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Zhong J, Zhang J, Zhang Y, Ge Y, He W, Liang C, Gao Y, Zhu Z, Machado RAR, Zhou W. Heat stress reprograms herbivory-induced defense responses in potato plants. BMC PLANT BIOLOGY 2024; 24:677. [PMID: 39014327 PMCID: PMC11253553 DOI: 10.1186/s12870-024-05404-x] [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: 11/29/2023] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
Climate change is predicted to increase the occurrence of extreme weather events such as heatwaves, which may thereby impact the outcome of plant-herbivore interactions. While elevated temperature is known to directly affect herbivore growth, it remains largely unclear if it indirectly influences herbivore performance by affecting the host plant they feed on. In this study, we investigated how transient exposure to high temperature influences plant herbivory-induced defenses at the transcript and metabolic level. To this end, we studied the interaction between potato (Solanum tuberosum) plants and the larvae of the potato tuber moth (Phthorimaea operculella) under different temperature regimes. We found that P. operculella larvae grew heavier on leaves co-stressed by high temperature and insect herbivory than on leaves pre-stressed by herbivory alone. We also observed that high temperature treatments altered phylotranscriptomic patterns upon herbivory, which changed from an evolutionary hourglass pattern, in which transcriptomic responses at early and late time points after elicitation are more variable than the ones in the middle, to a vase pattern. Specifically, transcripts of many herbivory-induced genes in the early and late defense stage were suppressed by HT treatment, whereas those in the intermediate stage peaked earlier. Additionally, we observed that high temperature impaired the induction of jasmonates and defense compounds upon herbivory. Moreover, using jasmonate-reduced (JA-reduced, irAOC) and -elevated (JA-Ile-elevated, irCYP94B3s) potato plants, we showed that high temperature suppresses JA signaling mediated plant-induced defense to herbivore attack. Thus, our study provides evidences on how temperature reprograms plant-induced defense to herbivores.
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Affiliation(s)
- Jian Zhong
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Jinyi Zhang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yadong Zhang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yang Ge
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenjing He
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengjuan Liang
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yulin Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zengrong Zhu
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China
- Hainan Institute, Zhejiang University, Sanya, 572000, China
| | - Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchatel, Neuchatel, 2000, Switzerland
| | - Wenwu Zhou
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, 310058, China.
- Hainan Institute, Zhejiang University, Sanya, 572000, China.
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2
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Li C, Yang Z, Xu X, Meng L, Liu S, Yang D. Conserved and specific gene expression patterns in the embryonic development of tardigrades. Evol Dev 2024; 26:e12476. [PMID: 38654704 DOI: 10.1111/ede.12476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/18/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
Tardigrades, commonly known as water bears, are enigmatic organisms characterized by their remarkable resilience to extreme environments despite their simple and compact body structure. To date, there is still much to understand about their evolutionary and developmental features contributing to their special body plan and abilities. This research provides preliminary insights on the conserved and specific gene expression patterns during embryonic development of water bears, focusing on the species Hypsibius exemplaris. The developmental dynamic expression analysis of the genes with various evolutionary age grades indicated that the mid-conserved stage of H. exemplaris corresponds to the period of ganglia and midgut development, with the late embryonic stage showing a transition from non-conserved to conserved state. Additionally, a comparison with Drosophila melanogaster highlighted the absence of certain pathway nodes in development-related pathways, such as Maml and Hairless, which are respectively the transcriptional co-activator and co-repressor of NOTCH regulated genes. We also employed Weighted Gene Co-expression Network Analysis (WGCNA) to investigate the expression patterns of tardigrade-specific genes during embryo development. Our findings indicated that the module containing the highest proportion of tardigrade-specific genes (TSGs) exhibits high expression levels before the mid-conserved stage, potentially playing a role in glutathione and lipid metabolism. These functions may be associated to the ecdysone synthesis and storage cell formation, which is unique to tardigrades.
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Affiliation(s)
- Chaoran Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhixiang Yang
- School of Life Sciences, Hebei University, Baoding, China
| | - Xiaofang Xu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Lingling Meng
- School of Life Sciences, Hebei University, Baoding, China
| | - Shihao Liu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Dong Yang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
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3
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Sartorius AM, Rokicki J, Birkeland S, Bettella F, Barth C, de Lange AMG, Haram M, Shadrin A, Winterton A, Steen NE, Schwarz E, Stein DJ, Andreassen OA, van der Meer D, Westlye LT, Theofanopoulou C, Quintana DS. An evolutionary timeline of the oxytocin signaling pathway. Commun Biol 2024; 7:471. [PMID: 38632466 PMCID: PMC11024182 DOI: 10.1038/s42003-024-06094-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Oxytocin is a neuropeptide associated with both psychological and somatic processes like parturition and social bonding. Although oxytocin homologs have been identified in many species, the evolutionary timeline of the entire oxytocin signaling gene pathway has yet to be described. Using protein sequence similarity searches, microsynteny, and phylostratigraphy, we assigned the genes supporting the oxytocin pathway to different phylostrata based on when we found they likely arose in evolution. We show that the majority (64%) of genes in the pathway are 'modern'. Most of the modern genes evolved around the emergence of vertebrates or jawed vertebrates (540 - 530 million years ago, 'mya'), including OXTR, OXT and CD38. Of those, 45% were under positive selection at some point during vertebrate evolution. We also found that 18% of the genes in the oxytocin pathway are 'ancient', meaning their emergence dates back to cellular organisms and opisthokonta (3500-1100 mya). The remaining genes (18%) that evolved after ancient and before modern genes were classified as 'medium-aged'. Functional analyses revealed that, in humans, medium-aged oxytocin pathway genes are highly expressed in contractile organs, while modern genes in the oxytocin pathway are primarily expressed in the brain and muscle tissue.
