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Schultz DT, Heath-Heckman EA, Winchell CJ, Kuo DH, Yu YS, Oberauer F, Kocot KM, Cho SJ, Simakov O, Weisblat DA. Acceleration of genome rearrangement in clitellate annelids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593736. [PMID: 38798472 PMCID: PMC11118384 DOI: 10.1101/2024.05.12.593736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Comparisons of multiple metazoan genomes have revealed the existence of ancestral linkage groups (ALGs), genomic scaffolds sharing sets of orthologous genes that have been inherited from ancestral animals for hundreds of millions of years (Simakov et al. 2022; Schultz et al. 2023) These ALGs have persisted across major animal taxa including Cnidaria, Deuterostomia, Ecdysozoa and Spiralia. Notwithstanding this general trend of chromosome-scale conservation, ALGs have been obliterated by extensive genome rearrangements in certain groups, most notably including Clitellata (oligochaetes and leeches), a group of easily overlooked invertebrates that is of tremendous ecological, agricultural and economic importance (Charles 2019; Barrett 2016). To further investigate these rearrangements, we have undertaken a comparison of 12 clitellate genomes (including four newly sequenced species) and 11 outgroup representatives. We show that these rearrangements began at the base of the Clitellata (rather than progressing gradually throughout polychaete annelids), that the inter-chromosomal rearrangements continue in several clitellate lineages and that these events have substantially shaped the evolution of the otherwise highly conserved Hox cluster.
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Affiliation(s)
- Darrin T. Schultz
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Elizabeth A.C. Heath-Heckman
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Christopher J. Winchell
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
| | - Dian-Han Kuo
- Department of Life Science & Museum of Zoology, National Taiwan University, No. 1 Section 4 Roosevelt Rd., Taipei 10617, Taiwan
| | - Yun-sang Yu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Fabian Oberauer
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - Kevin M. Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL 35487, USA
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1010, Austria
| | - David A. Weisblat
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
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2
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Álvarez-Campos P, García-Castro H, Emili E, Pérez-Posada A, Del Olmo I, Peron S, Salamanca-Díaz DA, Mason V, Metzger B, Bely AE, Kenny NJ, Özpolat BD, Solana J. Annelid adult cell type diversity and their pluripotent cellular origins. Nat Commun 2024; 15:3194. [PMID: 38609365 PMCID: PMC11014941 DOI: 10.1038/s41467-024-47401-6] [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: 07/28/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Many annelids can regenerate missing body parts or reproduce asexually, generating all cell types in adult stages. However, the putative adult stem cell populations involved in these processes, and the diversity of cell types generated by them, are still unknown. To address this, we recover 75,218 single cell transcriptomes of the highly regenerative and asexually-reproducing annelid Pristina leidyi. Our results uncover a rich cell type diversity including annelid specific types as well as novel types. Moreover, we characterise transcription factors and gene networks that are expressed specifically in these populations. Finally, we uncover a broadly abundant cluster of putative stem cells with a pluripotent signature. This population expresses well-known stem cell markers such as vasa, piwi and nanos homologues, but also shows heterogeneous expression of differentiated cell markers and their transcription factors. We find conserved expression of pluripotency regulators, including multiple chromatin remodelling and epigenetic factors, in piwi+ cells. Finally, lineage reconstruction analyses reveal computational differentiation trajectories from piwi+ cells to diverse adult types. Our data reveal the cell type diversity of adult annelids by single cell transcriptomics and suggest that a piwi+ cell population with a pluripotent stem cell signature is associated with adult cell type differentiation.
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Affiliation(s)
- Patricia Álvarez-Campos
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Helena García-Castro
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Elena Emili
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Alberto Pérez-Posada
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Irene Del Olmo
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sophie Peron
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - David A Salamanca-Díaz
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Vincent Mason
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Bria Metzger
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA
| | - Alexandra E Bely
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - Nathan J Kenny
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, Aotearoa, New Zealand
| | - B Duygu Özpolat
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA.
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA.
| | - Jordi Solana
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Living Systems Institute, University of Exeter, Exeter, UK.
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3
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Yao X, Liang C, Lv H, Liu W, Wang Q, Ding J, Li X, Wang J. Expanding the insight of ecological risk on the novel chiral pesticide mefentrifluconazole: Mechanism of enantioselective toxicity to earthworms (Eisenia fetida). JOURNAL OF HAZARDOUS MATERIALS 2024; 466:133585. [PMID: 38271877 DOI: 10.1016/j.jhazmat.2024.133585] [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: 11/27/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Continued application of new chiral fungicide mefentrifluconazole (MFZ) increases its risk to soil ecosystem. However, the toxicity of MFZ enantiomers to soil fauna and whether stereoselectivity exists remains poorly elucidated. Based on multilevel toxicity endpoints and transcriptomics, we investigated the negative effects of racemic, R-(-)-, and S-(+)-MFZ on Eisenia fetida. After exposure to S-(+) configuration at 4 mg/kg for 28 day, its reactive oxygen species levels were elevated by 15.4% compared to R-(-) configuration, inducing enantiospecific oxidative stress and transcriptional aberrations. The S-(+) isomer induced more severe cell membrane damage and apoptosis than the R-(-) isomer, and notably, the selectivity of apoptosis is probably dominated by the mitochondrial pathway. Mechanistically, differential mitochondrial stress lies in: S-(+) isomer specifically up-regulated mitochondrial cellular component compared to R-(-) isomer and identified more serious mitochondrial fission. Furthermore, S-(+) conformation down-regulated biological processes associated with ATP synthesis and metabolism, with specific inhibition of mitochondrial respiratory electron transport chain complex I and IV activity resulting in more severe electron flow disturbances. These ultimately mediated enantioselective ontogenetic process disorders, which were supported at phenotypic (weight loss), genetic, and protein (reverse modulate TCTP and Sox2 expression) levels. Our findings offer an important reference for elucidating the enantioselective toxicological mechanism of MFZ in soil fauna.
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Affiliation(s)
- Xiangfeng Yao
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Chunliu Liang
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Huijuan Lv
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wenrong Liu
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Qian Wang
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jia Ding
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xianxu Li
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jun Wang
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
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4
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Mitchell DG, Edgar A, Mateu JR, Ryan JF, Martindale MQ. The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor. Commun Biol 2024; 7:203. [PMID: 38374160 PMCID: PMC10876535 DOI: 10.1038/s42003-024-05901-7] [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: 06/29/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024] Open
Abstract
Regenerative potential is widespread but unevenly distributed across animals. However, our understanding of the molecular mechanisms underlying regenerative processes is limited to a handful of model organisms, restricting robust comparative analyses. Here, we conduct a time course of RNA-seq during whole body regeneration in Mnemiopsis leidyi (Ctenophora) to uncover gene expression changes that correspond with key events during the regenerative timeline of this species. We identified several genes highly enriched in this dataset beginning as early as 10 minutes after surgical bisection including transcription factors in the early timepoints, peptidases in the middle timepoints, and cytoskeletal genes in the later timepoints. We validated the expression of early response transcription factors by whole mount in situ hybridization, showing that these genes exhibited high expression in tissues surrounding the wound site. These genes exhibit a pattern of transient upregulation as seen in a variety of other organisms, suggesting that they may be initiators of an ancient gene regulatory network linking wound healing to the initiation of a regenerative response.
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Affiliation(s)
- Dorothy G Mitchell
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Júlia Ramon Mateu
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA.
- Department of Biology, University of Florida, Gainesville, FL, USA.
