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Whole genome evaluation analysis and preliminary Assembly of Oratosquilla oratoria (Stomatopoda: Squillidae)

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Abstract

Background

As the dominant species of Stomatopoda, Oratosquilla oratoria has not been fully cultivated artificially, and the fishery production mainly depends on marine fishing. Due to the lack of stomatopod genome, the development of molecular breeding of mantis shrimps still lags behind.

Methods and results

A survey analysis was performed to obtain the genome size, GC content and heterozygosity ratio in order to provide a fundation for subsequent whole-genome sequencing. The results showed that the estimated genome size of the O. oratoria was about 2.56 G, and the heterozygosity ratio was 1.81%, indicating that it is a complex genome. Then the sequencing data was preliminarily assembled with k-mer = 51 by SOAPdenovo software to obtain a genome size of 3.01G and GC content of 40.37%. According to ReapeatMasker and RepeatModerler analysis, the percentage of repeats in O. oratoria was 45.23% in the total genome, similar to 44% in Survey analysis. The MISA tool was used to analyze the simple sequence repeat (SSR) characteristics of genome sequences including Oratosquilla oratoria, Macrobrachium nipponense, Fenneropenaeus chinensis, Eriocheir japonica sinensis, Scylla paramamosain and Paralithodes platypus. All crustacean genomes showed similar SSRs characteristics, with the highest proportion of di-nucleotide repeat sequences. And AC/GT and AGG/CCT repeats were the main types of di-nucleotide and tri-nucleotide repeats in O. oratoria.

Conclusion

This study provided a reference for the genome assembly and annotation of the O. oratoria, and also provided a theoretical basis for the development of molecular markers of O. oratoria.

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Data availability

The datasets generated during the current study are available in the NCBI repository under BioProject: PRJNA935513.

References

  1. Ahyong ST (2012) The Marine Fauna of New Zealand: Mantis Shrimps (Crustacea: Stomatopoda). Wellington: NIWA (National Institute of Water and Atmospheric Research Ltd). NIWA Biodiversity Memoir (ISSN 1174-0043; 125)

  2. Zhao W, Yang QB, Chen X, Chen MQ, Wen WG (2019) A review of research on the biological properties and reproductive biology of some mantis shrimps. Marine Sci 43(4):105–114

  3. Gutekunst J, Andriantsoa R, Falckenhayn C, Hanna K, Stein W (2018) Clonal genome evolution and rapid invasive spread of the marbled crayfish. Nat Ecol Evol 2(3):567–573

    Article  Google Scholar 

  4. Veldsman WP, Ma KY, Hui JHL, Chan TF, Chu KH (2021) Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation. BMC Genomics 22(1):1–5

    Article  Google Scholar 

  5. Xu Z, Gao T, Xu Y, Li X, Tang J (2021) A chromosome-level reference genome of red swamp crayfish Procambarus clarkii provides insights into the gene families regarding growth or development in crustaceans. Genomics 113(5):3274–3284

    Article  CAS  PubMed  Google Scholar 

  6. Bachvaroff TR, Mcdonald RC, Plough LV, Chung JS (2021) Chromosome-level genome assembly of the blue crab Callinectes sapidus. G3 Genes|Genomes|Genetics 11(9):jkab212

    Article  PubMed  PubMed Central  Google Scholar 

  7. Tang B, Zhang D, Li H, Jiang S, Zhang H, Xuan F, Ge B, Wang Z, Liu Y, Sha Z (2020) Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus). GigaScience 9(1):giz161

    Article  PubMed  PubMed Central  Google Scholar 

  8. Xiong L, Wang Q, Qiu G (2012) large-scale isolation of microsatellites from chinese Mitten crab Eriocheir sinensis via a Solexa genomic survey. Int J Mole Sci 13(12):16333–16345

    Article  CAS  Google Scholar 

  9. Zhang D, Ding G, Ge B, Zhang H, Tang B (2011) Development and characterization of microsatellite loci of Oratosquilla oratoria (Crustacea: Squillidae). Conserv Genet Resour 4(1):147–150

    Article  CAS  Google Scholar 

  10. Dong X, Xing K, Sui Y, Liu H (2015) Genetic diversity of oratosqilla oratoria from four sea waters based on the mitochondrial coi gene sequences analysis. Marine Sci 39(7): 29–36

  11. Cloonan N, Arr F, Kolle G, Bba G, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature methods 5(7):613–619

    Article  CAS  PubMed  Google Scholar 

  12. Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764–770

    Article  PubMed  PubMed Central  Google Scholar 

  13. Ranallo-Benavidez T, Jaron K, Schatz M (2020) GenomeScope 2.0 and smudgeplot for reference-free profiling of polyploid genomes. Nat Commun 11(1):1432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinf (Oxford England) 24(5):713–714

    CAS  Google Scholar 

  15. Sebastian B, Thomas Thiel, Münch Uwe, Scholz Martin, Mascher,(2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33(16):2583–2585

    Article  Google Scholar 

  16. Tarailo-Graovac M, Chen N (2009) Using RepeatMasker to identify repetitive elements in genomic sequences. Current protoc Bioinform 4:1–4

  17. Robert C, Edgar (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797

    Article  Google Scholar 

  18. Sudhir K, Glen S, Koichiro T (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets. Mol Biology Evol 33:1870–1874

