Skip to main content

De novo assembly and annotation of the mangrove cricket genome

Abstract

Objectives

The mangrove cricket, Apteronemobius asahinai, shows endogenous activity rhythms that synchronize with the tidal cycle (i.e., a free-running rhythm with a period of ~ 12.4 h [the circatidal rhythm]). Little is known about the molecular mechanisms underlying the circatidal rhythm. We present the draft genome of the mangrove cricket to facilitate future molecular studies of the molecular mechanisms behind this rhythm.

Data description

The draft genome contains 151,060 scaffolds with a total length of 1.68 Gb (N50: 27 kb) and 92% BUSCO completeness. We obtained 28,831 predicted genes, of which 19,896 (69%) were successfully annotated using at least one of two databases (UniProtKB/SwissProt database and Pfam database).

Objective

Some animals in the intertidal zone, which is influenced by a tidal flooding and ebbing cycle of approximately 12.4 h, show a tidal rhythm in their activity [1,2,3]. This endogenous rhythm, which persists even under constant conditions, is known as a circatidal rhythm, and it occurs over a range of ~ 11.5 h (predatory mite) [4] to ~ 13.8 h (high-shore limpet) [5]. Although the molecular mechanisms underlying the circadian rhythm (i.e., an endogenous rhythm with a period of ~ 24 h) are well known [6], mechanistic studies of circatidal rhythms are limited [7, 8].

The mangrove cricket (Apteronemobius asahinai), an endemic species of mangrove forest floors, is also influenced by tides. This cricket shows a circatidal rhythm in its locomotor activity, with a period of ~ 12.6 h [9, 10]. This endogenous rhythm is not entrained by the light–dark cycle but by periodic inundations [11, 12]. The mangrove cricket is one of only a few model organisms studied for the purpose of understanding the molecular mechanisms of the circatidal rhythm. Previous work demonstrated that the circatidal rhythm was not disrupted by suppressing the expression of two circadian clock genes, period and Clock [13, 14]. These findings indicate that the molecular components of the circatidal clock differ from those of the circadian clock in the mangrove cricket. Recently, transcriptome analyses of this species were conducted to reveal circatidal clock-controlled genes [15] or to identify biological processes related to the circatidal rhythm [16]. Here, we provide the draft genome of the mangrove cricket. This information is expected to contribute to future molecular studies by enabling the use of molecular techniques such as GWAS.

Data description

Mangrove crickets were collected from a mangrove forest in Ginoza, Okinawa Prefecture, Japan. To generate highly homozygous individuals, we repeated sibling mating over 7 generations and used two adult males of the eighth generation for DNA extraction (for details, see Data file 1). Genomic DNA from the whole body of a male was extracted using the DNeasy® Blood & Tissue Kit (Qiagen). The NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) was used to construct a library from 500 ng sample DNA. Paired-end (2 × 150 bp) sequencing was performed on the Illumina HiSeq X platform. For long-read library preparation, genomic DNA from the whole body of another male was extracted using the DNeasy® Blood & Tissue Kit and Genomic-tip 20G Kit (both from Qiagen). Short DNA fragments were removed using Short Read Eliminator Kit (Circulomics). The library was constructed from 415 ng sample DNA using the Rapid Sequencing Kit (SQK-RAD004; Oxford Nanopore Technologies [ONT]). Sequencing was performed twice on the MinION Mk1b with a flow cell R9.4 (FLO-MIN106D; ONT). The Illumina and ONT platforms yielded 217.5 and 14.6 Gb of nucleotide sequence, respectively. The Illumina reads (Data file 2) were assembled and scaffolded using the CLC genomic workbench v20.0.4 [17]. The ONT reads (Data file 3) were trimmed for adapter and low-quality reads using Porechop v0.2.4 [18] and Nanofilt v2.8.0 [19], respectively, and then error-corrected using the Illumina reads by LoRDEC v0.9 [20]. Finally, the error-corrected ONT reads were subjected to gap closing in the scaffolds using TGS-Gapcloser v1.1.1 [21]. The final draft genome (Data file 4) consists of 151,060 scaffolds with a total length of 1,676,217,857 bp, average length of 11,096 bp, and N50 of 27,317 bp. BUSCO analysis using the online interface gVolante [22] identified 983 genes (92.21%) among the 1,066 arthropodal universal orthologs completely, and only 17 genes (1.59%) were missing, indicating high completeness of our draft genome.

