Skip to main content

First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima

Abstract

Objectives

American shad (Alosa sapidissima) is an important migratory fish under Alosinae and has long been valued for its economic, nutritional and cultural attributes. Overfishing and barriers across the passage made it vulnerable to sustain. To protect this valuable species, aquaculture action plans have been taken though there are no published genetic resources prevailing yet. Here, we reported the first de novo assembled and annotated transcriptome of A. sapidissima using blood and brain tissues.

Data description

We generated 160,481 and 129,040 non-redundant transcripts from brain and blood tissues. The entire work strategy involved RNA extraction, library preparation, sequencing, de novo assembly, filtering, annotation and validation. Both coding and non-coding transcripts were annotated against Swissprot and Pfam datasets. Nearly, 83% coding transcripts were functionally assigned. Protein clustering with clupeiform and non-clupeiform taxa revealed ~ 82% coding transcripts retained the orthologue relationship which improved confidence over annotation procedure. This study will serve as a useful resource in future for the research community to elucidate molecular mechanisms for several key traits like migration which is fascinating in clupeiform shads.

Objective

Alosa sapidissima is well discussed among the alosines for its biological, nutritional, and commercial calibre [1,2,3,4]. Their native range from the North Atlantic coast extends to several freshwater tributaries where come to reproduce by migrating, sometimes up to 1800 km upstream [5,6,7]. For high fecundity, marketable weight, and sport fishing, this anadromous fish receives an overwhelming demand, which drives up the exploitation. Numerous obstructions on their passage are limiting free movement and segregating the populations into patches [8,9,10,11,12]. Being sensitive to environmental changes, several reports have anticipated the extinction of shad species namely Tenualosa. reevesii, T. thibaudeaui, and Alosa killarnensis [13, 14]. Considering this risk, American shad restoration project and captive rearing has been undertaken in the USA and China, respectively. Despite these efforts, there is no large scale molecular information published to explain key traits that can strengthen a recovery program. Moreover, advanced omics technologies are producing vast amount of genomic data with precision. Therefore, we are reporting annotated transcriptomic resources from A. sapidissima for the first time. For a migratory species, it’s a challenge to maintain the ionic-balance in body fluid at a steady-state as it requires a rhythmic alteration between solvent and solutes contents. Moreover, a well-developed signaling system is also required to switch from salt to fresh water and vice versa, and to feed live prey [15,16,17,18]. So, the current transcriptomic resource from blood and brain will aim to understand key biological features from molecular level for this precious species. Nevertheless, the resource was initially produced to compare with other shads, but the effort was halted due to biological material transfer incompatibilities during COVID-19 pandemic. Besides, WGS study of A. sapidissimsa is under consideration by the G10K consortium [19]. Thereafter, it would be useful to share the data with scientific community to make better use of it.

Data description

A mature individual of 42 cm in SL was euthanized with MS222(1gL− 1) prior to extract brain and blood tissues, which were immediately placed in ALLProtect buffer and EDTA-stabilized anticoagulant tubes, respectively and later preserved in − 20 °C refrigerator [20]. Total RNA from each sample was extracted with TRIzol and 1 g was used to prepare cDNA libraries (~ 400 bp) for bridge amplification following the manufacturer’s instructions. Finally, the purified libraries were loaded into Illumina Novaseq with 2*150 bp paired-end configuration. Raw sequencing reads were trimmed where the base accuracy was strictly confined to 99.99% (Data file 5). To perform assembly, the processed reads were passed through Trinity-v2.11.0 [21, 22] assembler that constructed 195,742 and 158,817 transcripts from brain and blood samples, respectively (Data file 9). The primary number of transcripts was reduced to 160,481 and 129,040 after filtering and clustering non-redundant transcripts at 98% threshold. Quantitative analysis identified 41,572 bp and 17,242 bp from the brain and blood transcriptomes as the longest transcripts with N50 values of 2039 bp and 2096 bp (Data file 10). In both instances, the assembly length distribution remained uniform and comparable to one another (Data file 6). In addition, BUSCO searches against 3354 species from vertebrate lineages found 82.3% and 71.5% of complete universal single-copy genes from brain and blood transcriptomes (Data file 7).