    Article  Google Scholar 

  19. Balakrishnan S, Gao S, Lercher MJ, Hu S, Chen WH (2019) Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees. Nucleic Acids Res 47(W1):W270–W275

    Article  Google Scholar 

  20. Wang Q, Ren X, Liu P, Li J, Lv J, Wang J, Zhang H, Wei W, Zhou Y, He Y et al (2022) Improved genome assembly of chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication. Mol Ecol Resour 22(1):334–344

    Article  CAS  PubMed  Google Scholar 

  21. Jin S, Bian C, Jiang S, Han K, Xiong Y, Zhang W, Shi C, Qiao H, Gao Z, Li R et al (2021) A chromosome-level genome assembly of the oriental river prawn Macrobrachium nipponense.  GigaScience 10(1):giaa160

    Article  PubMed  PubMed Central  Google Scholar 

  22. Tang B, Wang Z, Liu Q, Wang Z, Ren Y, Guo H, Qi T, Li Y, Zhang H, Jiang S et al (2021) Chromosome-level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs. Mol Ecol Resour 21(2):511–525

    Article  PubMed  Google Scholar 

  23. Cui Z, Liu Y, Yuan J, Zhang X, Ventura T, Ma K, Sun S, Song C, Zhan D, Yang Y et al (2021) The chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation. Nat Commun 12(1):2395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Zhao M, Wang W, Zhang F, Ma C, Liu Z, Yang M, Chen W, Li Q, Cui M, Jiang K et al (2021) A chromosome-level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean. Mol Ecol Resour 21(4):1299–1317

    Article  CAS  PubMed  Google Scholar 

  25. Shi L, Yi S, Li Y (2018) Genome survey sequencing of red swamp crayfish Procambarus clarkii. Mol Biol Rep 45(5):799–806

    Article  CAS  PubMed  Google Scholar 

  26. Hamilton JP, Buell CR (2012) Advances in plant genome sequencing. Plant J 70(1):177–190

    Article  CAS  PubMed  Google Scholar 

  27. Shi MJ, Cheng YY, Zhang WT, Xia XQ (2016) The evolutionary mechanism of genome size. Chinese Sci Bull 61:3188–3195

    Article  Google Scholar 

  28. López-Flores I, Garrido-Ramos M (2012) The repetitive DNA content of eukaryotic genomes. Genome Dyn 7:1–28

    Article  PubMed  Google Scholar 

  29. Kapitonov V, Jurka J (1999) Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica 107:27–37

    Article  CAS  PubMed  Google Scholar 

  30. Schug M, Wetterstrand KA, Gaudette MS, Lim RH, Hutter CM, Aquadro CF (1998) The distribution and frequency of microsatellite loci in Drosophila melanogaster. Mol Ecol 7:57–70

    Article  CAS  PubMed  Google Scholar 

  31. Edwards Y, Elgar G, Clark MS, Bishop MJ (1998) The identification and characterization of microsatellites in the compact genome of the japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analyses. J Mol Biol 278(4):843–854

    Article  CAS  PubMed  Google Scholar 

  32. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921

    Article  CAS  PubMed  Google Scholar 

  33. Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6

    Article  CAS  PubMed  Google Scholar 

  34. Zhang J, Jibin Huang C (2016) Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus. Gene 575(2):524–530

    Article  PubMed  Google Scholar 

  35. Labbé J, Murat C, Morin E, Tacon FL, Martin F (2011) Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers. Curr Genet 57(2):75–88

    Article  PubMed  Google Scholar 

  36. Haydar K, Ying L, Wieland M (2005) Survey of simple sequence repeats in completed fungal genomes. Mol Biology Evol 22(3):639–649

    Article  Google Scholar 

  37. Zhang Y, Lou FR, Han ZQ (2019) Development of microsatellite markers in Oratosquilla oratoria Transcriptome. J Zhejiang Ocean Univ (Natl Sci) 38(2):95–99

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Acknowledgements

The work was funded by National Natural Science Foundation of China (32070526) and sponsored by “Qing Lan Project” & “333 Project”.

Funding

This study was supported by National Natural Science Foundation of China (32070526).

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Author notes

  1. Xiaoli Sun and Gang Wang have contributed equally to this paper.

Authors and Affiliations

  1. Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Yancheng Teachers University, Yancheng, 224051, China

    Xiaoli Sun, Gang Wang, Jie Yang, Wei Yu, Jiayue Xu, Boping Tang & Daizhen Zhang

  2. College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, China

    Xiaoli Sun

  3. Chemical and Biological Engineering College, Yancheng Institute of Technology, Yancheng, 224003, China

    Ge Ding

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  1. Xiaoli Sun
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Contributions

All authors contributed to the study conception and design. Methodology was performed by XS, and GW. Formal analysis, data curation and investigation were performed by JY, WY and JX. The original draft was written by GD and DZ. Writing-review and editing were performed by GW, XS and BT. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Daizhen Zhang.

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The authors have no relevant financial or non-financial interests to disclose.

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This article does not contain any studies with human participants performed by any of the authors. All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

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Sun, X., Wang, G., Yang, J. et al. Whole genome evaluation analysis and preliminary Assembly of Oratosquilla oratoria (Stomatopoda: Squillidae). Mol Biol Rep 50, 4165–4173 (2023). https://doi.org/10.1007/s11033-023-08356-x

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