1
|
De novo Assembly and Analysis of Tissue-Specific Transcriptomes of the Edible Red Sea Urchin Loxechinus albus Using RNA-Seq. BIOLOGY 2021; 10:biology10100995. [PMID: 34681094 PMCID: PMC8533317 DOI: 10.3390/biology10100995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023]
Abstract
Simple Summary Edible red sea urchin (Loxechinus albus) is an endemic species of echinoderm distributed along the Chilean coasts. This resource has been overexploited in recent years, depleting their natural populations. At present, there are few reported gene sequences available in public databases, restricting the molecular studies associated with aquaculture for this species. The aim of this study was to present the first annotated reference transcriptome of L. albus using NGS technologies and the differential expression transcripts analysis of the evaluated tissues. The transcriptome data obtained in this study will serve as a reference for future molecular research in the edible red sea urchin and other sea urchin species. Abstract Edible red sea urchin (Loxechinus albus) is an endemic echinoderm species of the Chilean coasts. The worldwide demand for high-quality gonads of this species has addressed the depletion of its natural populations. Studies on this sea urchin are limited, and genomic information is almost nonexistent. Hence, generate a transcriptome is crucial information that will considerably enrich molecular data and promote future findings for the L. albus aquaculture. Here, we obtained transcriptomic data of the edible red sea urchin by Illumina platform. Total RNA was extracted from gonads, intestines, and coelomocytes of juvenile urchins, and samples were sequenced using MiSeq Illumina technology. A total of 91,119,300 paired-end reads were de novo assembled, 185,239 transcripts produced, and a reference transcriptome created with 38.8% GC content and an N50 of 1769 bp. Gene ontology analysis revealed notable differences in the expression profiles between gonads, intestines, and coelomocytes, allowing the detection of transcripts associated with specific biological processes and KEGG pathways. These data were validated using 12 candidate transcripts by real-time qPCR. This dataset will provide a valuable molecular resource for L. albus and other species of sea urchins.
Collapse
|
2
|
Figueroa Á, Brante A, Cárdenas L. RNA-Seq reveals divergent gene expression between larvae with contrasting trophic modes in the poecilogonous polychaete Boccardia wellingtonensis. Sci Rep 2021; 11:14997. [PMID: 34294855 PMCID: PMC8298564 DOI: 10.1038/s41598-021-94646-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 07/12/2021] [Indexed: 12/01/2022] Open
Abstract
The polychaete Boccardia wellingtonensis is a poecilogonous species that produces different larval types. Females may lay Type I capsules, in which only planktotrophic larvae are present, or Type III capsules that contain planktotrophic and adelphophagic larvae as well as nurse eggs. While planktotrophic larvae do not feed during encapsulation, adelphophagic larvae develop by feeding on nurse eggs and on other larvae inside the capsules and hatch at the juvenile stage. Previous works have not found differences in the morphology between the two larval types; thus, the factors explaining contrasting feeding abilities in larvae of this species are still unknown. In this paper, we use a transcriptomic approach to study the cellular and genetic mechanisms underlying the different larval trophic modes of B. wellingtonensis. By using approximately 624 million high-quality reads, we assemble the de novo transcriptome with 133,314 contigs, coding 32,390 putative proteins. We identify 5221 genes that are up-regulated in larval stages compared to their expression in adult individuals. The genetic expression profile differed between larval trophic modes, with genes involved in lipid metabolism and chaetogenesis over expressed in planktotrophic larvae. In contrast, up-regulated genes in adelphophagic larvae were associated with DNA replication and mRNA synthesis.
Collapse
Affiliation(s)
- Álvaro Figueroa
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.
