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Xiang X, Poli D, Degnan BM, Degnan SM. Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont. Mar Biotechnol (NY) 2022; 24:722-732. [PMID: 35895230 PMCID: PMC9385839 DOI: 10.1007/s10126-022-10138-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Investigations of host-symbiont interactions can benefit enormously from a complete and reliable holobiont gene expression profiling. The most efficient way to acquire holobiont transcriptomes is to perform RNA-Seq on both host and symbionts simultaneously. However, optimal methods for capturing both host and symbiont mRNAs are still under development, particularly when the host is a eukaryote and the symbionts are bacteria or archaea. Traditionally, poly(A)-enriched libraries have been used to capture eukaryotic mRNA, but the ability of this method to adequately capture bacterial mRNAs is unclear because of the short half-life of the bacterial transcripts. Here, we address this gap in knowledge with the aim of helping others to choose an appropriate RNA-Seq approach for analysis of animal host-bacterial symbiont transcriptomes. Specifically, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont. Annotated genomes of the sponge host and the three most abundant bacterial symbionts, which can comprise up to 95% of the adult microbiome, are available. Importantly, this allows for transcriptomes to be accurately mapped to these genomes, and thus quantitatively assessed and compared. The two strategies that we compare here are (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq) and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). For the host sponge, we find no significant difference in transcriptomes generated by the two different mRNA capture methods. However, for the symbiont transcriptomes, we confirm the expectation that the rRNA-depleted-RNA-Seq performs much better than the Poly(A)-RNA-Seq. This comparison demonstrates that RNA-Seq by ribosomal RNA depletion is an effective and reliable method to simultaneously capture gene expression in host and symbionts and thus to analyse holobiont transcriptomes.
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Affiliation(s)
- Xueyan Xiang
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
- Present Address: BGI-Shenzhen, Shenzhen, 518083 China
| | - Davide Poli
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
- Present Address: School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Bernard M. Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Sandie M. Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD 4072 Australia
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Plese B, Kenny NJ, Rossi ME, Cárdenas P, Schuster A, Taboada S, Koutsouveli V, Riesgo A. Mitochondrial evolution in the Demospongiae (Porifera): Phylogeny, divergence time, and genome biology. Mol Phylogenet Evol 2020; 155:107011. [PMID: 33217579 DOI: 10.1016/j.ympev.2020.107011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/01/2022]
Abstract
The sponge class Demospongiae is the most speciose and morphologically diverse in the phylum Porifera, and the species within it are vital components of a range of ecosystems worldwide. Despite their ubiquity, a number of recalcitrant problems still remain to be solved regarding their phylogenetic inter-relationships, the timing of their appearance, and their mitochondrial biology, the latter of which is only beginning to be investigated. Here we generated 14 new demosponge mitochondrial genomes which, alongside previously published mitochondrial resources, were used to address these issues. In addition to phylogenomic analysis, we have used syntenic data and analysis of coding regions to forge a framework for understanding the inter-relationships between Demospongiae sub-classes and orders. We have also leveraged our new resources to study the mitochondrial biology of these clades in terms of codon usage, optimisation and gene expression, to understand how these vital cellular components may have contributed to the success of the Porifera. Our results strongly support a sister relationship between Keratosa and (Verongimorpha + Heteroscleromorpha), contradicting previous studies using nuclear markers. Our study includes one species of Clionaida, and show for the first time support for a grouping of Suberitida+(Clionaida+(Tethyida + Poecilosclerida). The findings of our phylogenetic analyses are supported by in-depth examination of structural and coding-level evidence from our mitochondrial data. A time-calibrated phylogeny estimated the origin of Demospongiae in the Cambrian (~529 Mya), and suggests that most demosponge order crown-groups emerged in the Mesozoic. This work therefore provides a robust basis for considering demosponge phylogenetic relationships, as well as essential mitochondrial data for understanding the biological basis for their success and diversity.
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Affiliation(s)
- Bruna Plese
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom.
| | - Nathan James Kenny
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Faculty of Health and Life Sciences, Oxford Brookes University, Headington Rd, Oxford OX3 0BP, United Kingdom(2).
| | - Maria Eleonora Rossi
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; School of Earth Sciences, University of Bristol, Life Science Building, 24 Tyndall Ave, Bristol BS8 1TH, United Kingdom.
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Husargatan 3, Uppsala 751 23, Sweden.
| | - Astrid Schuster
- Department of Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark; CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.
| | - Sergi Taboada
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Life Sciences, Universidad de Alcalá de Henares, 28871 Alcalá de Henares, Spain; Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, C/ José Antonio Novais, 12, Ciudad Universitaria, 28040 Madrid, Spain.
| | - Vasiliki Koutsouveli
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Husargatan 3, Uppsala 751 23, Sweden.
| | - Ana Riesgo
- Life Sciences Department, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales de Madrid (CSIC), c/ José Gutiérrez Abascal 2, 28006 Madrid, Spain.