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Affiliation(s)
- Alina M Sartorius
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Jaroslav Rokicki
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Centre of Research and Education in Forensic Psychiatry, Oslo University Hospital, Oslo, Norway
| | - Siri Birkeland
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Francesco Bettella
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Medical Genetics, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Claudia Barth
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Ann-Marie G de Lange
- Department of Psychology, University of Oslo, Oslo, Norway
- Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Marit Haram
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Department of Mental Health and Suicide, Norwegian Institute of Public Health, Oslo, Norway
| | - Alexey Shadrin
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Adriano Winterton
- Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway
| | - Nils Eiel Steen
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Emanuel Schwarz
- Hector Institute for Artificial Intelligence in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Dan J Stein
- SA MRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Dennis van der Meer
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Lars T Westlye
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Daniel S Quintana
- Norwegian Centre for Mental Disorders Research (NORMENT), Institute of Clinical Medicine and Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway.
- Department of Psychology, University of Oslo, Oslo, Norway.
- KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo and Oslo University Hospital, Oslo, Norway.
- NevSom, Department of Rare Disorders, Oslo University Hospital, Oslo, Norway.
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4
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Ma PF, Liu YL, Guo C, Jin G, Guo ZH, Mao L, Yang YZ, Niu LZ, Wang YJ, Clark LG, Kellogg EA, Xu ZC, Ye XY, Liu JX, Zhou MY, Luo Y, Yang Y, Soltis DE, Bennetzen JL, Soltis PS, Li DZ. Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance. Nat Genet 2024; 56:710-720. [PMID: 38491323 PMCID: PMC11018529 DOI: 10.1038/s41588-024-01683-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024]
Abstract
Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.
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Affiliation(s)
- Peng-Fei Ma
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Cen Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Guihua Jin
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ling Mao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yi-Zhou Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Liang-Zhong Niu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yu-Jiao Wang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lynn G Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 345 Bessey, Ames, IA, USA
| | | | - Zu-Chang Xu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xia-Ying Ye
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yan Luo
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Yang Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | | | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.
- Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
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5
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Ramon E, Obón-Santacana M, Khannous-Lleiffe O, Saus E, Gabaldón T, Guinó E, Bars-Cortina D, Ibáñez-Sanz G, Rodríguez-Alonso L, Mata A, García-Rodríguez A, Moreno V. Performance of a Shotgun Prediction Model for Colorectal Cancer When Using 16S rRNA Sequencing Data. Int J Mol Sci 2024; 25:1181. [PMID: 38256252 PMCID: PMC10816515 DOI: 10.3390/ijms25021181] [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: 12/14/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Colorectal cancer (CRC), the third most common cancer globally, has shown links to disturbed gut microbiota. While significant efforts have been made to establish a microbial signature indicative of CRC using shotgun metagenomic sequencing, the challenge lies in validating this signature with 16S ribosomal RNA (16S) gene sequencing. The primary obstacle is reconciling the differing outputs of these two methodologies, which often lead to divergent statistical models and conclusions. In this study, we introduce an algorithm designed to bridge this gap by mapping shotgun-derived taxa to their 16S counterparts. This mapping enables us to assess the predictive performance of a shotgun-based microbiome signature using 16S data. Our results demonstrate a reduction in performance when applying the 16S-mapped taxa in the shotgun prediction model, though it retains statistical significance. This suggests that while an exact match between shotgun and 16S data may not yet be feasible, our approach provides a viable method for comparative analysis and validation in the context of CRC-associated microbiome research.
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Affiliation(s)
- Elies Ramon
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
| | - Mireia Obón-Santacana
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Olfat Khannous-Lleiffe
- Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), 08028 Barcelona, Spain
| | - Elisabet Guinó
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - David Bars-Cortina
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
| | - Gemma Ibáñez-Sanz
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- Gastroenterology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Lorena Rodríguez-Alonso
- Gastroenterology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Alfredo Mata
- Digestive System Service, Moisés Broggi Hospital, 08970 Sant Joan Despí, Spain
| | - Ana García-Rodríguez
- Endoscopy Unit, Digestive System Service, Viladecans Hospital-IDIBELL, 08840 Viladecans, Spain
| | - Victor Moreno
- Colorectal Cancer Group, ONCOBELL Program, Institut de Recerca Biomedica de Bellvitge (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Unit of Biomarkers and Suceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona (UB), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
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6
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Ullrich KK, Glytnasi NE. oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data. Bioinformatics 2023; 39:btad657. [PMID: 37952198 PMCID: PMC10663984 DOI: 10.1093/bioinformatics/btad657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/22/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
SUMMARY For model species, single-cell RNA-based cell atlases are available. A good cell atlas includes all major stages in a species' ontogeny, and soon, they will be standard even for nonmodel species. Here, we propose a Python package called oggmap, which allows for the easy extraction of an orthomap (gene ages per orthogroup) for any given query species from OrthoFinder and other gene family data resources, like homologous groups from eggNOG or PLAZA. oggmap provides extracted gene ages for more than thousand eukaryotic species which can be further used to calculate gene age-weighted expression data from scRNA sequencing objects using the Python Scanpy toolkit. Not limited to one transcriptome evolutionary index, oggmap can visualize the individual gene category (e.g. age class, nucleotide diversity bin) and their corresponding expression profiles to investigate scRNA-based cell type assignments in an evolutionary context. AVAILABILITY AND IMPLEMENTATION oggmap source code is available at https://github.com/kullrich/oggmap, documentation is available at https://oggmap.readthedocs.io/en/latest/. oggmap can be installed via PyPi or directly used via a docker container.
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Affiliation(s)
- Kristian K Ullrich
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Nikoleta E Glytnasi
- Max Planck Research Group: Dynamics of Social Behavior, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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7
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Batista da Silva I, Aciole Barbosa D, Kavalco KF, Nunes LR, Pasa R, Menegidio FB. Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae). Sci Rep 2023; 13:12051. [PMID: 37491348 PMCID: PMC10368750 DOI: 10.1038/s41598-023-34198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/25/2023] [Indexed: 07/27/2023] Open
Abstract
Astyanax mexicanus is a well-known model species, that has two morphotypes, cavefish, from subterranean rivers and surface fish, from surface rivers. They are morphologically distinct due to many troglomorphic traits in the cavefish, such as the absence of eyes. Most studies on A. mexicanus are focused on eye development and protein-coding genes involved in the process. However, lncRNAs did not get the same attention and very little is known about them. This study aimed to fill this knowledge gap, identifying, describing, classifying, and annotating lncRNAs expressed in the embryo's eye tissue of cavefish and surface fish. To do so, we constructed a concise workflow to assemble and evaluate transcriptomes, annotate protein-coding genes, ncRNAs families, predict the coding potential, identify putative lncRNAs, map them and predict interactions. This approach resulted in the identification of 33,069 and 19,493 putative lncRNAs respectively mapped in cavefish and surface fish. Thousands of these lncRNAs were annotated and identified as conserved in human and several species of fish. Hundreds of them were validated in silico, through ESTs. We identified lncRNAs associated with genes related to eye development. This is the case of a few lncRNAs associated with sox2, which we suggest being isomorphs of the SOX2-OT, a lncRNA that can regulate the expression of sox2. This work is one of the first studies to focus on the description of lncRNAs in A. mexicanus, highlighting several lncRNA targets and opening an important precedent for future studies focusing on lncRNAs expressed in A. mexicanus.