| | - Antonio Brante
- Facultad de Ciencias, Centro de Investigación en Biodiversidad y Ambientes Sustentables, Universidad Católica de la Ssma, Concepción, Concepción, Chile
- Departamento Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Leyla Cárdenas
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Centro Fondap-IDEAL, Valdivia, Chile
| |
Collapse
|
3
|
Figueiredo D, Santos WS, Montoni F, Iwai LK, Silva Junior PI. Toposome: Source of antimicrobial molecules in the gonads of the sea urchin Lytechinus variegatus (Lamarck, 1816). FISH & SHELLFISH IMMUNOLOGY 2021; 109:51-61. [PMID: 33276094 DOI: 10.1016/j.fsi.2020.11.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Sea urchins live in a challenging environment that requires rapid and efficient responses against pathogens and invaders. This response may be also important in reproductive processes once males and females release their gametes into water. In addition, the gonads are organs with dual function: reproductive organ and nutrient reserve, therefore it needs efficient protective mechanisms to preserve the nutrients as well as the reproductive cells. The aim of this study was to evaluate the presence and characterize antimicrobial molecules in the male and female gonads of the sea urchin Lytechinus variegatus. Through HPLC purification, antimicrobial activity test and mass spectrometry several antimicrobial molecules were found in the gonads of both gender. Computational in silico analyses showed that they are fragments of a glycoprotein called toposome, also known as major yolk protein (MYP) which is one of the major proteins found in the gonads. Although different functions have been reported for this protein, this is the first description of a direct antimicrobial activity in Lytechinus variegatus. The results indicate that when undergoing proteolysis the toposome generates different fragments with antimicrobial activity which may indicate the importance of a rapid defense response strategy against invading microorganisms in the gonads used by both males and females sea urchins.
Collapse
Affiliation(s)
- Dal Figueiredo
- Laboratory for Applied Toxinology (LETA/CeTICS), Butantan Institute, São Paulo CEP, 05503-900, SP, Brazil; Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP, 05508-900, SP, Brazil
| | - W S Santos
- Laboratory for Applied Toxinology (LETA/CeTICS), Butantan Institute, São Paulo CEP, 05503-900, SP, Brazil
| | - Fabio Montoni
- Laboratory for Applied Toxinology (LETA/CeTICS), Butantan Institute, São Paulo CEP, 05503-900, SP, Brazil
| | - Leo Kei Iwai
- Laboratory for Applied Toxinology (LETA/CeTICS), Butantan Institute, São Paulo CEP, 05503-900, SP, Brazil
| | - P I Silva Junior
- Laboratory for Applied Toxinology (LETA/CeTICS), Butantan Institute, São Paulo CEP, 05503-900, SP, Brazil; Institute of Biomedical Sciences, University of São Paulo, São Paulo CEP, 05508-900, SP, Brazil.
| |
Collapse
|
4
|
Mongiardino Koch N, Thompson JR. A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data. Syst Biol 2020; 70:421-439. [PMID: 32882040 DOI: 10.1093/sysbio/syaa069] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 08/14/2020] [Accepted: 08/23/2020] [Indexed: 12/13/2022] Open
Abstract
Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.].
Collapse
Affiliation(s)
| | - Jeffrey R Thompson
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| |
Collapse
|
5
|
Pérez‐Portela R, Riesgo A, Wangensteen OS, Palacín C, Turon X. Enjoying the warming Mediterranean: Transcriptomic responses to temperature changes of a thermophilous keystone species in benthic communities. Mol Ecol 2020; 29:3299-3315. [DOI: 10.1111/mec.15564] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Rocío Pérez‐Portela
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona, and Research Institute of Biodiversity (IRBIO) Barcelona Spain
- Center for Advanced Studies of Blanes (CEAB, CSIC) Girona Spain
| | - Ana Riesgo
- Department of Life Sciences The Natural History Museum London UK
| | - Owen S. Wangensteen
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Cruz Palacín
- Department of Evolutionary Biology, Ecology and Environmental Sciences University of Barcelona, and Research Institute of Biodiversity (IRBIO) Barcelona Spain
| | - Xavier Turon
- Center for Advanced Studies of Blanes (CEAB, CSIC) Girona Spain
| |
Collapse
|
6
|
Détrée C, Navarro JM, Font A, Gonzalez M. Species vulnerability under climate change: Study of two sea urchins at their distribution margin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 728:138850. [PMID: 32570334 DOI: 10.1016/j.scitotenv.2020.138850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
In order to develop powerful predictions on the impact of climate change on marine organisms, it is critical to understand how abiotic drivers such as temperature can directly and indirectly affect marine organisms. Here, we evaluated and compared the physiological vulnerability of the leading-edge populations of two species of sea urchins Loxechinus albus and Pseudechinus magellanicus in response to predicted ocean warming and food limitation. After exposing sea urchins to a 60-day experimental period to contrasting temperature (1 °C, 7 °C and 14 °C corresponding respectively to the actual average summer temperature in Antarctica, the control treatment temperature and the predicted future temperature in the Strait of Magellan) and diet levels (ad libitum or food limitation), sea urchin stress tolerance was assessed. Sea urchins' physiology was measured at the organismal and sub-cellular level by studying the organisms energy balance (behavior, growth, gonad index, ingestion rate, O2 uptake, energy reserves) and the expression of genes associated with aerobic metabolism. Our results showed that at their distribution edge, and despite their distinct geographical repartition, both species might be resilient to ocean warming. However, the combination of ocean warming and food limitation reduced the stress tolerance of sea urchins. In a warming ocean, another strategy could be to migrate toward the pole to a cooler environment but incubation at 1 °C resulted in a diminution of both species' aerobic scope. Overall, if these engineer species are unable to acclimate to food limitation under future climate, population fitness could be affected with ecological and economic consequences.