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5
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [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: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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6
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Yuan Y, Teng H, Zhang T, Wang D, Gu H, Lv W. Toxicological effects induced by two carbamates on earthworms (Eisenia fetida): Acute toxicity, arrested regeneration and underlying mechanisms. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 269:115824. [PMID: 38096595 DOI: 10.1016/j.ecoenv.2023.115824] [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: 08/01/2023] [Revised: 11/03/2023] [Accepted: 12/10/2023] [Indexed: 01/12/2024]
Abstract
Eisenia fetida is recognised as advantageous model species in ecotoxicological and regeneration investigations. The intensive utilization of carbamate pesticides (CARs) imposes heavy residue burdens and grave hazards on edaphic environments as well as soil fauna therein. However, precise mechanisms whereby the specific CAR exerted toxic effects on earthworms remain largely elusive, notably from regenerative perspective. Herein, acute responses and regenerative toxicity of two carbamates (metolcarb, MEB and fenoxycarb, FEB) against E. fetida were dissected using biochemical, histological as well as molecular approaches following OECD guidelines at the cellular, tissue and organismal level. The acute toxicity data implied that MEB/FEB were very toxic/medium to extremely toxic, respectively in filter paper contact test and low to medium toxic/low toxic, respectively in artificial soil test. Chronic exposure to MEB and FEB at sublethal concentrations significantly mitigated the soluble protein content, protein abundance while enhanced the protein carbonylation level. Moreover, severely retarded posterior renewal of amputated earthworms was noticed in MEB and FEB treatments relative to the control group, with pronouncedly compromised morphology, dwindling segments and elevated cell apoptosis of blastema tissues, which were mediated by the rising Sox2 and decreasing TCTP levels. Taken together, these findings not only presented baseline toxicity cues for MEB and FEB exposure against earthworms, but also yielded mechanistic insights into regenerative toxicity upon CAR exposure, further contributing to the environmental risk assessment and benchmark formulation of agrochemical pollution in terrestrial ecosystem.
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Affiliation(s)
- Yongda Yuan
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Haiyuan Teng
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Tianshu Zhang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Dongsheng Wang
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Haotian Gu
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China.
| | - Weiguang Lv
- Eco-environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; Agricultural Environment and Farmland Conservation Experiment Station of Ministry Agriculture, Shanghai 201403, China.
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7
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Aigner GP, Peer V, Fiechtner B, Piechnik CA, Höckner M. Wound healing and Cadmium detoxification in the earthworm Lumbricus terrestris - a potential case for coelomocytes? Front Immunol 2023; 14:1272191. [PMID: 38116011 PMCID: PMC10728717 DOI: 10.3389/fimmu.2023.1272191] [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: 08/03/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023] Open
Abstract
Earthworms are affected by physical stress, like injury, and by exposure to xenobiotics, such as the toxic metal cadmium (Cd), which enters the environment mainly through industry and agriculture. The stress response to the single and the combination of both stressors was examined in regenerative and unharmed tissue of Lumbricus terrestris to reveal if the stress response to a natural insult like injury (amputation) interferes with Cd detoxification mechanisms. We characterized the roles of metallothionein 1 (MT1) and MT2 isoforms, heat shock protein 70 as well as immune biomarkers such as the toll-like receptors (TLR) single cysteine cluster TLR and multiple cysteine cluster TLR. The role of the activated transcription factors (ATFs) ATF2, ATF7, and the cAMP responsive element binding protein as putative regulatory intersection as well as a stress-dependent change of the essential trace elements zinc and calcium was analyzed. Phosphorylated AMP activated protein kinase, the cellular energy sensor, was measured to explore the energy demand, while the energy status was determined by detecting carbohydrate and protein levels. Taken together, we were able to show that injury rather than Cd is the driving force that separates the four treatment groups - Control, Cd exposure, Injury, Cd exposure and injury. Interestingly, we found that gene expression differed regarding the tissue section that was analyzed and we hypothesize that this is due to the migration of coelomocytes, earthworm immune cells, that take over a key role in protecting the organism from a variety of environmental challenges. Surprisingly, we discovered a role for MT1 in the response to multiple stressors and an isoform-specific function for the two newly characterized TLRs. In conclusion, we gathered novel information on the relation of innate immunity, wound healing, and Cd detoxification mechanisms in earthworms.
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Affiliation(s)
| | | | | | | | - Martina Höckner
- Department of Zoology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
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8
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Martín-Zamora FM, Davies BE, Donnellan RD, Guynes K, Martín-Durán JM. Functional genomics in Spiralia. Brief Funct Genomics 2023; 22:487-497. [PMID: 37981859 PMCID: PMC10658182 DOI: 10.1093/bfgp/elad036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.
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Affiliation(s)
- Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Rory D Donnellan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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9
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Paré L, Bideau L, Baduel L, Dalle C, Benchouaia M, Schneider SQ, Laplane L, Clément Y, Vervoort M, Gazave E. Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii. BMC Genomics 2023; 24:583. [PMID: 37784028 PMCID: PMC10546743 DOI: 10.1186/s12864-023-09602-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: 05/25/2023] [Accepted: 08/18/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Restorative regeneration, the capacity to reform a lost body part following amputation or injury, is an important and still poorly understood process in animals. Annelids, or segmented worms, show amazing regenerative capabilities, and as such are a crucial group to investigate. Elucidating the molecular mechanisms that underpin regeneration in this major group remains a key goal. Among annelids, the nereididae Platynereis dumerilii (re)emerged recently as a front-line regeneration model. Following amputation of its posterior part, Platynereis worms can regenerate both differentiated tissues of their terminal part as well as a growth zone that contains putative stem cells. While this regeneration process follows specific and reproducible stages that have been well characterized, the transcriptomic landscape of these stages remains to be uncovered. RESULTS We generated a high-quality de novo Reference transcriptome for the annelid Platynereis dumerilii. We produced and analyzed three RNA-sequencing datasets, encompassing five stages of posterior regeneration, along with blastema stages and non-amputated tissues as controls. We included two of these regeneration RNA-seq datasets, as well as embryonic and tissue-specific datasets from the literature to produce a Reference transcriptome. We used this Reference transcriptome to perform in depth analyzes of RNA-seq data during the course of regeneration to reveal the important dynamics of the gene expression, process with thousands of genes differentially expressed between stages, as well as unique and specific gene expression at each regeneration stage. The study of these genes highlighted the importance of the nervous system at both early and late stages of regeneration, as well as the enrichment of RNA-binding proteins (RBPs) during almost the entire regeneration process. CONCLUSIONS In this study, we provided a high-quality de novo Reference transcriptome for the annelid Platynereis that is useful for investigating various developmental processes, including regeneration. Our extensive stage-specific transcriptional analysis during the course of posterior regeneration sheds light upon major molecular mechanisms and pathways, and will foster many specific studies in the future.
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Affiliation(s)
- Louis Paré
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loïc Bideau
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loeiza Baduel
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Caroline Dalle
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Médine Benchouaia
- Département de biologie, GenomiqueENS, Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Stephan Q Schneider
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Lucie Laplane
- Université Paris I Panthéon-Sorbonne, CNRS UMR 8590 Institut d'Histoire et de Philosophie des Sciences et des Techniques (IHPST), Paris, France
- Gustave Roussy, UMR 1287, Villejuif, France
| | - Yves Clément
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Michel Vervoort
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Eve Gazave
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France.
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10
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Jia X, Lin W, Wang W. Regulation of chromatin organization during animal regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:19. [PMID: 37259007 DOI: 10.1186/s13619-023-00162-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/21/2023] [Indexed: 06/02/2023]
Abstract
Activation of regeneration upon tissue damages requires the activation of many developmental genes responsible for cell proliferation, migration, differentiation, and tissue patterning. Ample evidence revealed that the regulation of chromatin organization functions as a crucial mechanism for establishing and maintaining cellular identity through precise control of gene transcription. The alteration of chromatin organization can lead to changes in chromatin accessibility and/or enhancer-promoter interactions. Like embryogenesis, each stage of tissue regeneration is accompanied by dynamic changes of chromatin organization in regeneration-responsive cells. In the past decade, many studies have been conducted to investigate the contribution of chromatin organization during regeneration in various tissues, organs, and organisms. A collection of chromatin regulators were demonstrated to play critical roles in regeneration. In this review, we will summarize the progress in the understanding of chromatin organization during regeneration in different research organisms and discuss potential common mechanisms responsible for the activation of regeneration response program.