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Affiliation(s)
- Iuri Batista da Silva
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil
| | - David Aciole Barbosa
- Integrated Biotechnology Center, University of Mogi das Cruzes (UMC), Av. Dr. Cândido X. de Almeida and Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil
| | - Karine Frehner Kavalco
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil
| | - Luiz R Nunes
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, 09606-045, Brazil
| | - Rubens Pasa
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil.
| | - Fabiano B Menegidio
- Integrated Biotechnology Center, University of Mogi das Cruzes (UMC), Av. Dr. Cândido X. de Almeida and Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil.
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8
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Nesterenko M, Miroliubov A. From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala). F1000Res 2023; 11:583. [PMID: 36447930 PMCID: PMC9664023 DOI: 10.12688/f1000research.110492.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, a system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into "zombies". Despite all these amazing traits, there are no genomic or transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan Peltogaster reticulata: the externa, and the main, growing, and thoracic parts of the interna. We used all prepared data for the de novo assembly of the reference transcriptome. Next, a set of encoded proteins was determined, the expression levels of protein-coding genes in different parts of the parasite's body were calculated and lists of enriched bioprocesses were identified. We also in silico identified and analyzed sets of potential excretory / secretory proteins. Finally, we applied phylostratigraphy and evolutionary transcriptomics approaches to our data. Results: The assembled reference transcriptome included transcripts of 12,620 protein-coding genes and was the first for any rhizocephalan. Based on the results obtained, the spatial heterogeneity of protein-coding gene expression in different regions of the adult female body of P. reticulata was established. The results of both transcriptomic analysis and histological studies indicated the presence of germ-like cells in the lumen of the interna. The potential molecular basis of the interaction between the nervous system of the host and the parasite's interna was also determined. Given the prolonged expression of development-associated genes, we suggest that rhizocephalans "got stuck in their metamorphosis", even at the reproductive stage. Conclusions: The results of the first comparative transcriptomic analysis for Rhizocephala not only clarified but also expanded the existing ideas about the biology of these extraordinary parasites.
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Affiliation(s)
- Maksim Nesterenko
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, 199034, Russian Federation,Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation,
| | - Aleksei Miroliubov
- Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation
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9
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Zhong R, Zhu Y, Zhang H, Huo Y, Huang Y, Cheng W, Liang P. Integrated lipidomic and transcriptomic analyses reveal the mechanism of large yellow croaker roe phospholipids on lipid metabolism in normal-diet mice. Food Funct 2022; 13:12852-12869. [PMID: 36444685 DOI: 10.1039/d2fo02736d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large yellow croaker roe phospholipids (LYCRPLs) could regulate the accumulation of triglycerides and blood lipid levels. However, there exists little research on the mechanism of LYCRPLs on lipid metabolism in normal-diet mice. In this work, the mice on a normal diet were given low-dose, medium-dose, and high-dose LYCRPLs by intragastric administration for 6 weeks. At the same time, the physiological and biochemical indicators of the mice were determined, and the histomorphological observation of the liver and epididymal fat was carried out. In addition, we examined the gene expression and lipid metabolites in the liver of mice using transcriptomic and lipidomic and performed a correlation analysis. The results showed that LYCRPLs regulated the lipid metabolism of normal-diet mice by affecting the expression of the glycerolipid metabolism pathway, insulin resistance pathway, and cholesterol metabolism pathway. This study not only elucidated the main pathway by which LYCRPLs regulate lipid metabolism, but also laid a foundation for exploring LYCRPLs as functional food supplements.
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Affiliation(s)
- Rongbin Zhong
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian, China. .,Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, 350002, Fujian, China
| | - Yujie Zhu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian, China. .,Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, 350002, Fujian, China
| | - Huadan Zhang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian, China. .,Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, 350002, Fujian, China
| | - Yuming Huo
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian, China. .,Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, 350002, Fujian, China
| | - Ying Huang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian, China. .,Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, 350002, Fujian, China
| | - Wenjian Cheng
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian, China. .,Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, 350002, Fujian, China
| | - Peng Liang
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian, China. .,Engineering Research Centre of Fujian-Taiwan Special Marine Food Processing and Nutrition, Ministry of Education, Fuzhou, 350002, Fujian, China
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10
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Rokicki J, Kaufmann T, de Lange AMG, van der Meer D, Bahrami S, Sartorius AM, Haukvik UK, Steen NE, Schwarz E, Stein DJ, Nærland T, Andreassen OA, Westlye LT, Quintana DS. Oxytocin receptor expression patterns in the human brain across development. Neuropsychopharmacology 2022; 47:1550-1560. [PMID: 35347267 PMCID: PMC9205980 DOI: 10.1038/s41386-022-01305-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/04/2022] [Indexed: 12/31/2022]
Abstract
Oxytocin plays a vital role in social behavior and homeostatic processes, with animal models indicating that oxytocin receptor (OXTR) expression patterns in the brain influence behavior and physiology. However, the developmental trajectory of OXTR gene expression is unclear. By analyzing gene expression data in human post-mortem brain samples, from the prenatal period to late adulthood, we demonstrate distinct patterns of OXTR gene expression in the developing brain, with increasing OXTR expression along the course of the prenatal period culminating in a peak during early childhood. This early life OXTR expression peak pattern appears slightly earlier in a comparative macaque sample, which is consistent with the relative immaturity of the human brain during early life compared to macaques. We also show that a network of genes with strong spatiotemporal couplings with OXTR is enriched in several psychiatric illness and body composition phenotypes. Taken together, these results demonstrate that oxytocin signaling plays an important role in a diverse set of psychological and somatic processes across the lifespan.