Collapse
Affiliation(s)
- Camille Détrée
- Centro FONDAP de Investigación de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile; Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
| | - Jorge M Navarro
- Centro FONDAP de Investigación de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile; Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Alejandro Font
- Scientific Department, Chilean Antarctic Institute, Plaza Muñoz Gamero Punta Arenas, Chile
| | - Marcelo Gonzalez
- Scientific Department, Chilean Antarctic Institute, Plaza Muñoz Gamero Punta Arenas, Chile
| |
Collapse
|
7
|
Wang H, Ding J, Ding S, Chang Y. Transcriptome analysis to characterize the genes related to gonad growth and fatty acid metabolism in the sea urchin Strongylocentrotus intermedius. Genes Genomics 2019; 41:1397-1415. [PMID: 31485990 DOI: 10.1007/s13258-019-00864-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Sea urchin gonads of both sexes, commonly termed "roe", are highly valued seafood delicacies, and Strongylocentrotus intermedius is considered one of the tastiest sea urchins. In order to produce high-quality gonads for consumption and clarify the mechanism of gonad growth and development of the sea urchin, more genetic information, especially at the transcriptome level, is needed. OBJECTIVE A more thorough understanding of sea urchin gonad growth and development in both sexes could enable regulation of these processes at several stages with the aim of suppressing gametogenesis in order to produce high-quality gonads for consumption. METHODS The adult sea urchins S. intermedius were cultured for 3 months, and were sampled for the gonadal transcriptome analysis which has been performed on the RNAs of three male and female adults of S. intermedius in each gonad development stage. RESULTS Illumina sequencing raw sequence data was deposited in the NCBI Sequence Read Archive (SRA) database (PRJNA532998). It generated 560,196,356 raw reads and 548,956,944 clean reads were acquired, which were assembled into 107,850 transcripts with 44,124 genes. Comparative analysis showed the differentially expressed genes (DEGs) from 114 to 2566. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to determine the functional significance of these DEGs. We have selected 9 genes related to growth and 12 genes related to fatty acid biosynthesis and metabolism in sea urchin gonads. CONCLUSION These data for sea urchins were intended to provide markers for gonad growth and development that can be accumulated for use in aquaculture applications.
Collapse
Affiliation(s)
- Heng Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Jun Ding
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
| | - Siyu Ding
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China
| | - Yaqing Chang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, 116023, China.
| |
Collapse
|
8
|
Uthicke S, Deshpande NP, Liddy M, Patel F, Lamare M, Wilkins MR. Little evidence of adaptation potential to ocean acidification in sea urchins living in "Future Ocean" conditions at a CO 2 vent. Ecol Evol 2019; 9:10004-10016. [PMID: 31534709 PMCID: PMC6745858 DOI: 10.1002/ece3.5563] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/25/2019] [Accepted: 07/28/2019] [Indexed: 12/20/2022] Open
Abstract
Ocean acidification (OA) can be detrimental to calcifying marine organisms, with stunting of invertebrate larval development one of the most consistent responses. Effects are usually measured by short-term, within-generation exposure, an approach that does not consider the potential for adaptation. We examined the genetic response to OA of larvae of the tropical sea urchin Echinometra sp. C. raised on coral reefs that were either influenced by CO2 vents (pH ~ 7.9, future OA condition) or nonvent control reefs (pH 8.2). We assembled a high quality de novo transcriptome of Echinometra embryos (8 hr) and pluteus larvae (48 hr) and identified 68,056 SNPs. We tested for outlier SNPs and functional enrichment in embryos and larvae raised from adults from the control or vent sites. Generally, highest F ST values in embryos were observed between sites (intrinsic adaptation, most representative of the gene pool in the spawned populations). This comparison also had the highest number of outlier loci (40). In the other comparisons, classical adaptation (comparing larvae with adults from the control transplanted to either the control or vent conditions) and reverse adaptation (larvae from the vent site returned to the vent or explanted at the control), we only observed modest numbers of outlier SNPs (6-19) and only enrichment in two functional pathways. Most of the outliers detected were silent substitutions without adaptive potential. We conclude that there is little evidence of realized adaptation potential during early development, while some potential (albeit relatively low) exists in the intrinsic gene pool after more than one generation of exposure.