RepeatModeler v2.0.1 [23] estimated 2532 repeat sequences, which were utilized by RepeatMasker v4.0.9 [24] to mask the repetitive elements in the genome. The repeat sequences in the assembly comprised 572,734,587 bp (34.17% of the total length). The MAKER v2.31.11 [25] pipeline predicted 28,831 protein-coding genes in the hard-masked genome (Data files 5–7). The average coding sequence length was 997.08 bp, with an average intron length of 1000.45 bp and average number of exons per gene of 4.34. We annotated 16,528 genes (57.3%) via a BLASTP v2.10.1 + [26] search (E-value threshold of 1 × 10–10) against known proteins in the UniProtKB/SwissProt Database [27]. InterProScan v5.50–84.0 [28] identified 4537 domain families among 17,932 (62.3%) genes via a search of the Pfam database. As a result, 69% of the predicted genes were successfully annotated by at least one of the two methods.

Limitations

The genome size, assessed by the k-mer frequency distribution of the Illumina reads using KmerGenie v1.7051 [29], was estimated to be 1,610,998,267 bp. Based on this estimation, the sequencing depths obtained from the Illumina and ONT platforms were calculated to be 134× and 9× , respectively. Since the coverage of ONT reads was low, the usage of them were limited only to the gap closing. The genome size of the mangrove cricket is comparable with the three previously sequenced Gryllidae genomes: Teleogryllus occipitalis (1.93 Gb) [30], Teleogryllus oceanicus (2.05 Gb) [31], and Laupala kohalensis (1.6 Gb) [32].

Availability of data and materials

The data described in this Data note can be freely and openly accessed on DDBJ under BioProject ID: PRJDB11838 and the figshare database. Sequence reads have been deposited at DDBJ Sequence Read Archive under accession number DRX290103 (https://identifiers.org/insdc.sra:DRX290103) [34] and DRX290104 (https://identifiers.org/insdc.sra:DRX290104) [35]. The whole genome sequence data has been deposited at DDBJ under accession number BPSV01000000 (https://identifiers.org/ncbi/insdc:BPSV01000000) [36]. The other data files generated in the current study are available at the figshare database: Data file 1 (https://doi.org/10.6084/m9.figshare.16632781) [33], Data file 5–7 (https://doi.org/10.6084/m9.figshare.14746056) [37,38,39]. See Table 1 and references [33,34,35,36,37,38,39] for details.

Table 1 Overview of data files/data sets

Abbreviations

BUSCO:

Benchmarking Universal Single-Copy Orthologs

Gb:

Giga base pair

GWAS:

Genome-wide association studies

kb:

Kilo base pair

ONT:

Oxford Nanopore Technologies

References

  1. 1.

    Akiyama T. Circatidal swimming activity rhythm in a subtidal cumacean Dimorphostylis asiatica (Crustacea). Mar Biol. 1995;123:251–5.

    Article  Google Scholar 

  2. 2.

    Barnwell FH. Daily and tidal patterns of activity in individual fiddler crab (Genus Uca) from the Woods Hole region. Biol Bull. 1966;13:1–17.

    Article  Google Scholar 

  3. 3.

    Satoh A, Momoshita H, Hori M. Circatidal rhythmic behaviour in the coastal tiger beetle Callytron inspecularis in Japan. Biol Rhythm Res. 2006;37(2):147–55.

    Article  Google Scholar 

  4. 4.

    Treherne JE, Foster WA, Evns PD, Ruscoe CNE. Free-running activity rhythm in the natural environment. Nature. 1977;269:796–7.

    CAS  Article  Google Scholar 

  5. 5.