Implication of TransDecoder-v5.5.0 [22] predicted around 80% of assembled transcripts had an ORF, of which 48,579 and 40,948 transcripts were capable of producing functional proteins (Data file 11). Using Blastx, Blastp as well as a series of tools based on HMM, we annotated coding and non-coding transcripts with an e value cut-off at 10^-5. GO analysis ascertained 39,015 and 33,475 proteins had at least one relevant term with molecular function, cellular component or biological process. In both instances, search against Pfam database revealed 70% of proteins with a functional domain. According to the loaded Sqlite database from Trinotate [23], 83% of predicted proteins were functionally annotated. Moreover, we made an assembly and subsequent annotation combining the reads from both tissues. The entire effort and representative datasets can be found in Table 1 (Data file 1, Data file 4 and Data file 14-20). To draw the homologous relationship, we retrieved Refseq proteins of seven other species, including clupeiform and non-clupeiform species from NCBI repository (Data file 12). For brain and blood, we found that 40,304 and 34,301 proteins had orthologue relationships with other species accounting for > 82% of total proteins (Data file 13). Finally, to evaluate the phylogenetic relationships, one-to-one orthologue proteins were retrieved. As the datasets from brain tissue extracted more groups of homologue proteins, we used 204 one-to-one orthologue proteins from brain to reconstruct a phylogenetic tree. We have found that A. sapidissima was clustered well with the clupeiform clade that was supported with maximum bootstrap value (Data file 8). The constructed phylogeny supports several other previous phylogenetic studies regarding their position [32,33,34]. However, this present resource will leverage the whole genome study of A. sapidissima as well as provide a solid foundation to compare their impressive physiological and behavioral competence with other allies.

Table 1 Overview of all data files/data sets

Limitations

The sample was collected from freshwater captivity located at Songjiang District, Shanghai. Normally, when anadromous fish migrate to freshwater, they need to move against strong water currents and interact with particular abiotic factors. However, in captivity, possible absence of such physical properties might provide less chance to specific gene expression than during migration in the wild.

Availability of data and materials

Processed raw data has been deposited in NCBI with open access (https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR16474177 & https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR16474180). Method with its codes and references and all the final product of analysis has been submitted to figshare for public usage [24,25,26,27,28,29,30,31]. File type and specific accessible links can be found in Table 1.

Abbreviations

SL:

Standard Length

BUSCO:

Benchmarking Universal Single Copy Orthologs

ORF:

Open Reading Frame

HMM:

Hidden Markov Model

GO:

Gene Ontology

NCBI:

National Canter for Biotechnology Information

WGS:

Whole Genome Study

G10K:

The international Genome 10 K consortium

References

  1. Limburg KE. American Shad in its native range. Am Fish Soc Symp. 2003;35:125–40.

    Google Scholar 

  2. Bi YH, Chen XW. Mitochondrial genome of the American shad Alosa sapidissima. Mitochondrial DNA. 2011;22(1-2):9–11.

  3. Wang J, Yu ZS, Wang X, Yang SS, Zhang DG, Zhang Y. The next-generation sequencing reveals the complete mitochondrial genome of Alosa sapidissima (Perciformes: Clupeidae) with phylogenetic consideration. Mitochondrial DNA B. 2017;2(1):304–6.

    Article  Google Scholar 

  4. Guo YJ, Xing ZK, Yang G, Liu JL, Chen CX, Xu DW. American shad muscle nutrition composition determination and analysis. China Feed. 2010;8:39–40.

    Google Scholar 

  5. Brown BL, Smouse PE, Epifanio JM, Kobak CJ. Mitochondrial DNA mixed-stock analysis of American Shad: coastal harvests are dynamic and variable. Trans Am Fish Soc. 1999;128(6):977–94.