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Affiliation(s)
- Xiaohui Jia
- National Institute of Biological Sciences, Beijing, 102206, China
- China Agricultural University, Beijing, 100083, China
| | - Weifeng Lin
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Wei Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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11
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Shalaeva AY, Kozin VV. Cell Proliferation Indices in Regenerating Alitta virens (Annelida, Errantia). Cells 2023; 12:1354. [PMID: 37408190 DOI: 10.3390/cells12101354] [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: 03/31/2023] [Revised: 05/02/2023] [Accepted: 05/08/2023] [Indexed: 07/07/2023] Open
Abstract
In recent years, interest in the possible molecular regulators of cell proliferation and differentiation in a wide range of regeneration models has grown significantly, but the cell kinetics of this process remain largely a mystery. Here we try to elucidate the cellular aspects of regeneration by EdU incorporation in intact and posteriorly amputated annelid Alitta virens using quantitative analysis. We found that the main mechanism of blastema formation in A. virens is local dedifferentiation; mitotically active cells of intact segments do not significantly contribute to the blastemal cellular sources. Amputation-induced proliferation occurred predominantly within the epidermal and intestinal epithelium, as well as wound-adjacent muscle fibers, where clusters of cells at the same stage of the cell cycle were found. The resulting regenerative bud had zones of high proliferative activity and consisted of a heterogeneous population of cells that differed in their anterior-posterior positions and in their cell cycle parameters. The data presented allowed for the quantification of cell proliferation in the context of annelid regeneration for the first time. Regenerative cells showed an unprecedentedly high cycle rate and an exceptionally large growth fraction, making this regeneration model especially valuable for studying coordinated cell cycle entry in vivo in response to injury.
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Affiliation(s)
- Alexandra Y Shalaeva
- Department of Embryology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Vitaly V Kozin
- Department of Embryology, St. Petersburg State University, 199034 St. Petersburg, Russia
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12
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Lee CJ, Lee HY, Yu YS, Ryu KB, Lee H, Kim K, Shin SY, Gil YC, Cho SJ. Brain compartmentalization based on transcriptome analyses and its gene expression in Octopus minor. Brain Struct Funct 2023:10.1007/s00429-023-02647-6. [PMID: 37138199 DOI: 10.1007/s00429-023-02647-6] [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: 12/15/2022] [Accepted: 04/17/2023] [Indexed: 05/05/2023]
Abstract
Coleoid cephalopods have a high intelligence, complex structures, and large brain. The cephalopod brain is divided into supraesophageal mass, subesophageal mass and optic lobe. Although much is known about the structural organization and connections of various lobes of octopus brain, there are few studies on the brain of cephalopod at the molecular level. In this study, we demonstrated the structure of an adult Octopus minor brain by histomorphological analyses. Through visualization of neuronal and proliferation markers, we found that adult neurogenesis occurred in the vL and posterior svL. We also obtained specific 1015 genes by transcriptome of O. minor brain and selected OLFM3, NPY, GnRH, and GDF8 genes. The expression of genes in the central brain showed the possibility of using NPY and GDF8 as molecular marker of compartmentation in the central brain. This study will provide useful information for establishing a molecular atlas of cephalopod brain.
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Affiliation(s)
- Chan-Jun Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Hae-Youn Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Yun-Sang Yu
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Kyoung-Bin Ryu
- Clinical Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Hyerim Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Song Yub Shin
- Department of Cellular and Molecular Medicine, School of Medicine, Chosun University, Gwangju, 61452, Republic of Korea.
| | - Young-Chun Gil
- Department of Anatomy, College of Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
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13
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Lathakumari S, Seenipandian S, Balakrishnan S, Raj APMS, Sugiyama H, Namasivayam GP, Sivasubramaniam S. Identification of genes responsible for the social skill in the earthworm, Eudrilus eugeniae. GENE REPORTS 2023. [DOI: 10.1016/j.genrep.2023.101774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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14
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Rusin LY. Evolution of homology: From archetype towards a holistic concept of cell type. J Morphol 2023; 284:e21569. [PMID: 36789784 DOI: 10.1002/jmor.21569] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/10/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
The concept of homology lies in the heart of comparative biological science. The distinction between homology as structure and analogy as function has shaped the evolutionary paradigm for a century and formed the axis of comparative anatomy and embryology, which accept the identity of structure as a ground measure of relatedness. The advent of single-cell genomics overturned the classical view of cell homology by establishing a backbone regulatory identity of cell types, the basic biological units bridging the molecular and phenotypic dimensions, to reveal that the cell is the most flexible unit of living matter and that many approaches of classical biology need to be revised to understand evolution and diversity at the cellular level. The emerging theory of cell types explicitly decouples cell identity from phenotype, essentially allowing for the divergence of evolutionarily related morphotypes beyond recognition, as well as it decouples ontogenetic cell lineage from cell-type phylogeny, whereby explicating that cell types can share common descent regardless of their structure, function or developmental origin. The article succinctly summarizes current progress and opinion in this field and formulates a more generalistic view of biological cell types as avatars, transient or terminal cell states deployed in a continuum of states by the developmental programme of one and the same omnipotent cell, capable of changing or combining identities with distinct evolutionary histories or inventing ad hoc identities that never existed in evolution or development. It highlights how the new logic grounded in the regulatory nature of cell identity transforms the concepts of cell homology and phenotypic stability, suggesting that cellular evolution is inherently and massively network-like, with one-to-one homologies being rather uncommon and restricted to shallower levels of the animal tree of life.
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Affiliation(s)
- Leonid Y Rusin
- Laboratory for Mathematic Methods and Models in Bioinformatics, Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- EvoGenome Analytics LLC, Odintsovo, Moscow Region, Russia
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15
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Discovery and Mechanism of Action of a Novel Antimicrobial Peptide from an Earthworm. Microbiol Spectr 2023; 11:e0320622. [PMID: 36602379 PMCID: PMC9927515 DOI: 10.1128/spectrum.03206-22] [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] [Indexed: 01/06/2023] Open
Abstract
The robust innate immune system of the earthworm provides a potential source of natural antimicrobial peptides (AMPs). However, the cost and high rediscovery rate of direct separation and purification limits their discovery. Genome sequencing of numerous earthworm species facilitates the discovery of new antimicrobial peptides. Through predicting potential antimicrobial peptides in the open reading frames of the Eisenia andrei genome and sequence optimization, a novel antimicrobial peptide, named EWAMP-R (RIWWSGGWRRWRW), was identified. EWAMP-R demonstrated good activity against various bacteria, including drug-resistant strains. The antibacterial mechanisms of EWAMP-R were explored through molecular simulation and wet-laboratory experiments. These experiments demonstrated that the bacterial membrane may be one of the targets of EWAMP-R but that there may be different interactions with Gram-negative and Gram-positive bacterial membranes. EWAMP-R can disrupt bacterial membrane integrity; however, at low concentrations, it appears that EWAMP-R may get through the membrane of Escherichia coli instead of damaging it directly, implying the existence of a secondary response. Gene expression studies identified that in E. coli, only the apoptosis-like cell death (ALD) pathway was activated, while in Staphylococcus aureus, the MazEF pathway was also upregulated, limiting the influence of the ALD pathway. The different antimicrobial actions against Gram-positive and -negative bacteria can provide important information on the structure-activity relationship of AMPs and facilitate AMP design with higher specificity. This study identified a new source of antibacterial agents that has the potential to address the increasingly serious issue of antibiotic resistance. IMPORTANCE Drug-resistant bacteria are a great threat to public health and drive the search for new antibacterial agents. The living environment of earthworms necessitates a strong immune system, and therefore, they are potentially a rich resource of novel antibiotics. A novel AMP, EWAMP-R, with high antibacterial activity was found through in silico analysis of the Eisenia andrei genome. Molecular analysis investigating the interactions between EWAMP-R and the cell membrane demonstrated the importance of tryptophan and arginine residues to EWAMP-R activity. Additionally, the different secondary responses found between E. coli and S. aureus were in accordance with a common phenomenon where some antibacterial agents only target specific species of bacteria. These results provided useful molecular information to support further AMP research and design. Our study expands the sources of antimicrobial peptides and also helps to explain the adaptability of earthworms to their environment.
