 1.077 Gb (31.86 Mb Scaffold N50) in size with a repeat content of 23.24%. The BUSCO (Benchmarking Universal Single Copy Orthologues) completeness of the assembly is 93.5% when compared with Actinopterygii (ray finned fishes) data set. A total of 46316 protein coding genes were predicted. Sardinella longiceps is nutritionally rich with high levels of omega-3 polyunsaturated fatty acids (PUFA). The core genes for omega-3 PUFA biosynthesis, such as Elovl 1a and 1b,Elovl 2, Elovl 4a and 4b,Elovl 8a and 8b,and Fads 2, were observed in Sardinella longiceps. The presence of these genes may indicate the PUFA biosynthetic capability of Indian oil sardine, which needs to be confirmed functionally.
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Affiliation(s)
- Sandhya Sukumaran
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
| | - Wilson Sebastian
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - Oommen K Mathew
- Agrigenome Labs Pvt. Ltd., Kakkanad, Kochi, Kerala, 682042, India
| | - V G Vysakh
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - Prathibha Rohit
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - J K Jena
- ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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87
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Zhang Z, Li C, Li Q, Su X, Li J, Zhu L, Lin XJ, Shen J. Structure prediction of novel isoforms from uveal melanoma by AlphaFold. Sci Data 2023; 10:513. [PMID: 37542084 PMCID: PMC10403560 DOI: 10.1038/s41597-023-02429-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/28/2023] [Indexed: 08/06/2023] Open
Abstract
Alternative splicing is an important mechanism that enhances protein functional diversity. To date, our understanding of alternative splicing variants has been based on mRNA transcript data, but due to the difficulty in predicting protein structures, protein tertiary structures have been largely unexplored. However, with the release of AlphaFold, which predicts three-dimensional models of proteins, this challenge is rapidly being overcome. Here, we present a dataset of 315 predicted structures of abnormal isoforms in 18 uveal melanoma patients based on second- and third-generation transcriptome-sequencing data. This information comprises a high-quality set of structural data on recurrent aberrant isoforms that can be used in multiple types of studies, from those aimed at revealing potential therapeutic targets to those aimed at recognizing of cancer neoantigens at the atomic level.
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Affiliation(s)
- Zhe Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Chen Li
- High Performance Computing Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoming Su
- High Performance Computing Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lili Zhu
- Songjiang Research Institute and Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
| | - Xinhua James Lin
- High Performance Computing Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
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88
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Kuśmirek W. Estimated Nucleotide Reconstruction Quality Symbols of Basecalling Tools for Oxford Nanopore Sequencing. SENSORS (BASEL, SWITZERLAND) 2023; 23:6787. [PMID: 37571570 PMCID: PMC10422362 DOI: 10.3390/s23156787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Currently, one of the fastest-growing DNA sequencing technologies is nanopore sequencing. One of the key stages involved in processing sequencer data is the basecalling process, where the input sequence of currents measured on the nanopores of the sequencer reproduces the DNA sequences, called DNA reads. Many of the applications dedicated to basecalling, together with the DNA sequence, provide the estimated quality of the reconstruction of a given nucleotide (quality symbols are contained on every fourth line of the FASTQ file; each nucleotide in the FASTQ file corresponds to exactly one estimated nucleotide reconstruction quality symbol). Herein, we compare the estimated nucleotide reconstruction quality symbols (signs from every fourth line of the FASTQ file) reported by other basecallers. The conducted experiments consisted of basecalling the same raw datasets from the nanopore device by other basecallers and comparing the provided quality symbols, denoting the estimated quality of the nucleotide reconstruction. The results show that the estimated quality reported by different basecallers may vary, depending on the tool used, particularly in terms of range and distribution. Moreover, we mapped basecalled DNA reads to reference genomes and calculated matched and mismatched rates for groups of nucleotides with the same quality symbol. Finally, the presented paper shows that the estimated nucleotide reconstruction quality reported in the basecalling process is not used in any investigated tool for processing nanopore DNA reads.