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Affiliation(s)
- Jaroslav Rokicki
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.5510.10000 0004 1936 8921Department of Psychology, University of Oslo, Oslo, Norway ,grid.55325.340000 0004 0389 8485Centre of Research and Education in Forensic Psychiatry, Oslo University Hospital, Oslo, Norway
| | - Tobias Kaufmann
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.10392.390000 0001 2190 1447Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Ann-Marie G. de Lange
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.9851.50000 0001 2165 4204LREN, Centre for Research in Neurosciences - Department of Clinical Neurosciences, CHUV and University of Lausanne, Lausanne, Switzerland ,grid.4991.50000 0004 1936 8948Department of Psychiatry, University of Oxford, Oxford, UK
| | - Dennis van der Meer
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.5012.60000 0001 0481 6099School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Shahram Bahrami
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.5510.10000 0004 1936 8921Department of Psychology, University of Oslo, Oslo, Norway
| | - Alina M. Sartorius
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.5510.10000 0004 1936 8921Department of Psychology, University of Oslo, Oslo, Norway
| | - Unn K. Haukvik
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.55325.340000 0004 0389 8485Centre of Research and Education in Forensic Psychiatry, Oslo University Hospital, Oslo, Norway
| | - Nils Eiel Steen
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Emanuel Schwarz
- grid.7700.00000 0001 2190 4373Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Dan J. Stein
- grid.7836.a0000 0004 1937 1151SAMRC Unit on Risk & Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Terje Nærland
- grid.55325.340000 0004 0389 8485NevSom, Department of Rare Disorders, Oslo University Hospital, Oslo, Norway ,grid.5510.10000 0004 1936 8921KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Ole A. Andreassen
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.5510.10000 0004 1936 8921KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Lars T. Westlye
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.5510.10000 0004 1936 8921Department of Psychology, University of Oslo, Oslo, Norway ,grid.5510.10000 0004 1936 8921KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Daniel S. Quintana
- grid.5510.10000 0004 1936 8921NORMENT Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital, Oslo, Norway ,grid.5510.10000 0004 1936 8921Department of Psychology, University of Oslo, Oslo, Norway ,grid.55325.340000 0004 0389 8485NevSom, Department of Rare Disorders, Oslo University Hospital, Oslo, Norway ,grid.5510.10000 0004 1936 8921KG Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
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11
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Nesterenko M, Miroliubov A. From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala). F1000Res 2022; 11:583. [PMID: 36447930 PMCID: PMC9664023 DOI: 10.12688/f1000research.110492.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 09/16/2023] Open
Abstract
Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, a system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into "zombies". Despite all these amazing traits, there are no genomic or transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan Peltogaster reticulata: the externa, and the main, growing, and thoracic parts of the interna. We used all prepared data for the de novo assembly of the reference transcriptome. Next, a set of encoded proteins was determined, the expression levels of protein-coding genes in different parts of the parasite's body were calculated and lists of enriched bioprocesses were identified. We also in silico identified and analyzed sets of potential excretory / secretory proteins. Finally, we applied phylostratigraphy and evolutionary transcriptomics approaches to our data. Results: The assembled reference transcriptome included transcripts of 12,620 protein-coding genes and was the first for any rhizocephalan. Based on the results obtained, the spatial heterogeneity of protein-coding gene expression in different regions of the adult female body of P. reticulata was established. The results of both transcriptomic analysis and histological studies indicated the presence of germ-like cells in the lumen of the interna. The potential molecular basis of the interaction between the nervous system of the host and the parasite's interna was also determined. Given the prolonged expression of development-associated genes, we suggest that rhizocephalans "got stuck in their metamorphosis", even at the reproductive stage. Conclusions: The results of the first comparative transcriptomic analysis for Rhizocephala not only clarified but also expanded the existing ideas about the biology of these extraordinary parasites.
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Affiliation(s)
- Maksim Nesterenko
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, 199034, Russian Federation
- Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation
| | - Aleksei Miroliubov
- Laboratory of parasitic worms and protists, Zoological Institute of Russian Academy of Sciences, St Petersburg, 199034, Russian Federation
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12
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Xu T, Yang X, Jia Y, Li Z, Tang G, Li X, Wang B, Wang T, Lin J, Guo L, Ye K. A global survey of the transcriptome of the opium poppy (Papaver somniferum) based on single-molecule long-read isoform sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:607-620. [PMID: 35092713 DOI: 10.1111/tpj.15689] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Tun Xu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Xiaofei Yang
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yanyan Jia
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Zihang Li
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Guangbo Tang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xiujuan Li
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Tingjie Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Jiadong Lin
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Li Guo
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
- Faculty of Science, Leiden University, Leiden, The Netherlands
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13
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Bussi Y, Kapon R, Reich Z. Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy. PLoS One 2021; 16:e0258693. [PMID: 34648558 PMCID: PMC8516232 DOI: 10.1371/journal.pone.0258693] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/02/2021] [Indexed: 12/24/2022] Open
Abstract
Information theoretic approaches are ubiquitous and effective in a wide variety of bioinformatics applications. In comparative genomics, alignment-free methods, based on short DNA words, or k-mers, are particularly powerful. We evaluated the utility of varying k-mer lengths for genome comparisons by analyzing their sequence space coverage of 5805 genomes in the KEGG GENOME database. In subsequent analyses on four k-mer lengths spanning the relevant range (11, 21, 31, 41), hierarchical clustering of 1634 genus-level representative genomes using pairwise 21- and 31-mer Jaccard similarities best recapitulated a phylogenetic/taxonomic tree of life with clear boundaries for superkingdom domains and high subtree similarity for named taxons at lower levels (family through phylum). By analyzing ~14.2M prokaryotic genome comparisons by their lowest-common-ancestor taxon levels, we detected many potential misclassification errors in a curated database, further demonstrating the need for wide-scale adoption of quantitative taxonomic classifications based on whole-genome similarity.