    Article  Google Scholar 

  6. Rasmussen JL, Regier HA, Sparks RE, Taylor WW. Dividing the waters: the case for hydrologic separation of the north American Great Lakes and Mississippi River basins. J Great Lakes Res. 2011;37(3):588–92.

    Article  Google Scholar 

  7. Pearcy WG, Fisher JP. Ocean distribution of the American shad (Alosa sapidissima) along the Pacific coast of North America. Fish B-Noaa. 2011;109(4):440–53.

    Google Scholar 

  8. Harris JE, Hightower JE. Movement patterns of American Shad transported upstream of dams on the Roanoke River, North Carolina and Virginia. North Am J Fish Manage. 2011;31(2):240–56.

    Article  Google Scholar 

  9. Haro A, Castro-Santos T. Passage of American Shad: paradigms and realities. Mar Coast Fish. 2012;4(1):252–61.

    Article  Google Scholar 

  10. Grote AB, Bailey MM, Zydlewski JD. Movements and demography of spawning American Shad in the Penobscot River, Maine, prior to dam removal. Trans Am Fish Soc. 2014;143(2):552–63.

    Article  Google Scholar 

  11. Mulligan KB, Haro A, Noreika J. Effect of backwatering a streamgage weir on the passage performance of adult American Shad (Alosa sapidissima). J Ecohydraulics. 2021:1–13. https://doi.org/10.1080/24705357.2021.1945500.

  12. Hasselman DJ, Bentzen P, Narum SR, Quinn TP. Formation of population genetic structure following the introduction and establishment of non-native American shad (Alosa sapidissima) along the Pacific coast of North America. Biol Invasions. 2018;20(11):3123–43.

    Article  Google Scholar 

  13. Guo Q, Liu XJ, Ao XF, Qin JJ, Wu XP, Ouyang S. Fish diversity in the middle and lower reaches of the Ganjiang River of China: threats and conservation. PLoS One. 2018;13(11):e0205116. https://doi.org/10.1371/journal.pone.0205116.

  14. IUCN. The IUCN Red List of Threatened Species, vol. 2021-2; 2021.

    Google Scholar 

  15. Cao QQ, Gu J, Wang D, Liang FF, Zhang HY, Li XR, et al. Physiological mechanism of osmoregulatory adaptation in anguillid eels. Fish Physiol Biochem. 2018;44(2):423–33.

    CAS  Article  Google Scholar 

  16. Mohindra V, Dangi T, Tripathi RK, Kumar R, Singh RK, Jena JK, et al. Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies. Sci Rep. 2019;9(1):16511. https://doi.org/10.1038/s41598-019-52603-w.

  17. Xu GC, Bian C, Nie ZJ, Li J, Wang YY, Xu DP, et al. Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation. Gigascience. 2020;9(1):giz157. https://doi.org/10.1093/gigascience/giz157.

  18. Finlay RW, Poole R, Rogan G, Dillane E, Cotter D, Reed TE. Hyper- and hypo-osmoregulatory performance of Atlantic Salmon (Salmo salar) Smolts infected with Pomphorhynchus tereticollis (Acanthocephala). Front Ecol Evol. 2021;9(529). https://doi.org/10.3389/fevo.2021.689233.

  19. Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592(7856):737.

    CAS  Article  Google Scholar 

  20. Beekman JM, Reischl J, Henderson D, Bauer D, Ternes R, Peña C, et al. Recovery of microarray-quality RNA from frozen EDTA blood samples. J Pharmacol Toxicol Methods. 2009;59(1):44–9.

    CAS  Article  Google Scholar 

  21. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–U130.

    CAS  Article  Google Scholar 

  22. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, et al. De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494–512.

    CAS  Article  Google Scholar 

  23. Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, et al. A tissue-mapped axolotl De novo transcriptome enables identification of limb regeneration factors. Cell Rep. 2017;18(3):762–76.

    CAS  Article  Google Scholar 

  24. Sarker KK, Lu L, Huang J, Zhou T, Wang L, Hu Y, et al. First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima Figshare; 2021. https://doi.org/10.6084/m9.figshare.17056328.