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Affiliation(s)
- Wiktor Kuśmirek
- Institute of Computer Science, Warsaw University of Technology, 00-661 Warsaw, Poland
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89
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Yu Q, Xiong Y, Su X, Xiong Y, Dong Z, Zhao J, Shu X, Bai S, Lei X, Yan L, Ma X. Integrating Full-Length Transcriptome and RNA Sequencing of Siberian Wildrye ( Elymus sibiricus) to Reveal Molecular Mechanisms in Response to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2719. [PMID: 37514333 PMCID: PMC10385362 DOI: 10.3390/plants12142719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Drought is one of the most significant limiting factors affecting plant growth and development on the Qinghai-Tibet Plateau (QTP). Mining the drought-tolerant genes of the endemic perennial grass of the QTP, Siberian wildrye (Elymus sibiricus), is of great significance to creating new drought-resistant varieties which can be used in the development of grassland livestock and restoring natural grassland projects in the QTP. To investigate the transcriptomic responsiveness of E. sibiricus to drought stress, PEG-induced short- and long-term drought stress was applied to two Siberian wildrye genotypes (drought-tolerant and drought-sensitive accessions), followed by third- and second-generation transcriptome sequencing analysis. A total of 40,708 isoforms were detected, of which 10,659 differentially expressed genes (DEGs) were common to both genotypes. There were 2107 and 2498 unique DEGs in the drought-tolerant and drought-sensitive genotypes, respectively. Additionally, 2798 and 1850 DEGs were identified in the drought-tolerant genotype only under short- and long-term conditions, respectively. DEGs numbering 1641 and 1330 were identified in the drought-sensitive genotype only under short- and long-term conditions, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that all the DEGs responding to drought stress in E. sibiricus were mainly associated with the mitogen-activated protein kinase (MAKP) signaling pathway, plant hormone signal transduction, the linoleic acid metabolism pathway, the ribosome pathway, and plant circadian rhythms. In addition, Nitrate transporter 1/Peptide transporter family protein 3.1 (NPF3.1) and Auxin/Indole-3-Acetic Acid (Aux/IAA) family protein 31(IAA31) also played an important role in helping E. sibiricus resist drought. This study used transcriptomics to investigate how E. sibiricus responds to drought stress, and may provide genetic resources and references for research into the molecular mechanisms of drought resistance in native perennial grasses and for breeding drought-tolerant varieties.
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Affiliation(s)
- Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoli Su
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhixiao Dong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Shu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Lijun Yan
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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90
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Liu Q, Wang F, Xu Y, Lin C, Li X, Xu W, Wang H, Zhu Y. Molecular Mechanism Underlying the Sorghum sudanense (Piper) Stapf. Response to Osmotic Stress Determined via Single-Molecule Real-Time Sequencing and Next-Generation Sequencing. PLANTS (BASEL, SWITZERLAND) 2023; 12:2624. [PMID: 37514239 PMCID: PMC10385767 DOI: 10.3390/plants12142624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023]
Abstract
Drought, as a widespread environmental factor in nature, has become one of the most critical factors restricting the yield of forage grass. Sudangrass (Sorghum sudanense (Piper) Stapf.), as a tall and large grass, has a large biomass and is widely used as forage and biofuel. However, its growth and development are limited by drought stress. To obtain novel insight into the molecular mechanisms underlying the drought response and excavate drought tolerance genes in sudangrass, the first full-length transcriptome database of sudangrass under drought stress at different time points was constructed by combining single-molecule real-time sequencing (SMRT) and next-generation transcriptome sequencing (NGS). A total of 32.3 Gb of raw data was obtained, including 20,199 full-length transcripts with an average length of 1628 bp after assembly and correction. In total, 11,921 and 8559 up- and down-regulated differentially expressed genes were identified between the control group and plants subjected to drought stress. Additionally, 951 transcription factors belonging to 50 families and 358 alternative splicing events were found. A KEGG analysis of 158 core genes exhibiting continuous changes over time revealed that 'galactose metabolism' is a hub pathway and raffinose synthase 2 and β-fructofuranosidase are key genes in the response to drought stress. This study revealed the molecular mechanism underlying drought tolerance in sudangrass. Furthermore, the genes identified in this study provide valuable resources for further research into the response to drought stress.