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16
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Angileri KM, Bagia NA, Feschotte C. Transposon control as a checkpoint for tissue regeneration. Development 2022; 149:dev191957. [PMID: 36440631 PMCID: PMC10655923 DOI: 10.1242/dev.191957] [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: 03/11/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022]
Abstract
Tissue regeneration requires precise temporal control of cellular processes such as inflammatory signaling, chromatin remodeling and proliferation. The combination of these processes forms a unique microenvironment permissive to the expression, and potential mobilization of, transposable elements (TEs). Here, we develop the hypothesis that TE activation creates a barrier to tissue repair that must be overcome to achieve successful regeneration. We discuss how uncontrolled TE activity may impede tissue restoration and review mechanisms by which TE activity may be controlled during regeneration. We posit that the diversification and co-evolution of TEs and host control mechanisms may contribute to the wide variation in regenerative competency across tissues and species.
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Affiliation(s)
- Krista M. Angileri
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Nornubari A. Bagia
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
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17
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del Olmo I, Verdes A, Álvarez‐Campos P. Distinct patterns of gene expression during regeneration and asexual reproduction in the annelid Pristina leidyi. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:405-420. [PMID: 35604322 PMCID: PMC9790225 DOI: 10.1002/jez.b.23143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/03/2022] [Accepted: 05/04/2022] [Indexed: 12/30/2022]
Abstract
Regeneration, the ability to replace lost body parts, is a widespread phenomenon in the animal kingdom often connected to asexual reproduction or fission, since the only difference between the two appears to be the stimulus that triggers them. Both developmental processes have largely been characterized; however, the molecular toolkit and genetic mechanisms underlying these events remain poorly unexplored. Annelids, in particular the oligochaete Pristina leidyi, provide a good model system to investigate these processes as they show diverse ways to regenerate, and can reproduce asexually through fission under laboratory conditions. Here, we used a comparative transcriptomics approach based on RNA-sequencing and differential gene expression analyses to understand the molecular mechanisms involved in anterior regeneration and asexual reproduction. We found 291 genes upregulated during anterior regeneration, including several regeneration-related genes previously reported in other annelids such as frizzled, paics, and vdra. On the other hand, during asexual reproduction, 130 genes were found upregulated, and unexpectedly, many of them were related to germline development during sexual reproduction. We also found important differences between anterior regeneration and asexual reproduction, with the latter showing a gene expression profile more similar to that of control individuals. Nevertheless, we identified 35 genes that were upregulated in both conditions, many of them related to cell pluripotency, stem cells, and cell proliferation. Overall, our results shed light on the molecular mechanisms that control anterior regeneration and asexual reproduction in annelids and reveal similarities with other animals, suggesting that the genetic machinery controlling these processes is conserved across metazoans.
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Affiliation(s)
- Irene del Olmo
- Department of Biology (Zoology)Universidad Autónoma de MadridMadridSpain
| | - Aida Verdes
- Department of Biodiversity and Evolutionary BiologyMuseo Nacional de Ciencias Naturales de MadridMadridSpain
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18
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Li J, Wang J, Zhang P, Wang R, Mei Y, Sun Z, Fei L, Jiang M, Ma L, E W, Chen H, Wang X, Fu Y, Wu H, Liu D, Wang X, Li J, Guo Q, Liao Y, Yu C, Jia D, Wu J, He S, Liu H, Ma J, Lei K, Chen J, Han X, Guo G. Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types. Nat Genet 2022; 54:1711-1720. [PMID: 36229673 DOI: 10.1038/s41588-022-01197-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 08/31/2022] [Indexed: 11/09/2022]
Abstract
Despite extensive efforts to generate and analyze reference genomes, genetic models to predict gene regulation and cell fate decisions are lacking for most species. Here, we generated whole-body single-cell transcriptomic landscapes of zebrafish, Drosophila and earthworm. We then integrated cell landscapes from eight representative metazoan species to study gene regulation across evolution. Using these uniformly constructed cross-species landscapes, we developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory sequences at the single-cell level. We systematically compared cell-type-specific transcription factors to reveal conserved genetic regulation in vertebrates and invertebrates. Our work provides a valuable resource and offers a new strategy for studying regulatory grammar in diverse biological systems.
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Affiliation(s)
- Jiaqi Li
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Jingjing Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
| | - Peijing Zhang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Renying Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuqing Mei
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongyi Sun
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weigao E
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Xinru Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hanyu Wu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Daiyuan Liu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xueyi Wang
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingyu Li
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qile Guo
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuan Liao
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, China
| | - Chengxuan Yu
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Danmei Jia
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital School of Medicine, Zhejiang University, Hangzhou, China
| | - Shibo He
- College of Control Science and Engineering, Zhejiang University, Hangzhou, China
| | - Huanju Liu
- Women's Hospital and Institute of Genetics, Zhenjiang University School of Medicine, Hangzhou, China
| | - Jun Ma
- Women's Hospital and Institute of Genetics, Zhenjiang University School of Medicine, Hangzhou, China
| | - Kai Lei
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jiming Chen
- College of Control Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, China.
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China. .,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China. .,Zhejiang Provincial Key Laboratory for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, China. .,Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China.
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19
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Perry I, Hernadi SB, Cunha L, Short S, Marchbank A, Spurgeon DJ, Orozco-terWengel P, Kille P. Molecular insights into high-altitude adaption and acclimatisation of Aporrectodea caliginosa. Life Sci Alliance 2022; 5:5/11/e202201513. [PMID: 35977843 PMCID: PMC9386962 DOI: 10.26508/lsa.202201513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
A megabase genome assembly for Aporrectodea caliginosa is presented with transcriptomic and SNP-based evidence for acclimatisation and adaption to extreme weather conditions found at high altitude. Here, we explore the high-altitude adaptions and acclimatisation of Aporrectodea caliginosa. Population diversity is assessed through mitochondrial barcoding, identifying closely related populations across the island of Pico (Azores). We present the first megabase N50 assembly size (1.2 Mbp) genome for A. caliginosa. High- and low-altitude populations were exposed experimentally to a range of oxygen and temperature conditions, simulating altitudinal conditions, and the transcriptomic responses explored. SNP densities are assessed to identify signatures of selective pressure and their link to differentially expressed genes. The high-altitude A. caliginosa population had lower differential expression and fewer co-expressed genes between conditions, indicating a more condition-refined epigenetic response. Genes identified as under adaptive pressure through Fst and nucleotide diversity in the high-altitude population clustered around the differentially expressed an upstream environmental response control gene, HMGB1. The high-altitude population of A. caliginosa indicated adaption and acclimatisation to high-altitude conditions and suggested resilience to extreme weather events. This mechanistic understanding could help offer a strategy in further identifying other species capable of maintaining soil fertility in extreme environments.
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Affiliation(s)
- Iain Perry
- Organisms and Environment, Cardiff University, Wales, UK .,Wales Gene Park, Cardiff University, Wales, UK
| | | | - Luis Cunha
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal.,School of Applied Sciences, University of South Wales, Wales, UK
| | - Stephen Short
- Organisms and Environment, Cardiff University, Wales, UK.,UK Centre for Ecology and Hydrology, Maclean Building, Wallingford, UK
| | | | - David J Spurgeon
- UK Centre for Ecology and Hydrology, Maclean Building, Wallingford, UK
| | | | - Peter Kille
- Organisms and Environment, Cardiff University, Wales, UK
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20
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Seudre O, Martín-Zamora FM, Rapisarda V, Luqman I, Carrillo-Baltodano AM, Martín-Durán JM. The Fox Gene Repertoire in the Annelid Owenia fusiformis Reveals Multiple Expansions of the foxQ2 Class in Spiralia. Genome Biol Evol 2022; 14:evac139. [PMID: 36099507 PMCID: PMC9539403 DOI: 10.1093/gbe/evac139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Fox genes are a large and conserved family of transcription factors involved in many key biological processes, including embryogenesis and body patterning. Although the role of Fox genes has been studied in an array of model systems, comprehensive comparative studies in Spiralia-a large clade of invertebrate animals including molluscs and annelids-are scarce but much needed to better understand the evolutionary history of this gene family. Here, we reconstruct and functionally characterize the Fox gene complement in the annelid Owenia fusiformis, a slow evolving species and member of the sister group to all remaining annelids. The genome of O. fusiformis contains at least a single ortholog for 20 of the 22 Fox gene classes that are ancestral to Bilateria, including an ortholog of the recently discovered foxT class. Temporal and spatial expression dynamics reveal a conserved role of Fox genes in gut formation, mesoderm patterning, and apical organ and cilia formation in Annelida and Spiralia. Moreover, we uncover an ancestral expansion of foxQ2 genes in Spiralia, represented by 11 paralogs in O. fusiformis. Notably, although all foxQ2 copies have apical expression in O. fusiformis, they show variable spatial domains and staggered temporal activation, which suggest cooperation and sub-functionalization among foxQ2 genes for the development of apical fates in this annelid. Altogether, our study informs the evolution and developmental roles of Fox genes in Annelida and Spiralia generally, providing the basis to explore how regulatory changes in Fox gene expression might have contributed to developmental and morphological diversification in Spiralia.