Collapse
Affiliation(s)
- Sven Uthicke
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | - Nandan P. Deshpande
- Systems Biology InitiativeSchool of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyNSWAustralia
| | - Michelle Liddy
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Frances Patel
- Australian Institute of Marine ScienceTownsvilleQldAustralia
| | - Miles Lamare
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Marc R. Wilkins
- Systems Biology InitiativeSchool of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyNSWAustralia
| |
Collapse
|
9
|
Wong JM, Gaitán-Espitia JD, Hofmann GE. Transcriptional profiles of early stage red sea urchins (Mesocentrotus franciscanus) reveal differential regulation of gene expression across development. Mar Genomics 2019; 48:100692. [PMID: 31227413 DOI: 10.1016/j.margen.2019.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 12/17/2022]
Abstract
The red sea urchin, Mesocentrotus franciscanus, is an ecologically important kelp forest species that also serves as a valuable fisheries resource. In this study, we have assembled and annotated a developmental transcriptome for M. franciscanus that represents eggs and six stages of early development (8- to 16-cell, morula, hatched blastula, early gastrula, prism and early pluteus). Characterization of the transcriptome revealed distinct patterns of gene expression that corresponded to major developmental and morphological processes. In addition, the period during which maternally-controlled transcription was terminated and the zygotic genome was activated, the maternal-to-zygotic transition (MZT), was found to begin during early cleavage and persist through the hatched blastula stage, an observation that is similar to the timing of the MZT in other sea urchin species. The presented developmental transcriptome will serve as a useful resource for investigating, in both an ecological and fisheries context, how the early developmental stages of this species respond to environmental stressors.
Collapse
Affiliation(s)
- Juliet M Wong
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Juan D Gaitán-Espitia
- The Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong Special Administrative Region.
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
| |
Collapse
|
10
|
Olivares A, Avila-Poveda OH. An ovotestis event in the gonochoric sea urchin Loxechinus albus (Echinodermata: Echinoidea). BRAZ J BIOL 2018; 79:548-551. [PMID: 30304296 DOI: 10.1590/1519-6984.188534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/23/2018] [Indexed: 11/21/2022] Open
Affiliation(s)
- Alberto Olivares
- Departamento de Biotecnologia, Facultad de Ciencias del Mar y Recursos Biologicos, Universidad de Antofagasta, CP 02800, Antofagasta, Chile
| | - Omar Hernando Avila-Poveda
- Facultad de Ciencias del Mar - FACIMAR, Universidad Autonoma de Sinaloa - UAS, CP 80000, Mazatlan, Sinaloa, Mexico.,Direccion de Catedras-CONACYT, Consejo Nacional de Ciencia y Tecnologia - CONACYT, CP 03940, Ciudad de Mexico, Mexico
| |
Collapse
|
11
|
Wu K, Jia Z, Wang Q, Wei Z, Zhou Z, Liu X. Identification, expression analysis, and the regulating function on C/EBPs of KLF10 in Dalian purple sea urchin, Strongylocentrotus nudus. Genome 2017; 60:837-849. [PMID: 28891718 DOI: 10.1139/gen-2017-0033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Accumulating evidence indicates that Krüppel-like factors (KLFs) play important roles in fat biology via the regulation of CCAAT/enhancer binding proteins (C/EBPs). However, KLFs and C/EBPs have not been identified from Strongylocentrotus nudus, and their roles in this species are not clear. In this study, the full-length cDNA of S. nudus KLF10 (SnKLF10) and three cDNA fragments of S. nudus C/EBPs (SnC/EBPs) were obtained. Examination of tissue distribution and expression patterns during gonadal development implied that SnKLF10 and SnC/EBPs play important roles in gonadal lipogenesis. The presence of transcription factor-binding sites (TFBSs) for KLFs in SnC/EBPs, and the results of an over-expression assay, revealed that SnKLF10 negatively regulates the transcription of SnC/EBPs. In addition, the core promoter regions of SnC/EBPs were determined, and multiple TFBSs for transcription factor (TFs) were identified, which are potential regulators of SnC/EBP transcription. Taken together, these results suggest that SnC/EBP genes are potential targets of SnKLF10, and that SnKLF10 plays a role in lipogenesis by repressing the transcription of SnC/EBPs. These findings provide information for further studies of KLF10 in invertebrates and provide new insight into the regulatory mechanisms of C/EBP transcription.