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Affiliation(s)
- Qiuxu Liu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Fangyan Wang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Yalin Xu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Chaowen Lin
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xiangyan Li
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Wenzhi Xu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Hong Wang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Yongqun Zhu
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
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91
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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] [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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92
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Liu F, Sun X, Wang L, Zhou K, Yao Q, Zhan RL. Transcriptomic and proteomic analyses of Mangifera indica in response to Xanthomonas critis pv. mangiferaeindicae. Front Microbiol 2023; 14:1220101. [PMID: 37469435 PMCID: PMC10352610 DOI: 10.3389/fmicb.2023.1220101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Mango is an important tropical fruit with the reputation of "Tropical Fruit King." It is widely cultivated in tropical and subtropical regions. Mango bacterial leaf spot, which is caused by Xanthomonas critis pv. mangiferaeindicae (Xcm), poses a great threat to the development of mango planting industry. In this study, we used RNA sequencing and data-independent acquisition techniques to compare the transcriptome and proteome of the highly resistant cultivar "Renong No.1" (RN) and the highly susceptible cultivar "Keitt" (KT) in response to Xcm infection at different stages (0, 2, and 6 days). A total of 14,397 differentially expressed genes (DEGs) were identified in the transcriptome of the two varieties, and 4,400 and 8,926 genes were differentially expressed in RN and KT, respectively. Among them, 217 DEGs were related to plant hormone signaling pathway, and 202 were involved in the maintenance of cellular redox homeostasis. A total of 3,438 differentially expressed proteins (DEPs) were identified in the proteome of the two varieties. Exactly 1,542 and 1,700 DEPs were detected in RN and KT, respectively. In addition, 39 DEPs were related to plant hormone signaling pathway, whereas 68 were involved in the maintenance of cellular redox homeostasis. Through cross-validation of the two omics, 1,470 genes were found to be expressed in both groups, and a large number of glutathione metabolism-related genes, such as HSP26-A, G6PD4, and GPX2, were up-regulated in both omics. Peroxisome-related genes, such as LACS6, LACS9, PED1, GLO4, and HACL, were up-regulated or down-regulated in both omics. ABCB11, SAPK2, MYC2, TAG7, PYL1, and other genes related to indole-3-acetic acid and abscisic acid signal transduction and plant-pathogen interaction were up-regulated or down-regulated in both omics. We also used weighted gene co-expression network analysis to combine physiological and biochemical data (superoxide dismutase and catalase activity changes) with transcriptome and proteome data and finally identified three hub genes/proteins (SAG113, SRK2A, and ABCB1) that play an important role in plant hormone signal transduction. This work was the first study of gene/protein changes in resistant and susceptible mango varieties, and its results improved our understanding of the molecular mechanism of mango resistance to Xcm.
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Affiliation(s)
- Feng Liu
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Xin Sun
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Lulu Wang
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Kaibing Zhou
- College of Horticulture, Hainan University, Haikou, China
| | - Quansheng Yao
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Ru-lin Zhan
- Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Key Laboratory of Tropical Fruit Biology, Ministry of Agriculture, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, Guangdong, China
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93
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Cracco A, Tomescu AI. Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT. Genome Res 2023; 33:1198-1207. [PMID: 37253540 PMCID: PMC10538363 DOI: 10.1101/gr.277615.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/16/2023] [Indexed: 06/01/2023]
Abstract
Compacted de Bruijn graphs are one of the most fundamental data structures in computational genomics. Colored compacted de Bruijn graphs are a variant built on a collection of sequences and associate to each k-mer the sequences in which it appears. We present GGCAT, a tool for constructing both types of graphs, based on a new approach merging the k-mer counting step with the unitig construction step, as well as on numerous practical optimizations. For compacted de Bruijn graph construction, GGCAT achieves speed-ups of 3× to 21× compared with the state-of-the-art tool Cuttlefish 2. When constructing the colored variant, GGCAT achieves speed-ups of 5× to 39× compared with the state-of-the-art tool BiFrost. Additionally, GGCAT is up to 480× faster than BiFrost for batch sequence queries on colored graphs.