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Affiliation(s)
- Océane Seudre
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Valentina Rapisarda
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Imran Luqman
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - Allan M Carrillo-Baltodano
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NSUnited Kingdom
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21
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Long read genome assemblies complemented by single cell RNA-sequencing reveal genetic and cellular mechanisms underlying the adaptive evolution of yak. Nat Commun 2022; 13:4887. [PMID: 36068211 PMCID: PMC9448747 DOI: 10.1038/s41467-022-32164-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
Wild yak (Bos mutus) and domestic yak (Bos grunniens) are adapted to high altitude environment and have ecological, economic, and cultural significances on the Qinghai-Tibetan Plateau (QTP). Currently, the genetic and cellular bases underlying adaptations of yak to extreme conditions remains elusive. In the present study, we assembled two chromosome-level genomes, one each for wild yak and domestic yak, and screened structural variants (SVs) through the long-read data of yak and taurine cattle. The results revealed that 6733 genes contained high-FST SVs. 127 genes carrying special type of SVs were differentially expressed in lungs of the taurine cattle and yak. We then constructed the first single-cell gene expression atlas of yak and taurine cattle lung tissues and identified a yak-specific endothelial cell subtype. By integrating SVs and single-cell transcriptome data, we revealed that the endothelial cells expressed the highest proportion of marker genes carrying high-FST SVs in taurine cattle lungs. Furthermore, we identified pathways which were related to the medial thickness and formation of elastic fibers in yak lungs. These findings provide new insights into the high-altitude adaptation of yak and have important implications for understanding the physiological and pathological responses of large mammals and humans to hypoxia. The genetic bases of yak adaptations to extreme conditions remains elusive. This study compares yak and cattle at a genomic and transcriptomic level, revealing a new type of endothelial cell and candidate genes related with elastic fiber formation in yak lungs that might contribute to high altitude adaptation.
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22
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Lee Y, Kim B, Jung J, Koh B, Jhang SY, Ban C, Chi WJ, Kim S, Yu J. Chromosome-level genome assembly of Plazaster borealis sheds light on the morphogenesis of multiarmed starfish and its regenerative capacity. Gigascience 2022; 11:6636911. [PMID: 35809048 PMCID: PMC9270726 DOI: 10.1093/gigascience/giac063] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/22/2022] [Accepted: 05/31/2022] [Indexed: 01/04/2023] Open
Abstract
Background Plazaster borealis has a unique morphology, displaying multiple arms with a clear distinction between disk and arms, rather than displaying pentaradial symmetry, a remarkable characteristic of echinoderms. Herein we report the first chromosome-level reference genome of P. borealis and an essential tool to further investigate the basis of the divergent morphology. Findings In total, 57.76 Gb of a long read and 70.83 Gb of short-read data were generated to assemble a de novo 561-Mb reference genome of P. borealis, and Hi-C sequencing data (57.47 Gb) were used for scaffolding into 22 chromosomal scaffolds comprising 92.38% of the genome. The genome completeness estimated by BUSCO was 98.0% using the metazoan set, indicating a high-quality assembly. Through the comparative genome analysis, we identified evolutionary accelerated genes known to be involved in morphogenesis and regeneration, suggesting their potential role in shaping body pattern and capacity of regeneration. Conclusion This first chromosome-level genome assembly of P. borealis provides fundamental insights into echinoderm biology, as well as the genomic mechanism underlying its unique morphology and regeneration.
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Affiliation(s)
- Yujung Lee
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea
| | - Bongsang Kim
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea.,Department of Agricultural and Life Sciences and Research Institute of Population Genomics, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaehoon Jung
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea.,Department of Agricultural and Life Sciences and Research Institute of Population Genomics, Seoul National University, Seoul 08826, Republic of Korea
| | - Bomin Koh
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea
| | - So Yun Jhang
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Chaeyoung Ban
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea
| | - Won-Jae Chi
- Department of Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Soonok Kim
- Department of Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Jaewoong Yu
- Department of Research, eGnome, Inc., 26 Beobwon-ro 9-gil, Sonpa-gu, Seoul 05836, Republic of Korea
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Hyams Y, Panov J, Rosner A, Brodsky L, Rinkevich Y, Rinkevich B. Transcriptome landscapes that signify Botrylloides leachi (Ascidiacea) torpor states. Dev Biol 2022; 490:22-36. [PMID: 35809632 DOI: 10.1016/j.ydbio.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/18/2022]
Abstract
Harsh environments enforce the expression of behavioural, morphological, physiological, and reproductive rejoinders, including torpor. Here we study the morphological, cellular, and molecular alterations in torpor architype in the colonial urochordate Botrylloides aff. leachii by employing whole organism Transmission electron (TEM) and light microscope observations, RNA sequencing, real-time polymerase chain reaction (qPCR) quantification of selected genes, and immunolocalization of WNT, SMAD and SOX2 gene expressions. On the morphological level, torpor starts with gradual regression of all zooids and buds which leaves the colony surviving as condensed vasculature remnants that may be 'aroused' to regenerate fully functional colonies upon changes in the environment. Simultaneously, we observed altered distributions of hemolymph cell types. Phagocytes doubled in number, while the number of morula cells declined by half. In addition, two new circulating cell types were observed, multi-nucleated and bacteria-bearing cells. RNA sequencing technology revealed marked differences in gene expression between different organism compartments and states: active zooids and ampullae, and between mid-torpor and naive colonies, or naive and torpid colonies. Gene Ontology term enrichment analyses further showed disparate biological processes. In torpid colonies, we observed overall 233 up regulated genes. These genes included NR4A2, EGR1, MUC5AC, HMCN2 and. Also, 27 transcription factors were upregulated in torpid colonies including ELK1, HDAC3, RBMX, MAZ, STAT1, STAT4 and STAT6. Interestingly, genes involved in developmental processes such as SPIRE1, RHOA, SOX11, WNT5A and SNX18 were also upregulated in torpid colonies. We further validated the dysregulation of 22 genes during torpor by utilizing qPCR. Immunohistochemistry of representative genes from three signaling pathways revealed high expression of these genes in circulated cells along torpor. WNT agonist administration resulted in early arousal from torpor in 80% of the torpid colonies while in active colonies WNT agonist triggered the torpor state. Abovementioned results thus connote unique transcriptome landscapes associated with Botrylloides leachii torpor.