Collapse
Affiliation(s)
- Kaikai Wu
- a College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
| | - Zhiying Jia
- a College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
| | - Qi'ai Wang
- a College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
| | - Zhenlin Wei
- b Biological Science Department, Dezhou University, Dezhou, Shandong 253023, China
| | - Zunchun Zhou
- c Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian, Liaoning 116023, China
| | - Xiaolin Liu
- a College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
| |
Collapse
|
12
|
Jia Z, Wang Q, Wu K, Wei Z, Zhou Z, Liu X. De novo transcriptome sequencing and comparative analysis to discover genes involved in ovarian maturity in Strongylocentrotus nudus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017. [PMID: 28622611 DOI: 10.1016/j.cbd.2017.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Strongylocentrotus nudus is an edible sea urchin, mainly harvested in China. Correlation studies indicated that S. nudus with larger diameter have a prolonged marketing time and better palatability owing to their precocious gonads and extended maturation process. However, the molecular mechanism underlying this phenomenon is still unknown. Here, transcriptome sequencing was applied to study the ovaries of adult S. nudus with different shell diameters to explore the possible mechanism. In this study, four independent cDNA libraries were constructed, including two from the big size urchins and two from the small ones using a HiSeq™2500 platform. A total of 88,581 unigenes were acquired with a mean length of 1354bp, of which 66,331 (74.88%) unigenes could be annotated using six major publicly available databases. Comparative analysis revealed that 353 unigenes were differentially expressed (with log2(ratio)≥1, FDR≤0.001) between the two groups. Of these, 20 differentially expressed genes (DEGs) were selected to confirm the accuracy of RNA-seq data by quantitative real-time RT-PCR. Furthermore, gene ontology and KEGG pathway enrichment analyses were performed to find the putative genes and pathways related to ovarian maturity. Eight unigenes were identified as significant DEGs involved in reproduction related pathways; these included Mos, Cdc20, Rec8, YP30, cytochrome P450 2U1, ovoperoxidase, proteoliaisin, and rendezvin. Our research fills the gap in the studies on the S. nudus ovaries using transcriptome analysis.
Collapse
Affiliation(s)
- Zhiying Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Qiai Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Kaikai Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhenlin Wei
- Biological Science Department, Dezhou University, Dezhou 253023, Shandong, China
| | - Zunchun Zhou
- Liaoning Key Lab of Marine Fishery Molecular Biology, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, Liaoning, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| |
Collapse
|
13
|
Gaitán-Espitia JD, Hofmann GE. Gene expression profiling during the embryo-to-larva transition in the giant red sea urchin Mesocentrotus franciscanus. Ecol Evol 2017; 7:2798-2811. [PMID: 28428870 PMCID: PMC5395446 DOI: 10.1002/ece3.2850] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 01/20/2017] [Accepted: 02/01/2017] [Indexed: 01/24/2023] Open
Abstract
In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo‐to‐larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins. From these transcripts, ~80% were functionally annotated allowing the identification of ~2,600 functional, structural, and regulatory genes involved in developmental process. Analysis of expression profiles between gastrula and pluteus stages of M. franciscanus revealed 791 differentially expressed genes with 251 GO overrepresented terms. For gastrula, up‐regulated GO terms were mainly linked to cell differentiation and signal transduction involved in cell cycle checkpoints. In the pluteus stage, major GO terms were associated with phosphoprotein phosphatase activity, muscle contraction, and olfactory behavior, among others. Our evolutionary comparative analysis revealed that several of these genes and functional pathways are highly conserved among echinoids, holothuroids, and ophiuroids.
Collapse
Affiliation(s)
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology University of California Santa Barbara CA USA
| |
Collapse
|