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Affiliation(s)
- Andrea Cracco
- Department of Computer Science, University of Verona, 37134 Verona, Italy;
| | - Alexandru I Tomescu
- Department of Computer Science, University of Helsinki, Helsinki 00560, Finland
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94
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Mou CY, Li Q, Huang ZP, Ke HY, Zhao H, Zhao ZM, Duan YL, Li HD, Xiao Y, Qian ZM, Du J, Zhou J, Zhang L. PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense. BMC Genomics 2023; 24:340. [PMID: 37340366 DOI: 10.1186/s12864-023-09442-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/11/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Oriental river prawn (Macrobrachium nipponense) is one of the most dominant species in shrimp farming in China, which is a rich source of protein and contributes to a significant impact on the quality of human life. Thus, more complete and accurate annotation of gene models are important for the breeding research of oriental river prawn. RESULTS A full-length transcriptome of oriental river prawn muscle was obtained using the PacBio Sequel platform. Then, 37.99 Gb of subreads were sequenced, including 584,498 circular consensus sequences, among which 512,216 were full length non-chimeric sequences. After Illumina-based correction of long PacBio reads, 6,599 error-corrected isoforms were identified. Transcriptome structural analysis revealed 2,263 and 2,555 alternative splicing (AS) events and alternative polyadenylation (APA) sites, respectively. In total, 620 novel genes (NGs), 197 putative transcription factors (TFs), and 291 novel long non-coding RNAs (lncRNAs) were identified. CONCLUSIONS In summary, this study offers novel insights into the transcriptome complexity and diversity of this prawn species, and provides valuable information for understanding the genomic structure and improving the draft genome annotation of oriental river prawn.
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Affiliation(s)
- Cheng-Yan Mou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Zhi-Peng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Hong-Yu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Zhong-Meng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Yuan-Liang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Hua-Dong Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Yu Xiao
- Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, China
| | - Zhou-Ming Qian
- Chengdu Eaters Agricultural Group Co., Ltd, Chengdu, Sichuan, 610000, China
| | - Jun Du
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China.
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China.
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95
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Mastrorosa FK, Miller DE, Eichler EE. Applications of long-read sequencing to Mendelian genetics. Genome Med 2023; 15:42. [PMID: 37316925 PMCID: PMC10266321 DOI: 10.1186/s13073-023-01194-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/18/2023] [Indexed: 06/16/2023] Open
Abstract
Advances in clinical genetic testing, including the introduction of exome sequencing, have uncovered the molecular etiology for many rare and previously unsolved genetic disorders, yet more than half of individuals with a suspected genetic disorder remain unsolved after complete clinical evaluation. A precise genetic diagnosis may guide clinical treatment plans, allow families to make informed care decisions, and permit individuals to participate in N-of-1 trials; thus, there is high interest in developing new tools and techniques to increase the solve rate. Long-read sequencing (LRS) is a promising technology for both increasing the solve rate and decreasing the amount of time required to make a precise genetic diagnosis. Here, we summarize current LRS technologies, give examples of how they have been used to evaluate complex genetic variation and identify missing variants, and discuss future clinical applications of LRS. As costs continue to decrease, LRS will find additional utility in the clinical space fundamentally changing how pathological variants are discovered and eventually acting as a single-data source that can be interrogated multiple times for clinical service.
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Affiliation(s)
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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96
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Berthelier J, Furci L, Asai S, Sadykova M, Shimazaki T, Shirasu K, Saze H. Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana. Nat Commun 2023; 14:3248. [PMID: 37277361 DOI: 10.1038/s41467-023-38954-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, ParasiTE, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.