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Affiliation(s)
- Yosef Hyams
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 9753, Tel Shikmona, Haifa, 3109701, Israel; Marine Biology Department, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, 31905, Israel.
| | - Julia Panov
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, 31905, Israel; Sagol Department of Neurobiology, University of Haifa, Haifa, 3498838, Israel
| | - Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 9753, Tel Shikmona, Haifa, 3109701, Israel
| | - Leonid Brodsky
- Tauber Bioinformatics Research Center, University of Haifa, Haifa, 31905, Israel
| | - Yuval Rinkevich
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum Munchen, Max-Lebsche-Platz 31, 81377, München, Germany
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 9753, Tel Shikmona, Haifa, 3109701, Israel
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24
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Yang X, Shang G, Wang X. Biochemical, transcriptomic, gut microbiome responses and defense mechanisms of the earthworm Eisenia fetida to salt stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113684. [PMID: 35623149 DOI: 10.1016/j.ecoenv.2022.113684] [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: 01/09/2022] [Revised: 05/05/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
The accumulation of sodium chloride (NaCl) in soil is a worldwide problem with detrimental effects on the survival of soil animals. The effects of NaCl on earthworms remain unclear. Here, we show that the growth rate, cocoon production rate, annetocin precursor (ANN) mRNA level, and superoxide dismutase and catalase activities in earthworms were reduced under NaCl stress, whereas the mortality rate, reactive oxygen species (ROS) and malondialdehyde activity level increased. Histological damage to the earthworm body wall and intestine were observed under NaCl stress. NaCl stress increased DNA damage in the seminal vesicle and coelomocytes. The mRNA level of lumbrokinase, 1,3-beta-glucanse, coelomic cytolytic factor (CCF1), and alpha-amylase was significantly down-regulated, whereas that of earthworm excitatory peptides2 (EEP2) was up-regulated. From 16 S rRNA sequencing, the earthworm gut microbiota diversity decreased under NaCl stress. However, Verminephrobacter, Kluyvera, Lactobacillus, and Ochrobactrum increased under NaCl stress. These findings contribute to the risk assessment of the salt stress on soil organisms.
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Affiliation(s)
- Xuelian Yang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Organic Recycling Research Institute (Suzhou) of China Agricultural University, Suzhou 215128, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing 100193, China
| | - Guangshen Shang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xing Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing 100193, China.
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25
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Arumugaperumal A, Sudalaimani DK, Arumugaswami V, Sivasubramaniam S. Draft Genome Sequence of the Earthworm Eudrilus eugeniae. Curr Genomics 2022; 23:118-125. [PMID: 36778974 PMCID: PMC9878837 DOI: 10.2174/1389202923666220401095626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Earthworms are annelids. They play a major role in agriculture and soil fertility. Vermicompost is the best organic manure for plant crops. Eudrilus eugeniae is an earthworm well suited for efficient vermicompost production. The worm is also used to study the cell and molecular biology of regeneration, molecular toxicology, developmental biology, etc., because of its abilities like high growth rate, rapid reproduction, tolerability toward wide temperature range, and less cost of maintenance. Objective: The whole genome has been revealed only for Eisenia andrei and Eisenia fetida. Methods: In the present work, we sequenced the genome of E. eugeniae using the Illumina platform and generated 160,684,383 paired-end reads. Results: The reads were assembled into a draft genome of size 488 Mb with 743,870 contigs and successfully annotated 24,599 genes. Further, 208 stem cell-specific genes and 3,432 non-coding genes were identified. Conclusion: The sequence and annotation details were hosted in a web application available at https://sudhakar-sivasubramaniam-labs.shinyapps.io/eudrilus_genome/.
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Affiliation(s)
| | | | | | - Sudhakar Sivasubramaniam
- Address correspondence to this author at the Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu- 627012, India; Tel: +91 9940998936; E-mail:
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26
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El-Aziz FEZAA, Ismail MS, Askary AE, El-Kott AF, Tantawy AA. The assessment of the protective impact of spidroin extract against UV-A radiation damage by using earthworms (Aporrectodea caliginosa) as a robust human skin model via macroscopic and histological observations. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:44906-44916. [PMID: 35141825 PMCID: PMC9200702 DOI: 10.1007/s11356-022-18861-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Numerous studies have confirmed the damage caused by excessive exposure to ultraviolet-A rays. Malignant melanoma and skin cancer are two of the most serious health consequences. Thus, the UV-A protectant is intended to protect the skin, especially the two primary layers of skin (epidermis that represents the interface between the body and its surroundings and dermis). Spider silk is the most powerful natural fibre due to its regeneration, biocompatibility, antimicrobial, wound healing, antiseptic, and blood clotting properties. This work targeted to determine the protective effect of spidroin extract against UV-A radiation damage. Earthworms Aporrectodea caliginosa were collected from Assiut University's farm. Each set of ten earthworms was separated into six groups and placed in a plastic container. Webs of spiders collected from trees and old houses. Spidroin was extracted and utilised in this work to determine the potential effects of topical application on UV-A protection. The experiment is divided into two sections: (1) UV-A exposure and (2) the use of spidroin extract to protect the earthworms from ultraviolet radiation. Two control groups (1،2) of worms were not received UV-A exposure, and four groups (3,4,5,6) were exposed to UVR-A. In contrast, groups (5,6) were received spidroin extract before exposure to UV-A. Each group from the groups (3,4,5,6) was exposed for three consecutive days (¼ hour/day, ½ hour/day, and 1 h/day), using a UV-Lamp with a wavelength of 366 nm. The histopathological changes revealed that after 1⁄4 h of UV exposure, the cuticle was swollen with a slightly detached epithelium. The cuticle was down after 1⁄2 h of exposure, and the epidermis was totally damaged and necrosed. After 1 h, the exposure showed destruction of the epidermis in the circular muscle with a loss of muscle filament integrity, varying size, and altered nucleus form, along with mild disintegration of longitudinal muscle. Spidroin extract is critical for earthworm protection against UV-A radiation damage and able to regeneration. For the first time, morphological and histological analysis was established to detect the Spidroin extract evaluated for topical application on earthworms. Earthworms can be considered as a robust human skin model prior to UV-A exposure. It induces a complete protective effect against UV-A radiation damage in earthworms.
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Affiliation(s)
| | - May S Ismail
- Pharmaceutics Department, Faculty of Pharmacy, South Valley University, Qena, Egypt
| | - Ahmad El Askary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O.Box 11099, Taif, 21944, Saudi Arabia
| | - Attalla F El-Kott
- Biology Department, Faculty of Science, King Khalid University, Abha, 61421, Saudi Arabia
- Zoology Department, College of Science, Damanhour University, Damanhour, 22511, Egypt
| | - Ahmed A Tantawy
- Biotechnology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
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27
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Discordant Genome Assemblies Drastically Alter the Interpretation of Single-Cell RNA Sequencing Data Which Can Be Mitigated by a Novel Integration Method. Cells 2022; 11:cells11040608. [PMID: 35203259 PMCID: PMC8870202 DOI: 10.3390/cells11040608] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
Advances in sequencing and assembly technology have led to the creation of genome assemblies for a wide variety of non-model organisms. The rapid production and proliferation of updated, novel assembly versions can create vexing problems for researchers when multiple-genome assembly versions are available at once, requiring researchers to work with more than one reference genome. Multiple-genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells, as single-cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. Using the Astyanax mexicanus, this study highlights how the interpretation of a single-cell dataset from the same sample changes when aligned to its two different available genome assemblies. We found that the number of cells and expressed genes detected were drastically different when aligning to the different assemblies. When the genome assemblies were used in isolation with their respective annotations, cell-type identification was confounded, as some classic cell-type markers were assembly-specific, whilst other genes showed differential patterns of expression between the two assemblies. To overcome the problems posed by multiple-genome assemblies, we propose that researchers align to each available assembly and then integrate the resultant datasets to produce a final dataset in which all genome alignments can be used simultaneously. We found that this approach increased the accuracy of cell-type identification and maximised the amount of data that could be extracted from our single-cell sample by capturing all possible cells and transcripts. As scRNAseq becomes more widely available, it is imperative that the single-cell community is aware of how genome assembly alignment can alter single-cell data and their interpretation, especially when reviewing studies on non-model organisms.