    Gray DR, Hodgson AN. Endogenous rhythms of locomotor activity in the high-shore limpet, Helcion pectunculus (Patellogastropoda). Anim Behav. 1999;57:387–91.

    CAS  Article  Google Scholar 

  6. 6.

    Dunlap JC, Loros JJ, DeCoursey PJ. Chronobiology: Biological Timekeeping. Massachusetts: Sinauer; 2004.

  7. 7.

    Bulla M, Oudman T, Bijleveld AI, Piersma T, Kyriacou CP. Marine biorhythms: bridging chronobiology and ecology. Philos Trans R Soc B. 2017;372:20160253.

    Article  Google Scholar 

  8. 8.

    Zhang L, Hastings MH, Green EW, Tauber E, Sladek M, Webster SG, et al. Dissociation of circadian and circatidal timekeeping in the marine crustacean Eurydice pulchra. Curr Biol. 2013;23:1863–73.

    CAS  Article  Google Scholar 

  9. 9.

    Satoh A. Constant light disrupts the circadian but not the circatidal rhythm in mangrove crickets. Biol Rhythm Res. 2017;48:459–63.

    Article  Google Scholar 

  10. 10.

    Satoh A, Yoshioka E, Numata H. Circatidal activity rhythm in the mangrove cricket Apteronemobius asahinai. Biol Lett. 2008;4:233–6.

    Article  Google Scholar 

  11. 11.

    Satoh A, Yoshioka E, Numata H. Entrainment of the cricatidal activity rhythm of the mangrove cricket, Apteronemobius asahinai, to periodic inundations. Anim Behav. 2009;78:189–94.

    Article  Google Scholar 

  12. 12.

    Sakura K, Numata H. Contact with water functions as a Zeitgeber for the circatidal rhythm in the mangrove cricket Apteronemobius asahinai. Biol Rhythm Res. 2017;48:887–95.

    Article  Google Scholar 

  13. 13.

    Takekata H, Matsuura Y, Goto SG, Satoh A, Numata H. RNAi of the circadian clock gene period disrupts the circadian rhythm but not the circatidal rhythm in the mangrove cricket. Biol Lett. 2012;8:488–91.

    CAS  Article  Google Scholar 

  14. 14.

    Takekata H, Numata H, Shiga S, Goto SG. Silencing the circadian clock gene Clock using RNAi reveals dissociation of the circatidal clock from the circadian clock in the mangrove cricket. J Insect Physiol. 2014;68:16–22.

    CAS  Article  Google Scholar 

  15. 15.

    Satoh A, Terai Y. Circatidal gene expression in the mangrove cricket Apteronemobius asahinai. Sci Rep. 2019;9:3719.

    Article  Google Scholar 

  16. 16.

    Takekata H, Tachibana S, Motooka D, Nakamura S, Goto SG. Possible biological processes controlled by the circatidal clock in the mangrove cricket inferred from transcriptome analysis. Biol Rhythm Res. 2020. https://doi.org/10.1080/09291016.2020.1838747.

    Article  Google Scholar 

  17. 17.

    CLC Genomic Workbench. https://www.qiagenbioinformatics.com/.

  18. 18.

    Wick R. Porechop. 2018. https://github.com/rrwick/Porechop/.

  19. 19.

    De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long read sequencing data. Bioinformatics. 2018;34:2666–9.

    Article  Google Scholar 

  20. 20.

    Salmela L, Rivals E. LoRDEC: accurate and efficient long read error correction. Bioinformatics. 2014;30:3506–14.

    CAS  Article  Google Scholar 

  21. 21.

    Xu M, Guo L, Gu S, Wang O, Zhang R, Peters BA, et al. TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads. GigaScience. 2020;9:giaa094.

  22. 22.

    Nishimura O, Hara Y, Kuraku S. gVolante for standardizing completeness assessment of genome and transcriptome assemblies. Bioinformatics. 2017;33:3635–7.

    CAS  Article  Google Scholar 

  23. 23.

    Smit AFA, Hubley R. RepeatModeler Open-2.0. http://www.repeatmasker.org.

  24. 24.