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Grants
- JP20H02995 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP22H00364 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05909 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05913 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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Affiliation(s)
- Jérémy Berthelier
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
| | - Leonardo Furci
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Shuta Asai
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Munissa Sadykova
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Tomoe Shimazaki
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
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97
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Francis WR, Eitel M, Vargas S, Garcia-Escudero CA, Conci N, Deister F, Mah JL, Guiglielmoni N, Krebs S, Blum H, Leys SP, Wörheide G. The genome of the reef-building glass sponge Aphrocallistes vastus provides insights into silica biomineralization. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230423. [PMID: 37351491 PMCID: PMC10282587 DOI: 10.1098/rsos.230423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Well-annotated and contiguous genomes are an indispensable resource for understanding the evolution, development, and metabolic capacities of organisms. Sponges, an ecologically important non-bilaterian group of primarily filter-feeding sessile aquatic organisms, are underrepresented with respect to available genomic resources. Here we provide a high-quality and well-annotated genome of Aphrocallistes vastus, a glass sponge (Porifera: Hexactinellida) that forms large reef structures off the coast of British Columbia (Canada). We show that its genome is approximately 80 Mb, small compared to most other metazoans, and contains nearly 2500 nested genes, more than other genomes. Hexactinellida is characterized by a unique skeletal architecture made of amorphous silicon dioxide (SiO2), and we identified 419 differentially expressed genes between the osculum, i.e. the vertical growth zone of the sponge, and the main body. Among the upregulated ones, mineralization-related genes such as glassin, as well as collagens and actins, dominate the expression profile during growth. Silicateins, suggested being involved in silica mineralization, especially in demosponges, were not found at all in the A. vastus genome and suggests that the underlying mechanisms of SiO2 deposition in the Silicea sensu stricto (Hexactinellida + Demospongiae) may not be homologous.
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Affiliation(s)
- Warren R. Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Catalina A. Garcia-Escudero
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Conci
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Deister
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jasmine L. Mah
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Nadège Guiglielmoni
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050 Brussels, Belgium
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sally P. Leys
- Department of Biological Sciences, University of Alberta, Edmonton, Canada T6G 2E9
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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98
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Zhang Y, Wei Y, Meng J, Wang Y, Nie S, Zhang Z, Wang H, Yang Y, Gao Y, Wu J, Li T, Liu X, Zhang H, Gu L. Chromosome-scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1490-1505. [PMID: 36971060 DOI: 10.1111/tpj.16201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 02/15/2023] [Accepted: 03/13/2023] [Indexed: 06/17/2023]
Abstract
Australian pine (Casuarina spp.) is extensively planted in tropical and subtropical regions for wood production, shelterbelts, environmental protection, and ecological restoration due to their superior biological characteristics, such as rapid growth, wind and salt tolerance, and nitrogen fixation. To analyze the genomic diversity of Casuarina, we sequenced the genomes and constructed de novo genome assemblies of the three most widely planted Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana. We generated chromosome-scale genome sequences using both Pacific Biosciences (PacBio) Sequel sequencing and chromosome conformation capture technology (Hi-C). The total genome sizes for C. equisetifolia, C. glauca, and C. cunninghamiana are 268 942 579 bp, 296 631 783 bp, and 293 483 606 bp, respectively, of which 25.91, 27.15, and 27.74% were annotated as repetitive sequences. We annotated 23 162, 24 673, and 24 674 protein-coding genes in C. equisetifolia, C. glauca, and C. cunninghamiana, respectively. We then collected branchlets from male and female individuals for whole-genome bisulfite sequencing (BS-seq) to explore the epigenetic regulation of sex determination in these three species. Transcriptome sequencing (RNA-seq) revealed differential expression of phytohormone-related genes between male and female plants. In summary, we generated three chromosome-level genome assemblies and comprehensive DNA methylation and transcriptome datasets from both male and female material for three Casuarina species, providing a basis for the comprehensive investigation of genomic diversity and functional gene discovery of Casuarina in the future.