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Affiliation(s)
- Yuval Bussi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ruti Kapon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Reich
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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14
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Jin G, Ma PF, Wu X, Gu L, Long M, Zhang C, Li DZ. New Genes Interacted with Recent Whole Genome Duplicates in the Fast Stem Growth of Bamboos. Mol Biol Evol 2021; 38:5752-5768. [PMID: 34581782 PMCID: PMC8662795 DOI: 10.1093/molbev/msab288] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
As drivers of evolutionary innovations, new genes allow organisms to explore new niches. However, clear examples of this process remain scarce. Bamboos, the unique grass lineage diversifying into the forest, have evolved with a key innovation of fast growth of woody stem, reaching up to 1 m/day. Here, we identify 1,622 bamboo-specific orphan genes that appeared in recent 46 million years, and 19 of them evolved from noncoding ancestral sequences with entire de novo origination process reconstructed. The new genes evolved gradually in exon−intron structure, protein length, expression specificity, and evolutionary constraint. These new genes, whether or not from de novo origination, are dominantly expressed in the rapidly developing shoots, and make transcriptomes of shoots the youngest among various bamboo tissues, rather than reproductive tissue in other plants. Additionally, the particularity of bamboo shoots has also been shaped by recent whole-genome duplicates (WGDs), which evolved divergent expression patterns from ancestral states. New genes and WGDs have been evolutionarily recruited into coexpression networks to underline fast-growing trait of bamboo shoot. Our study highlights the importance of interactions between new genes and genome duplicates in generating morphological innovation.
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Affiliation(s)
- Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Xiaopei Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, 60637, USA
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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15
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Bodenhausen N, Deslandes-Hérold G, Waelchli J, Held A, van der Heijden MGA, Schlaeppi K. Relative qPCR to quantify colonization of plant roots by arbuscular mycorrhizal fungi. MYCORRHIZA 2021; 31:137-148. [PMID: 33475800 PMCID: PMC7910240 DOI: 10.1007/s00572-020-01014-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/15/2020] [Indexed: 05/13/2023]
Abstract
Arbuscular mycorrhiza fungi (AMF) are beneficial soil fungi that can promote the growth of their host plants. Accurate quantification of AMF in plant roots is important because the level of colonization is often indicative of the activity of these fungi. Root colonization is traditionally measured with microscopy methods which visualize fungal structures inside roots. Microscopy methods are labor-intensive, and results depend on the observer. In this study, we present a relative qPCR method to quantify AMF in which we normalized the AMF qPCR signal relative to a plant gene. First, we validated the primer pair AMG1F and AM1 in silico, and we show that these primers cover most AMF species present in plant roots without amplifying host DNA. Next, we compared the relative qPCR method with traditional microscopy based on a greenhouse experiment with Petunia plants that ranged from very high to very low levels of AMF root colonization. Finally, by sequencing the qPCR amplicons with MiSeq, we experimentally confirmed that the primer pair excludes plant DNA while amplifying mostly AMF. Most importantly, our relative qPCR approach was capable of discriminating quantitative differences in AMF root colonization and it strongly correlated (Spearman Rho = 0.875) with quantifications by traditional microscopy. Finally, we provide a balanced discussion about the strengths and weaknesses of microscopy and qPCR methods. In conclusion, the tested approach of relative qPCR presents a reliable alternative method to quantify AMF root colonization that is less operator-dependent than traditional microscopy and offers scalability to high-throughput analyses.
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Affiliation(s)
- Natacha Bodenhausen
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Soil Sciences, Research Institute of Organic Agriculture FiBL, Frick, Switzerland
| | - Gabriel Deslandes-Hérold
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Jan Waelchli
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Alain Held
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Klaus Schlaeppi
- Plant Soil Interactions, Department of Agroecology and Environment, Agroscope, Zurich, Switzerland.
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
- Plant Microbe Interactions, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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16
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Futo M, Opašić L, Koska S, Čorak N, Široki T, Ravikumar V, Thorsell A, Lenuzzi M, Kifer D, Domazet-Lošo M, Vlahoviček K, Mijakovic I, Domazet-Lošo T. Embryo-Like Features in Developing Bacillus subtilis Biofilms. Mol Biol Evol 2021; 38:31-47. [PMID: 32871001 PMCID: PMC7783165 DOI: 10.1093/molbev/msaa217] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Correspondence between evolution and development has been discussed for more than two centuries. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure. For instance, it has been increasingly recognized that multicellular behavior underlies biofilm formation in bacteria. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed toward later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants, and fungi. Given that most cells on Earth reside in the form of biofilms and that biofilms represent the oldest known fossils, we anticipate that the widely adopted vision of the first life as a single-cell and free-living organism needs rethinking.
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Affiliation(s)
- Momir Futo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Luka Opašić
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sara Koska
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Nina Čorak
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tin Široki
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Vaishnavi Ravikumar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Annika Thorsell
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maša Lenuzzi
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Domagoj Kifer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Mirjana Domazet-Lošo
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
- School of Biosciences, University of Skövde, Skövde, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
- Catholic University of Croatia, Zagreb, Croatia
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17
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Xie Y, Chang J, Kwan HS. Carbon metabolism and transcriptome in developmental paths differentiation of a homokaryotic Coprinopsis cinerea strain. Fungal Genet Biol 2020; 143:103432. [PMID: 32681999 DOI: 10.1016/j.fgb.2020.103432] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/01/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
Abstract
The balance and interplay between sexual and asexual reproduction is one of the most intriguing mysteries in the study of fungi. The choice of developmental strategy reflects the ability of fungi to adapt to the changing environment. However, the evolution of developmental paths and the metabolic regulation during differentiation and morphogenesis are poorly understood. Here, an analysis was performed of carbohydrate metabolism and gene expression regulation during the early differentiation process from the vegetative mycelium, to the differentiated structures, fruiting body, oidia and sclerotia, of a homokaryotic fruiting Coprinopsis cinerea strain A43mutB43mut pab1-1 #326. Changes during morphogenesis and the evolution of developmental strategies were followed. Conversion between glucose and glycogen and between glucose and beta-glucan were the main carbon flows in the differentiation processes. Genes related to carbohydrate transport and metabolism were significantly differentially expressed among paths. Sclerotia displayed a set of specifically up-regulated genes that were enriched in the carbon metabolism and energy production and conversion processes. Evolutionary transcriptomic analysis of four developmental paths showed that all transcriptomes were under the purifying selection, and the more stressful the environment, the younger the transcriptome age. Oidiation has the lowest value of transcriptome age index (TAI) and transcriptome divergence index (TDI), while the fruiting process has the highest of both indexes. These findings provide new insights into the regulations of carbon metabolism and gene expressions during the early stages of fungal developmental paths differentiation, and improve our understanding of the evolutionary process of life history and reproductive strategy in fungi.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Jinhui Chang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region.