    Smit AFA, Hubley R, Green P. RepeatMasker Open-4.0. 2013–2015. http://www.repeatmasker.org.

  25. 25.

    Holt C, Yandell M. MAKER2: an annotation pipeline and genome database management tool for second-generation genome projects. BMC Bioinformatics. 2011;12:491.

    Article  Google Scholar 

  26. 26.

    Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and application. BMC Bioinformatics. 2009;10:421.

    Article  Google Scholar 

  27. 27.

    Uniprot. https://www.uniprot.org/. Accessed 19 Nov 2020.

  28. 28.

    Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014;30:1236–40.

    CAS  Article  Google Scholar 

  29. 29.

    Chikhi R, Medvedev P. Informed and automated k-mer size selection for genome assembly. Bioinformatics. 2013;30:31–7.

    Article  Google Scholar 

  30. 30.

    Kataoka K, Minri R, Ide K, Ogura A, Takeyama H, Takeda M, et al. The draft genome dataset of the Asian cricket Teleogryllus occipitalis for molecular research toward entomophagy. Front Genet. 2020;11:470.

    CAS  Article  Google Scholar 

  31. 31.

    Pascoal S, Risse JE, Zhang X, Blaxter M, Cezard T, Challis RJ, et al. Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild. Evol Lett. 2019;4:19–33.

    Article  Google Scholar 

  32. 32.

    Blankers T, Oh KP, Bombarely A, Shaw KL. The genomic architecture of a rapid island radiation: recombination rate variation, chromosome structure, and genome assembly of the Hawaiian cricket Laupala. Genetics. 2018;209:1329–44.

    CAS  Article  Google Scholar 

  33. 33.

    Satoh A, Takasu M, Yano K, Terai Y. Materials and Methods.pdf. figshare. 2021. https://doi.org/10.6084/m9.figshare.16632781.

  34. 34.

    Satoh A, Terai Y. HiSeq X Ten paired end sequencing of SAMD00330124. DDBJ Sequence Read Archive. 2021. https://identifiers.org/insdc.sra:DRX290103.

  35. 35.

    Satoh A, Terai Y. MinION sequencing of SAMD00330124. DDBJ Sequence Read Archive. 2021. https://identifiers.org/insdc.sra:DRX290104.

  36. 36.

    Satoh A, Terai Y. Apteronemobius asahinai, whole genome shotgun sequencing project. DDBJ. 2021. https://identifiers.org/ncbi/insdc:BPSV01000000.

  37. 37.

    Satoh A, Takasu M, Yano K, Terai Y. Apteronemobius_asahinai.gff. figshare. 2021. https://doi.org/10.6084/m9.figshare.14746056.

  38. 38.

    Satoh A, Takasu M, Yano K, Terai Y. Apteronemobius_asahinai_proteins.fasta. figshare. 2021. https://doi.org/10.6084/m9.figshare.14746056.

  39. 39.

    Satoh A, Takasu M, Yano K, Terai Y. Apteronemobius_asahinai_transcripts.fasta. figshare. 2021. https://doi.org/10.6084/m9.figshare.14746056.

Download references

Acknowledgements

We thank Mr. Masashi Inoue for his support in the in silico analyses. Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics.

Funding

This work was supported by JSPS KAKENHI Grant Number JP18K06330 to AS, and Research Funding for Computational Software Supporting Program form Meiji University to KY.

Author information

Affiliations

Authors

Contributions

AS and YT designed the project. AS collected crickets in the field. MT established inbred lines. AS and YT performed the molecular experiments. AS and YT performed the in silico analyses. AS wrote the manuscript. KY supported the in silico analyses.

Corresponding author

Correspondence to Aya Satoh.

Ethics declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Satoh, A., Takasu, M., Yano, K. et al. De novo assembly and annotation of the mangrove cricket genome. BMC Res Notes 14, 387 (2021). https://doi.org/10.1186/s13104-021-05798-z

Download citation

Keywords

  • Apteronemobius asahinai
  • Circatidal rhythm
  • Illumina
  • Nanopore