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Affiliation(s)
- Yong Zhang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Yongcheng Wei
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Jingxiang Meng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Yujiao Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Sen Nie
- Fujian Academy of Forestry Sciences, Fuzhou, Fujian, 350012, China
| | - Zeyu Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiyuan Wang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongkang Yang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ji Wu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tuhe Li
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xuqing Liu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianfeng Gu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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99
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Zhu W, Liao X. LCAT: an isoform-sensitive error correction for transcriptome sequencing long reads. Front Genet 2023; 14:1166975. [PMID: 37292144 PMCID: PMC10245045 DOI: 10.3389/fgene.2023.1166975] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/04/2023] [Indexed: 06/10/2023] Open
Abstract
As the carrier of genetic information, RNA carries the information from genes to proteins. Transcriptome sequencing technology is an important way to obtain transcriptome sequences, and it is also the basis for transcriptome research. With the development of third-generation sequencing, long reads can cover full-length transcripts and reflect the composition of different isoforms. However, the high error rate of third-generation sequencing affects the accuracy of long reads and downstream analysis. The current error correction methods seldom consider the existence of different isoforms in RNA, which makes the diversity of isoforms a serious loss. Here, we introduce LCAT (long-read error correction algorithm for transcriptome sequencing data), a wrapper algorithm of MECAT, to reduce the loss of isoform diversity while keeping MECAT's error correction performance. The experimental results show that LCAT can not only improve the quality of transcriptome sequencing long reads but also retain the diversity of isoforms.
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Affiliation(s)
- Wufei Zhu
- Department of Endocrinology, Yichang Central People’s Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
| | - Xingyu Liao
- Computer, Electrical and Mathematical Sciences, and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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100
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Zhao X, Sun X, Chen Y, Wu H, Liu Y, Jiang Y, Xie F, Chen Y. Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass. FRONTIERS IN PLANT SCIENCE 2023; 14:1158035. [PMID: 37229126 PMCID: PMC10204806 DOI: 10.3389/fpls.2023.1158035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/30/2023] [Indexed: 05/27/2023]
Abstract
Kentucky bluegrass (Poa pratensis L.) is an eminent turfgrass species with a complex genome, but it is sensitive to rust (Puccinia striiformis). The molecular mechanisms of Kentucky bluegrass in response to rust still remain unclear. This study aimed to elucidate differentially expressed lncRNAs (DELs) and genes (DEGs) for rust resistance based on the full-length transcriptome. First, we used single-molecule real-time sequencing technology to generate the full-length transcriptome of Kentucky bluegrass. A total of 33,541 unigenes with an average read length of 2,233 bp were obtained, which contained 220 lncRNAs and 1,604 transcription factors. Then, the comparative transcriptome between the mock-inoculated leaves and rust-infected leaves was analyzed using the full-length transcriptome as a reference genome. A total of 105 DELs were identified in response to rust infection. A total of 15,711 DEGs were detected (8,278 upregulated genes, 7,433 downregulated genes) and were enriched in plant hormone signal transduction and plant-pathogen interaction pathways. Additionally, through co-location and expression analysis, it was found that lncRNA56517, lncRNA53468, and lncRNA40596 were highly expressed in infected plants and upregulated the expression of target genes AUX/IAA, RPM1, and RPS2, respectively; meanwhile, lncRNA25980 decreased the expression level of target gene EIN3 after infection. The results suggest that these DEGs and DELs are important candidates for potentially breeding the rust-resistant Kentucky bluegrass.
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Affiliation(s)
- Xueying Zhao
- College of Horticulture, Northeast Agricultural University, Harbin, China
| | - Xiaoyang Sun
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yang Chen
- College of Life Science, Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Hanfu Wu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yujiao Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Fuchun Xie
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yajun Chen
- College of Horticulture, Northeast Agricultural University, Harbin, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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