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18
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Arendsee Z, Li J, Singh U, Seetharam A, Dorman K, Wurtele ES. phylostratr: a framework for phylostratigraphy. Bioinformatics 2020; 35:3617-3627. [PMID: 30873536 DOI: 10.1093/bioinformatics/btz171] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/27/2019] [Accepted: 03/13/2019] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION The goal of phylostratigraphy is to infer the evolutionary origin of each gene in an organism. This is done by searching for homologs within increasingly broad clades. The deepest clade that contains a homolog of the protein(s) encoded by a gene is that gene's phylostratum. RESULTS We have created a general R-based framework, phylostratr, to estimate the phylostratum of every gene in a species. The program fully automates analysis: selecting species for balanced representation, retrieving sequences, building databases, inferring phylostrata and returning diagnostics. Key diagnostics include: detection of genes with inferred homologs in old clades, but not intermediate ones; proteome quality assessments; false-positive diagnostics, and checks for missing organellar genomes. phylostratr allows extensive customization and systematic comparisons of the influence of analysis parameters or genomes on phylostrata inference. A user may: modify the automatically generated clade tree or use their own tree; provide custom sequences in place of those automatically retrieved from UniProt; replace BLAST with an alternative algorithm; or tailor the method and sensitivity of the homology inference classifier. We show the utility of phylostratr through case studies in Arabidopsis thaliana and Saccharomyces cerevisiae. AVAILABILITY AND IMPLEMENTATION Source code available at https://github.com/arendsee/phylostratr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zebulun Arendsee
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
| | - Jing Li
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
| | - Arun Seetharam
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Karin Dorman
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Department of Statistics, Iowa State University, Ames, IA, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, USA.,Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA.,Center for Metabolic Biology, Iowa State University, Ames, IA, USA
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19
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Wang J, Zhang L, Lian S, Qin Z, Zhu X, Dai X, Huang Z, Ke C, Zhou Z, Wei J, Liu P, Hu N, Zeng Q, Dong B, Dong Y, Kong D, Zhang Z, Liu S, Xia Y, Li Y, Zhao L, Xing Q, Huang X, Hu X, Bao Z, Wang S. Evolutionary transcriptomics of metazoan biphasic life cycle supports a single intercalation origin of metazoan larvae. Nat Ecol Evol 2020; 4:725-736. [PMID: 32203475 DOI: 10.1038/s41559-020-1138-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 02/06/2020] [Indexed: 12/16/2022]
Abstract
The transient larva-bearing biphasic life cycle is the hallmark of many metazoan phyla, but how metazoan larvae originated remains a major enigma in animal evolution. There are two hypotheses for larval origin. The 'larva-first' hypothesis suggests that the first metazoans were similar to extant larvae, with later evolution of the adult-added biphasic life cycle; the 'adult-first' hypothesis suggests that the first metazoans were adult forms, with the biphasic life cycle arising later via larval intercalation. Here, we investigate the evolutionary origin of primary larvae by conducting ontogenetic transcriptome profiling for Mollusca-the largest marine phylum characterized by a trochophore larval stage and highly variable adult forms. We reveal that trochophore larvae exhibit rapid transcriptome evolution with extraordinary incorporation of novel genes (potentially contributing to adult shell evolution), and that cell signalling/communication genes (for example, caveolin and innexin) are probably crucial for larval evolution. Transcriptome age analysis of eight metazoan species reveals the wide presence of young larval transcriptomes in both trochozoans and other major metazoan lineages, therefore arguing against the prevailing larva-first hypothesis. Our findings support an adult-first evolutionary scenario with a single metazoan larval intercalation, and suggest that the first appearance of proto-larva probably occurred after the divergence of direct-developing Ctenophora from a metazoan ancestor.
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Affiliation(s)
- Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shanshan Lian
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenkui Qin
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuan Zhu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Dai
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Jiankai Wei
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Naina Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Bo Dong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Dong
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Dexu Kong
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhifeng Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Sinuo Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Xia
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Liang Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,The Sars-Fang Centre, Ocean University of China, Qingdao, China.
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20
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Friedman DA, York RA, Hilliard AT, Gordon DM. Gene expression variation in the brains of harvester ant foragers is associated with collective behavior. Commun Biol 2020; 3:100. [PMID: 32139795 PMCID: PMC7057964 DOI: 10.1038/s42003-020-0813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/10/2020] [Indexed: 01/10/2023] Open
Abstract
Natural selection on collective behavior acts on variation among colonies in behavior that is associated with reproductive success. In the red harvester ant (Pogonomyrmex barbatus), variation among colonies in the collective regulation of foraging in response to humidity is associated with colony reproductive success. We used RNA-seq to examine gene expression in the brains of foragers in a natural setting. We find that colonies differ in the expression of neurophysiologically-relevant genes in forager brains, and a fraction of these gene expression differences are associated with two colony traits: sensitivity of foraging activity to humidity, and forager brain dopamine to serotonin ratio. Loci that were correlated with colony behavioral differences were enriched in neurotransmitter receptor signaling & metabolic functions, tended to be more central to coexpression networks, and are evolving under higher protein-coding sequence constraint. Natural selection may shape colony foraging behavior through variation in gene expression.
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Affiliation(s)
| | | | | | - Deborah M Gordon
- Stanford University, Department of Biology, Stanford, CA, 94305, USA.