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28
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Amorim MJB, Gansemans Y, Gomes SIL, Van Nieuwerburgh F, Scott-Fordsmand JJ. Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system. Lab Anim (NY) 2021; 50:285-294. [PMID: 34489599 PMCID: PMC8460440 DOI: 10.1038/s41684-021-00831-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023]
Abstract
Enchytraeids (Annelida) are soil invertebrates with worldwide distribution that have served as ecotoxicology models for over 20 years. We present the first high-quality reference genome of Enchytraeus crypticus, assembled from a combination of Pacific Bioscience single-molecule real-time and Illumina sequencing platforms as a 525.2 Mbp genome (910 gapless scaffolds and 18,452 genes). We highlight isopenicillin, acquired by horizontal gene transfer and conferring antibiotic function. Significant gene family expansions associated with regeneration (long interspersed nuclear elements), the innate immune system (tripartite motif-containing protein) and response to stress (cytochrome P450) were identified. The ACE (Angiotensin-converting enzyme) - a homolog of ACE2, which is involved in the coronavirus SARS-CoV-2 cell entry - is also present in E. crypticus. There is an obvious potential of using E. crypticus as a model to study interactions between regeneration, the innate immune system and aging-dependent decline.
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Affiliation(s)
- Mónica J B Amorim
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal.
| | - Yannick Gansemans
- Department of Pharmaceutics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Susana I L Gomes
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal
| | - Filip Van Nieuwerburgh
- Department of Pharmaceutics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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29
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Sahu R, Sahu SK, Nishank SS. de novo transcriptome profile of two earthworms Lampito mauritii and Drawida calebi during regeneration. Biochem Biophys Rep 2021; 27:101092. [PMID: 34409173 PMCID: PMC8361223 DOI: 10.1016/j.bbrep.2021.101092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/26/2022] Open
Abstract
Earthworms have remarkable ability to regenerate its tail and head region. However the list of genes expressed in this regeneration process has been less explored baring a few species. The current study involves the de novo transcriptome sequencing of intact tail and regenerating tail (15 day post amputation) of earthworms belonging to two different genera Lampito mauritii (Kinberg, 1867) and Drawida calebi (Gates, 1945). This study contains one de-novo and one reference based transcriptome analysis each from one genus of two earthworm genera. From a total of 119.92 million (150 × 2) reads, 112.95 million high quality adapter free reads were utilized in analysis. Assembly of high-quality reads was performed separately for Lampito mauritii (LM sample) and Drawida calebi (DC sample) that resulted in 66368 and 1,61,289 transcripts respectively. About 25.21% of transcripts were functionally annotated for DC sample and 38.27% for LM samples against Annelida sequences. A total of 239 genes were expressed exclusively in regenerated tissue compared to intact sample in DC whereas about 241 genes were exclusively expressed in regenerated tissue of LM compared to its intact sample. Majority of genes in Drawida and Lampito were dedicated to immune response, maintenance of cytoskeleton, resisting oxidative stress and promoting neuronal regeneration for cell-cell communication during tail regeneration. Upregulation of genes such as beta catenin, Sox, notch, FGF, frizzled. Similarity with annelid worm Capitella telesta.
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Affiliation(s)
- Ranjan Sahu
- Post Graduate Department of Zoology, Utkal University, Vani Vihar, Bhubaneswar, 751004, Odisha, India
| | - Sanjat Kumar Sahu
- Dept. of Environment Science, Sambalpur University, Jyoti Vihar, Burla, 768019, Odisha, India
| | - Sudhansu Sekhar Nishank
- Post Graduate Department of Zoology, Utkal University, Vani Vihar, Bhubaneswar, 751004, Odisha, India
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30
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Kostyuchenko RP, Kozin VV. Comparative Aspects of Annelid Regeneration: Towards Understanding the Mechanisms of Regeneration. Genes (Basel) 2021; 12:1148. [PMID: 34440322 PMCID: PMC8392629 DOI: 10.3390/genes12081148] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 01/12/2023] Open
Abstract
The question of why animals vary in their ability to regenerate remains one of the most intriguing questions in biology. Annelids are a large and diverse phylum, many members of which are capable of extensive regeneration such as regrowth of a complete head or tail and whole-body regeneration, even from few segments. On the other hand, some representatives of both of the two major annelid clades show very limited tissue regeneration and are completely incapable of segmental regeneration. Here we review experimental and descriptive data on annelid regeneration, obtained at different levels of organization, from data on organs and tissues to intracellular and transcriptomic data. Understanding the variety of the cellular and molecular basis of regeneration in annelids can help one to address important questions about the role of stem/dedifferentiated cells and "molecular morphallaxis" in annelid regeneration as well as the evolution of regeneration in general.
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Affiliation(s)
- Roman P. Kostyuchenko
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia;
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Bideau L, Kerner P, Hui J, Vervoort M, Gazave E. Animal regeneration in the era of transcriptomics. Cell Mol Life Sci 2021; 78:3941-3956. [PMID: 33515282 PMCID: PMC11072743 DOI: 10.1007/s00018-021-03760-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 12/27/2022]
Abstract
Animal regeneration, the ability to restore a lost body part, is a process that has fascinated scientists for centuries. In this review, we first present what regeneration is and how it relates to development, as well as the widespread and diverse nature of regeneration in animals. Despite this diversity, animal regeneration includes three common mechanistic steps: initiation, induction and activation of progenitors, and morphogenesis. In this review article, we summarize and discuss, from an evolutionary perspective, the recent data obtained for a variety of regeneration models which have allowed to identify key shared mechanisms that control these main steps of animal regeneration. This review also synthesizes the wealth of high-throughput mRNA sequencing data (bulk mRNA-seq) concerning regeneration which have been obtained in recent years, highlighting the major advances in the regeneration field that these studies have revealed. We stress out that, through a comparative approach, these data provide opportunities to further shed light on the evolution of regeneration in animals. Finally, we point out how the use of single-cell mRNA-seq technology and integration with epigenomic approaches may further help researchers to decipher mechanisms controlling regeneration and their evolution in animals.
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Affiliation(s)
- Loïc Bideau
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France
| | - Pierre Kerner
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Michel Vervoort
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France.
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France.
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Wang Z, Bai Y, Nie H, Xu Q, Yin Z, Zhang Y, Yin X, Yan X. Molecular mechanisms of wound healing and regeneration of siphon in the Manila clam Ruditapes philippinarum revealed by transcriptomic analysis. Genomics 2021; 113:1011-1025. [PMID: 33626340 DOI: 10.1016/j.ygeno.2021.02.010] [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: 08/11/2020] [Revised: 01/24/2021] [Accepted: 02/18/2021] [Indexed: 10/22/2022]
Abstract
Ruditapes philippinarum is an economically important marine shellfish aquaculture species, and it has the ability to regenerate its siphons. To gain a greater understanding of the molecular mechanisms at work during siphon regeneration and to provide evidence for morphological regeneration, we examined transcriptome responses of siphon tissue of R. philippinarum during regeneration and observed regenerative siphons under the stereomicroscope. The overall process of siphon regeneration was dissected based on the morphological changes of siphon and the identification of up-regulated key differentially expressed genes (DEGs). The protein biosynthesis and metabolism played important roles in wound healing and siphon regeneration of R. philippinarum. Transcriptomic analysis identified the Wnt and TGF-β signaling pathways by focusing on the function and expression pattern of genes in these pathways during siphon regeneration. In addition, we carried out a genome-wide identification and phylogenetic analysis of TGF-β superfamily in R. philippinarum. The expression profiles of the TGF-β superfamily genes were analyzed in eight adult tissues (adductor muscle, mantle, foot, gill, siphon, digestive gland, gonad, and labial palp) and regenerative siphon. This study shed new light on the process of morphological regeneration and regenerative mechanism of siphon of R. philippinarum.
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Affiliation(s)
- Zhengxing Wang
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Yitian Bai
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China.
| | - Qiaoyue Xu
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Zhihui Yin
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Yanming Zhang
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China
| | - Xuwang Yin
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China.
| | - Xiwu Yan
- College of Fisheries and Life Science, Dalian Ocean University, 116023 Dalian, China; Engineering Research Center of Shellfish Culture and Breeding in Liaoning Province, Dalian Ocean University, 116023 Dalian, China.