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Calcino AD, Fernandez-Valverde SL, Taft RJ, Degnan BM. Diverse RNA interference strategies in early-branching metazoans. BMC Evol Biol 2018; 18:160. [PMID: 30382896 PMCID: PMC6211395 DOI: 10.1186/s12862-018-1274-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Micro RNAs (miRNAs) and piwi interacting RNAs (piRNAs), along with the more ancient eukaryotic endogenous small interfering RNAs (endo-siRNAs) constitute the principal components of the RNA interference (RNAi) repertoire of most animals. RNAi in non-bilaterians - sponges, ctenophores, placozoans and cnidarians - appears to be more diverse than that of bilaterians, and includes structurally variable miRNAs in sponges, an enormous number of piRNAs in cnidarians and the absence of miRNAs in ctenophores and placozoans. RESULTS Here we identify thousands of endo-siRNAs and piRNAs from the sponge Amphimedon queenslandica, the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis using a computational approach that clusters mapped small RNA sequences and annotates each cluster based on the read length and relative abundance of the constituent reads. This approach was validated on 11 small RNA libraries in Drosophila melanogaster, demonstrating the successful annotation of RNAi-associated loci with properties consistent with previous reports. In the non-bilaterians we uncover seven new miRNAs from Amphimedon and four from Nematostella as well as sub-populations of candidate cis-natural antisense transcript (cis-NAT) endo-siRNAs. We confirmed the absence of miRNAs in Mnemiopsis but detected an abundance of endo-siRNAs in this ctenophore. Analysis of putative piRNA structure suggests that conserved localised secondary structures in primary transcripts may be important for the production of mature piRNAs in Amphimedon and Nematostella, as is also the case for endo-siRNAs. CONCLUSION Together, these findings suggest that the last common ancestor of extant animals did not have the entrained RNAi system that typifies bilaterians. Instead it appears that bilaterians, cnidarians, ctenophores and sponges express unique repertoires and combinations of miRNAs, piRNAs and endo-siRNAs.
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Affiliation(s)
- Andrew D Calcino
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Integrative Zoology, University of Vienna, Althanstraße 1, 4A-1090, Vienna, Austria
| | - Selene L Fernandez-Valverde
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: CONACYT, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio). CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia.,Illumina Inc, San Diego, California, 92122, USA
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
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Kim H, Kim HJ, Jung YH, Yu C, An YR, Han D, Kang DW. The complete mitochondrial genome of sponge Halichondria okadai (Demospongiae, Suberitida, Halichondriidae) from Korea water. Mitochondrial DNA B Resour 2017; 2:873-874. [PMID: 33474017 PMCID: PMC7799822 DOI: 10.1080/23802359.2017.1407693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/17/2017] [Indexed: 11/18/2022] Open
Abstract
The mitogenome sequence of Sponge Halichondria okadai (Kadota, 1922) (Suberitida, Halichondriidae) was determined for the first time in this study. The circular genome is 20,722 bp in length, containing 14 protein coding genes (PCGs), two ribosomal RNAs (rRNAs), and 25 transfer RNAs (tRNAs). The nucleotide composition of mitogenome consists of 29.5% A, 14.2% C, 21.5% G, 34.7% T, showing a high content of A + T similar to the other Suberitid sponges. These results will be useful for inferring the phylogenetic relationships among the members of family Halichondriidae within the Suberitids.
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Affiliation(s)
- Hana Kim
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea Ecosystem, Seocheon-gun, Republic of Korea
- Department of Biological Sciences, Inha University, Incheon, Republic of Korea
| | - Hyung June Kim
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea Ecosystem, Seocheon-gun, Republic of Korea
| | - Yun Hwan Jung
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea Ecosystem, Seocheon-gun, Republic of Korea
| | - Cheol Yu
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea Ecosystem, Seocheon-gun, Republic of Korea
| | - Yong Rock An
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea Ecosystem, Seocheon-gun, Republic of Korea
| | - Donguk Han
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea Ecosystem, Seocheon-gun, Republic of Korea
| | - Dong Won Kang
- Department of Taxonomy and Systematics, National Marine Biodiversity Institute of Korea Ecosystem, Seocheon-gun, Republic of Korea
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Wang D, Zhang Y, Huang D. The complete mitochondrial genome of sponge Halichondria ( Halichondria) sp. (Demospongiae, Suberitida, Halichondriidae). Mitochondrial DNA B Resour 2016; 1:512-514. [PMID: 33473538 PMCID: PMC7800652 DOI: 10.1080/23802359.2016.1192516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we found out the complete mitochondrial genome of Halichondria (Halichondria) sp., a common demosponge in China. This is the first complete mitochondrial report on the genus Halichondria. The mitochondrial genome of Halichondria (Halichondria) sp. is 20 746 bp in length, with 14 protein-coding genes, two rRNA genes and 25 tRNA genes. When compared with the complete mitochondrial genome of Hymeniacidon sinapium, our phylogenetic result suggested that Halichondria (Halichondria) sp. converged well according to morphological result.
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Affiliation(s)
- Dexiang Wang
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China
| | - Yuan Zhang
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China
| | - Dan Huang
- State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, China
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Zhang Y, Huang D, Wang D, Ding S. The complete mitochondrial genome of sponge Tethya sp. (Demospongiae, Tethyida, Tethyidae). Mitochondrial DNA B Resour 2016; 1:472-474. [PMID: 33473525 PMCID: PMC7799499 DOI: 10.1080/23802359.2016.1186518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The complete mitochondrial genome of Tethya sp. was studied. This is the second complete mitochondrial report on the family Tethyidae. The mitochondrial genome of Tethya sp. is 20,582 bp in length, containing 14 protein-coding genes and 25 tRNA genes, with 2 rRNA genes. Our phylogenetic result suggested that Tethya sp. converged well with Tethya actinia, which further verified the morphological result. We anticipate our study to shed light on future molecular studies of demosponges.
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Affiliation(s)
- Yuan Zhang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China.,Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, China
| | - Dan Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China.,Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, China
| | - Dexiang Wang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China.,Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, China
| | - Shaoxiong Ding
- Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen, China
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