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21
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Kapili BJ, Barnett SE, Buckley DH, Dekas AE. Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment. ISME JOURNAL 2020; 14:971-983. [PMID: 31907368 PMCID: PMC7082343 DOI: 10.1038/s41396-019-0584-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 12/18/2022]
Abstract
Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. However, we know little about the identity and activity of diazotrophs in deep-sea sediments, a habitat covering nearly two-thirds of the planet. Here, we identify candidate diazotrophs from Pacific Ocean sediments collected at 2893 m water depth using 15N-DNA stable isotope probing and a novel pipeline for nifH sequence analysis. Together, these approaches detect an unexpectedly diverse assemblage of active diazotrophs, including members of the Acidobacteria, Firmicutes, Nitrospirae, Gammaproteobacteria, and Deltaproteobacteria. Deltaproteobacteria, predominately members of the Desulfobacterales and Desulfuromonadales, are the most abundant diazotrophs detected, and display the most microdiversity of associated nifH sequences. Some of the detected lineages, including those within the Acidobacteria, have not previously been shown to fix nitrogen. The diazotrophs appear catabolically diverse, with the potential for using oxygen, nitrogen, iron, sulfur, and carbon as terminal electron acceptors. Therefore, benthic diazotrophy may persist throughout a range of geochemical conditions and provide a stable source of fixed nitrogen over geologic timescales. Our results suggest that nitrogen-fixing communities in deep-sea sediments are phylogenetically and catabolically diverse, and open a new line of inquiry into the ecology and biogeochemical impacts of deep-sea microorganisms.
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Affiliation(s)
- Bennett J Kapili
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA.
| | - Samuel E Barnett
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA.
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22
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Leiboff S, Hake S. Reconstructing the Transcriptional Ontogeny of Maize and Sorghum Supports an Inverse Hourglass Model of Inflorescence Development. Curr Biol 2019; 29:3410-3419.e3. [PMID: 31587998 DOI: 10.1016/j.cub.2019.08.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/29/2019] [Accepted: 08/19/2019] [Indexed: 12/31/2022]
Abstract
Assembling meaningful comparisons between species is a major limitation in studying the evolution of organismal form. To understand development in maize and sorghum, closely related species with architecturally distinct inflorescences, we collected RNA-seq profiles encompassing inflorescence body-plan specification in both species. We reconstructed molecular ontogenies from 40 B73 maize tassels and 47 BTx623 sorghum panicles and separated them into transcriptional stages. To discover new markers of inflorescence development, we used random forest machine learning to determine stage by RNA-seq. We used two descriptions of transcriptional conservation to identify hourglass-like stages during inflorescence development. Despite a relatively short 12 million years since their last common ancestor, we found maize and sorghum inflorescences are most different during their hourglass-like stages of development, following an inverse-hourglass model of development. We discuss whether agricultural selection may account for the rapid divergence signatures in these species and the observed separation of evolutionary pressure and developmental reprogramming.
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Affiliation(s)
- Samuel Leiboff
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California, Berkeley, Albany, CA 94710, USA.
| | - Sarah Hake
- Plant Gene Expression Center, U.S. Department of Agriculture-Agricultural Research Service and University of California, Berkeley, Albany, CA 94710, USA
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23
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Draceni Y, Pechmann S. Pervasive convergent evolution and extreme phenotypes define chaperone requirements of protein homeostasis. Proc Natl Acad Sci U S A 2019; 116:20009-20014. [PMID: 31527276 PMCID: PMC6778244 DOI: 10.1073/pnas.1904611116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Maintaining protein homeostasis is an essential requirement for cell and organismal viability. An elaborate regulatory system within cells, the protein homeostasis network, safeguards that proteins are correctly folded and functional. At the heart of this regulatory system lies a class of specialized protein quality control enzymes called chaperones that are tasked with assisting proteins in their folding, avoiding aggregation and degradation. Failure and decline of protein homeostasis are directly associated with conditions of aging and aging-related neurodegeneration. However, it is not clear what tips the balance of protein homeostasis and leads to onset of aging and diseases. Here, using a comparative genomics approach we report general principles of maintaining protein homeostasis across the eukaryotic tree of life. Expanding a previous study of 16 eukaryotes to the quantitative analysis of 216 eukaryotic genomes, we find a strong correlation between the composition of eukaryotic chaperone networks and genome complexity that is distinct for different species kingdoms. Organisms with pronounced phenotypes clearly buck this trend. Northobranchius furzeri, the shortest-lived vertebrate and a widely used model for fragile protein homeostasis, is found to be chaperone limited while Heterocephalus glaber as the longest-lived rodent and thus an especially robust organism is characterized by above-average numbers of chaperones. Strikingly, the relative size of chaperone networks is found to generally correlate with longevity in Metazoa. Our results thus indicate that the balance in protein homeostasis may be a key variable in explaining organismal robustness.
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Affiliation(s)
- Yasmine Draceni
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Sebastian Pechmann
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
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24
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Shackleton M, Rees GN, Watson G, Campbell C, Nielsen D. Environmental DNA reveals landscape mosaic of wetland plant communities. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00689] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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25
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Mahendran SM, Keystone EC, Krawetz RJ, Liang K, Diamandis EP, Chandran V. Elucidating the endogenous synovial fluid proteome and peptidome of inflammatory arthritis using label-free mass spectrometry. Clin Proteomics 2019; 16:23. [PMID: 31160890 PMCID: PMC6542032 DOI: 10.1186/s12014-019-9243-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/24/2019] [Indexed: 12/20/2022] Open
Abstract
Background Inflammatory arthritis (IA) is an immunological disorder in which loss of immune tolerance to endogenous self-antigens perpetuates synovitis and eventual destruction of the underlying cartilage and bone. Pathological changes in the joint are expected to be represented by synovial fluid (SF) proteins and peptides. In the present study, a mass spectrometry-based approach was utilized for the identification of key protein and peptide mediators of IA. Methods Age-matched SF samples from 10 rheumatoid arthritis patients, 10 psoriatic arthritis patients and 10 cadaveric controls were subjected to an integrated proteomic and peptidomic protocol using liquid chromatography tandem mass spectrometry. Significant differentially abundant proteins and peptides were identified between cohorts according to the results of a Mann-Whitney U test coupled to the Benjamini-Hochberg correction for multiple hypothesis testing. Fold change ratios were computed for each protein and peptide according to their log-transformed extracted ion current. Pathway analysis and antimicrobial peptide (AMP) prediction were conducted to clarify the pathophysiological relevance of identified proteins and peptides to IA. Results We determined that 144 proteins showed significant differential abundance between the IA and control SF proteomes, of which 11 protein candidates were selected for future follow-up studies. Similar analyses applied to our peptidomic data identified 15 peptide sequences, originating from 4 protein precursors, to have significant differential abundance in IA compared to the control SF peptidome. Pathway enrichment analysis of the IA SF peptidome along with AMP prediction suggests a possible mechanistic role of microbes in eliciting an immune response which drives the development of IA. Conclusions The discovery-phase data generated herein has provided a basis for the identification of candidates with the greatest potential to serve as novel serum biomarkers specific to inflammatory arthritides. Moreover, these findings facilitate the understanding of possible disease mechanisms specific to each subtype.