    Book  Google Scholar 

  25. Sarker KK, Lu L, Huang J, Zhou T, Wang L, Hu Y, et al. First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima. Sequence Read Archive. 2021. https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR16474177.

  26. Sarker KK, Lu L, Huang J, Zhou T, Wang L, Hu Y, et al. First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima. Sequence Read Archive. 2021. https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR16474180.

  27. Sarker KK, Lu L, Huang J, Zhou T, Wang L, Hu Y, et al. First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima Figshare; 2021. https://doi.org/10.6084/m9.figshare.17054852.

    Book  Google Scholar 

  28. Sarker KK, Lu L, Huang J, Zhou T, Wang L, Hu Y, et al. First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima Figshare; 2021. https://doi.org/10.6084/m9.figshare.17054948.

    Book  Google Scholar 

  29. Sarker KK, Lu L, Huang J, Zhou T, Wang L, Hu Y, et al. First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima: Figshare; 2021. https://doi.org/10.6084/m9.figshare.16834564.v2.

  30. Sarker KK, Lu L, Huang J, Zhou T, Wang L, Hu Y, et al. First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima Figshare; 2021. https://doi.org/10.6084/m9.figshare.16834546.v2.

    Book  Google Scholar 

  31. Sarker KK, Lu L, Huang J, Zhou T, Wang L, Hu Y, et al. First report of de novo assembly and annotation from brain and blood transcriptome of ananadromous shad, Alosa sapidissima Figshare 2022; 2022. https://doi.org/10.6084/m9.figshare.19308326.v1.

    Book  Google Scholar 

  32. Bloom DD, Lovejoy NR. The evolutionary origins of diadromy inferred from a time-calibrated phylogeny for Clupeiformes (herring and allies). P Roy Soc B-Biol Sci. 2014;281(1778):20132081. https://doi.org/10.1098/rspb.2013.2081.

  33. Bloom DD, Burns MD, Schriever TA. Evolution of body size and trophic position in migratory fishes: a phylogenetic comparative analysis of Clupeiformes (anchovies, herring, shad and allies). Biol J Linn Soc. 2018;125(2):302–14.

    Article  Google Scholar 

  34. Hughes LC, Orti G, Huang Y, Sun Y, Baldwin CC, Thompson AW, et al. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proc Natl Acad Sci U S A. 2018;115(24):6249–54.

    CAS  Article  Google Scholar 

Download references

Acknowledgements

Our thanks go to the management team at the Lab of Molecular systematics and ecology for maintaining the High Performance Computation Server (HPCS) and supporting our data analysis. We also want to express our gratitude Mr. Roland Nathan Mandal and Miss. Irin Sultana for their technical support.

Funding

This work was supported by “Science and Technology Commission of Shanghai Municipality (19410740500)” and “Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding project”. Except funding, funder has no role in study design, sample collection, data analysis, and interpretation, or in manuscript writing.

Author information

Authors and Affiliations

Authors

Contributions

C.L. and K.K.S. designed the project and wrote the primary manuscript. L.J., L.W. and Y.H. collected and prepared the samples. K.K.S., L.L., J.H. and T.Z. performed the data analysis. All authors contributed in manuscript editing and revising the manuscript. The author(s) read and approved the final manuscript.

Corresponding author

Correspondence to Chenhong Li.

Ethics declarations

Ethics approval and consent to participate

All experimental procedures including specimen handling were approved by the Animal Ethics Committee of Shanghai Ocean University, China.

Consent for publication

Not applicable.

Competing interests

Authors are declaring no competing of 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

Sarker, K.K., Lu, L., Huang, J. et al. First report of de novo assembly and annotation from brain and blood transcriptome of an anadromous shad, Alosa sapidissima. BMC Genom Data 23, 22 (2022). https://doi.org/10.1186/s12863-022-01043-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s12863-022-01043-z

Keywords

  • Alosa sapidissima
  • De novo transcriptome
  • Brain & Blood
  • Annotation