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33
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Identification and expression of adenosine deaminases acting on tRNA (ADAT) during early tail regeneration of the earthworm. Genes Genomics 2021; 43:295-301. [PMID: 33575975 DOI: 10.1007/s13258-020-01031-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND RNA editing is a widespread phenomenon in all metazoans. One of the common RNA editing event is the chemical conversion of adenosine to inosine (A-to-I) catalyzed by adenosine deaminases acting on tRNA (ADAT). During D. melanogaster development, the ADAT1 transcript was found to localize mainly to the central nervous system including brain and ventral nerve cord during brain development. Although an earthworm adenosine deaminases acting on mRNA (ADAR) has been identified and its possible implication in earthworm regeneration has been investigated, there is little accumulated information on ADAT and tRNA editing in the annelid including terrestrial earthworms. OBJECTIVE This study aimed to investigate the molecular characteristics and the expression pattern of earthworm ADAT during tail regeneration to understand its physiological significance. METHODS Nucleotide sequence of Ean-ADAT was retrieved from the genome assembly of Eisenia andrei via Basic Local Alignment Search Tool (BLAST). The genome assembly of Eisenia andrei was downloaded from National Genomics Data Center ( http://bigd.big.ac.cn/gwh/ ). The alignment and phylogenetic relationship of the core deaminase domains of ADATs and ADARs were analyzed. Its temporal expression during early tail regeneration was measured using real-time PCR. RESULTS The open reading frame of Ean-ADAT consists of 1719 nucleotides encoding 573 amino acids. Domain analysis indicates that Ean-ADAT has a deaminase domain composed of 498 amino acids and a predicted nuclear localization signal at the N-terminal. Its subcellular localization was predicted to be nuclear. The core deaminase region of Ean-ADAT encompasses the three active-site motifs, including zinc-chelating residues and a glutamate residue for catalytic activity. In addition, Ean-ADAT shares highly conserved RNA recognition region flanking the third cysteine of the deaminase motif with other ADAT1s even from the yeast. Multiple sequence alignment and phylogenetic analysis indicate that Ean-ADAT shows greater similarity to vertebrate ADARs than to yeast Tad1p. Ean-ADAT mRNA expression began to remarkably decrease before 12 h post-amputation, showing a tendency to gradual decrease until 7 dpa and then it slightly rebounded at 10 dpa. CONCLUSIONS Our results demonstrate that Ean-ADAT belongs to a class of ADAT1s and support the hypothesis of a common evolutionary origin for ADARs and ADATs. The temporal expression of Ean-ADAT could suggest that its activity is unrelated to the molecular mechanisms of dedifferentiation.
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Amynthas corticis genome reveals molecular mechanisms behind global distribution. Commun Biol 2021; 4:135. [PMID: 33514865 PMCID: PMC7846840 DOI: 10.1038/s42003-021-01659-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 01/05/2021] [Indexed: 01/30/2023] Open
Abstract
Earthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.
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Sur A, Meyer NP. Resolving Transcriptional States and Predicting Lineages in the Annelid Capitella teleta Using Single-Cell RNAseq. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.618007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Evolution and diversification of cell types has contributed to animal evolution. However, gene regulatory mechanisms underlying cell fate acquisition during development remains largely uncharacterized in spiralians. Here we use a whole-organism, single-cell transcriptomic approach to map larval cell types in the annelid Capitella teleta at 24- and 48-h post gastrulation (stages 4 and 5). We identified eight unique cell clusters (undifferentiated precursors, ectoderm, muscle, ciliary-band, gut, neurons, neurosecretory cells, and protonephridia), thus helping to identify uncharacterized molecular signatures such as previously unknown neurosecretory cell markers in C. teleta. Analysis of coregulatory programs in individual clusters revealed gene interactions that can be used for comparisons of cell types across taxa. We examined the neural and neurosecretory clusters more deeply and characterized a differentiation trajectory starting from dividing precursors to neurons using Monocle3 and velocyto. Pseudotime analysis along this trajectory identified temporally-distinct cell states undergoing progressive gene expression changes over time. Our data revealed two potentially distinct neural differentiation trajectories including an early trajectory for brain neurosecretory cells. This work provides a valuable resource for future functional investigations to better understanding neurogenesis and the transitions from neural precursors to neurons in an annelid.
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Yoon YB, Yu YS, Park BJ, Cho SJ, Park SC. Identification and Spatiotemporal Expression of Adenosine Deaminases Acting on RNA (ADAR) during Earthworm Regeneration: Its Possible Implication in Muscle Redifferentiation. BIOLOGY 2020; 9:biology9120448. [PMID: 33291433 PMCID: PMC7762157 DOI: 10.3390/biology9120448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022]
Abstract
Simple Summary Among the animal species capable of regenerating missing body parts, a species of earthworm, Perionyx excavatus, has the most powerful regeneration capacity, which can completely and regenerate an amputated head and tail. Earthworm regeneration is a form of epimorphosis, a simple mode of development in adults that occurs around the sites of damage rather than throughout the body. In order to achieve this process, the earthworm must have molecular tools via which a variety of cell and tissue types can be precisely recovered from the pluripotent (or possibly totipotent) blastemal cells. Adenosine to inosine (A-to-I) RNA editing catalyzed by adenosine deaminases acting on RNA (ADAR) can generate substantial transcriptome and proteome variability and provide an ideal tool for cell and tissue re-specification. To understand the role of ADAR during earthworm regeneration, the molecular characteristics of an ADAR gene identified from P. excavatus (Pex-ADAR) were analyzed, and its spatial and temporal expression patterns were observed during regeneration. Domain analysis showed that Pex-ADAR is a member of the ADAR1 class. Its expression level primarily increases when and where muscle redifferentiation is actively taking place, suggesting that the RNA-editing enzyme Pex-ADAR is involved in muscle redifferentiation. Abstract Adenosine deaminases acting on RNA (ADAR) catalyze the hydrolytic deamination of adenosine (A) to produce inosine (I) in double-stranded RNA substrates. A-to-I RNA editing has increasingly broad physiological significance in development, carcinogenesis, and environmental adaptation. Perionyx excavatus is an earthworm with potent regenerative potential; it can regenerate the head and tail and is an advantageous model system to investigate the molecular mechanisms of regeneration. During RNA sequencing analysis of P. excavatus regenerates, we identified an ADAR homolog (Pex-ADAR), which led us to examine its spatial and temporal expression to comprehend how Pex-ADAR is linked to regeneration. At first, in domain analysis, we discovered that Pex-ADAR only has one double-stranded RNA-binding domain (dsRBD) and a deaminase domain without a Z-DNA-binding domain (ZBD). In addition, a comparison of the core deaminase domains of Pex-ADAR with those of other ADAR family members indicated that Pex-ADAR comprises the conserved three active-site motifs and a glutamate residue for catalytic activity. Pex-ADAR also shares 11 conserved residues, a characteristic of ADAR1, supporting that Pex-ADAR is a member of ADAR1 class. Its temporal expression was remarkably low in the early stages of regeneration before suddenly increasing at 10 days post amputation (dpa) when diverse cell types and tissues were being regenerated. In situ hybridization of Pex-ADAR messenger RNA (mRNA) indicated that the main expression was observed in regenerating muscle layers and related connective tissues. Taken together, the present results demonstrate that an RNA-editing enzyme, Pex-ADAR, is implicated in muscle redifferentiation during earthworm regeneration.
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Affiliation(s)
- Yoo Bin Yoon
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (Y.B.Y.); (B.J.P.)
| | - Yun-Sang Yu
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea;
| | - Beom Jun Park
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (Y.B.Y.); (B.J.P.)
| | - Sung-Jin Cho
- School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju 28644, Korea;
- Correspondence: (S.-J.C.); (S.C.P.); Tel.: +82-43-261-2294 (S.-J.C.); +82-2-820-5212 (S.C.P.)
| | - Soon Cheol Park
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea; (Y.B.Y.); (B.J.P.)
- Correspondence: (S.-J.C.); (S.C.P.); Tel.: +82-43-261-2294 (S.-J.C.); +82-2-820-5212 (S.C.P.)
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