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Affiliation(s)
- Shalini M Mahendran
- 1Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada.,2Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON Canada
| | - Edward C Keystone
- 3Department of Rheumatology, Mount Sinai Hospital, Toronto, ON Canada
| | - Roman J Krawetz
- 4McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB Canada.,5Department of Surgery, University of Calgary, Calgary, AB Canada.,6Department of Anatomy and Cell Biology, University of Calgary, Calgary, AB Canada
| | - Kun Liang
- 7Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON Canada
| | - Eleftherios P Diamandis
- 1Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada.,2Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON Canada.,8Department of Clinical Biochemistry, University Health Network, Toronto, ON Canada
| | - Vinod Chandran
- 1Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada.,9Centre for Prognosis Studies in Rheumatic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON Canada.,10Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON Canada.,11Institute of Medical Science, University of Toronto, Toronto, ON Canada
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26
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Wu L, Ferger KE, Lambert JD. Gene Expression Does Not Support the Developmental Hourglass Model in Three Animals with Spiralian Development. Mol Biol Evol 2019; 36:1373-1383. [DOI: 10.1093/molbev/msz065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
It has been proposed that animals have a pattern of developmental evolution resembling an hourglass because the most conserved development stage—often called the phylotypic stage—is always in midembryonic development. Although the topic has been debated for decades, recent studies using molecular data such as RNA-seq gene expression data sets have largely supported the existence of periods of relative evolutionary conservation in middevelopment, consistent with the phylotypic stage and the hourglass concepts. However, so far this approach has only been applied to a limited number of taxa across the tree of life. Here, using established phylotranscriptomic approaches, we found a surprising reverse hourglass pattern in two molluscs and a polychaete annelid, representatives of the Spiralia, an understudied group that contains a large fraction of metazoan body plan diversity. These results suggest that spiralians have a divergent midembryonic stage, with more conserved early and late development, which is the inverse of the pattern seen in almost all other organisms where these phylotranscriptomic approaches have been reported. We discuss our findings in light of proposed reasons for the phylotypic stage and hourglass model in other systems.
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Affiliation(s)
- Longjun Wu
- Department of Biology, University of Rochester, Rochester, NY
| | - Kailey E Ferger
- Department of Biology, University of Rochester, Rochester, NY
| | - J David Lambert
- Department of Biology, University of Rochester, Rochester, NY
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27
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Liu J, Robinson-Rechavi M. Developmental Constraints on Genome Evolution in Four Bilaterian Model Species. Genome Biol Evol 2018; 10:2266-2277. [PMID: 30137380 PMCID: PMC6130771 DOI: 10.1093/gbe/evy177] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
Developmental constraints on genome evolution have been suggested to follow either an early conservation model or an "hourglass" model. Both models agree that late development strongly diverges between species, but debate on which developmental period is the most conserved. Here, based on a modified "Transcriptome Age Index" approach, that is, weighting trait measures by expression level, we analyzed the constraints acting on three evolutionary traits of protein coding genes (strength of purifying selection on protein sequences, phyletic age, and duplicability) in four species: Nematode worm Caenorhabditis elegans, fly Drosophila melanogaster, zebrafish Danio rerio, and mouse Mus musculus. In general, we found that both models can be supported by different genomic properties. Sequence evolution follows an hourglass model, but the evolution of phyletic age and of duplicability follow an early conservation model. Further analyses indicate that stronger purifying selection on sequences in the middle development are driven by temporal pleiotropy of these genes. In addition, we report evidence that expression in late development is enriched with retrogenes, which usually lack efficient regulatory elements. This implies that expression in late development could facilitate transcription of new genes, and provide opportunities for acquisition of function. Finally, in C. elegans, we suggest that dosage imbalance could be one of the main factors that cause depleted expression of high duplicability genes in early development.
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Affiliation(s)
- Jialin Liu
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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28
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Wang B, Regulski M, Tseng E, Olson A, Goodwin S, McCombie WR, Ware D. A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Res 2018; 28:921-932. [PMID: 29712755 PMCID: PMC5991521 DOI: 10.1101/gr.227462.117] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 04/12/2018] [Indexed: 12/15/2022]
Abstract
Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared expression profiles of both protein-coding and noncoding transcripts in 11 matched tissues using single-molecule, long-read, deep RNA sequencing. This comparative analysis revealed large numbers of novel isoforms in both species. Evolutionarily young genes were likely to be generated in reproductive tissues and usually had fewer isoforms than old genes. We also observed similarities and differences in alternative splicing patterns and activities, both among tissues and between species. The maize subgenomes exhibited no bias in isoform generation; however, genes in the B genome were more highly expressed in pollen tissue, whereas genes in the A genome were more highly expressed in endosperm. We also identified a number of splicing events conserved between maize and sorghum. In addition, we generated comprehensive and high-resolution maps of poly(A) sites, revealing similarities and differences in mRNA cleavage between the two species. Overall, our results reveal considerable splicing and expression diversity between sorghum and maize, well beyond what was reported in previous studies, likely reflecting the differences in architecture between these two species.
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Affiliation(s)
- Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | | | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.,USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York 14853, USA
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