Chromosome-level genome assembly and annotation of the skinnycheek lanternfish Benthosema ptertum.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
30 Oct 2024
30 Oct 2024
Historique:
received:
29
04
2024
accepted:
23
10
2024
medline:
31
10
2024
pubmed:
31
10
2024
entrez:
31
10
2024
Statut:
epublish
Résumé
Lanternfish not only boast the most abundant biomass among marine fish species but also play a vital role in marine ecosystems. As one of the lanternfish species with the highest global catch, the skinnycheek lanternfish (Benthosema pterotum) is widely distributed in the Indo-Pacific region, playing a pivotal role in the marine biological pump. This study constructed the first chromosome-level genome of B. pterotum using a combination of short-read sequencing, PacBio, and Hi-C sequencing technologies. The genome size of B. pterotum is 1,272.53 Mb, with a contig N50 of 810 Kb and a scaffold N50 of 54.49 M. More than 99.65% of contigs were successfully anchored onto 24 pseudochromosomes, and 95.7% of BUSCO genes were identified within the genome, demonstrating the high level of completeness in genome assembly. A total of 24,934 protein-coding genes were predicted, of which 99.02% were functionally annotated. The successful assembly of a high-quality genome for B. pterotum provides valuable genetic resources for better understanding its biological characteristics and potentially those of all lanternfish species.
Identifiants
pubmed: 39477948
doi: 10.1038/s41597-024-04039-9
pii: 10.1038/s41597-024-04039-9
doi:
Types de publication
Journal Article
Dataset
Langues
eng
Sous-ensembles de citation
IM
Pagination
1178Informations de copyright
© 2024. The Author(s).
Références
WoRMS Editorial Board. World Register of Marine Species. Available from https://www.marinespecies.org/ at VLIZ. https://www.marinespecies.org/aphia.php?p=popup&name=citation , https://doi.org/10.14284/170 (2023).
Fricke, R., Eschmeyer, W. & Fong, J. D. Eschmeyer’s catalog of fishes. Available at http://researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp . https://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp (2024).
Haygood, M. G., Edwards, D. B., Mowlds, G. & Rosenblatt, R. H. Bioluminescence of myctophid and stomiiform fishes is not due to bacterial luciferase. J. Exp. Zool. 270, 225–231 (1994).
doi: 10.1002/jez.1402700212
Yano, D., Bessho-Uehara, M., Paitio, J., Iwasaka, M. & Oba, Y. 14-3-3 proteins are luciferases candidate proteins from lanternfish Diaphus watasei. Photochem Photobiol Sci 22, 263–277 (2022).
doi: 10.1007/s43630-022-00311-2
pubmed: 36197650
Homaei, A., Khajeh, K., Sariri, R. & Kamrani, E. An emphatic study on the luciferin-luciferase bioluminescence system of Benthosema pterotum. Fish Physiol Biochem 49, 1409–1419 (2023).
doi: 10.1007/s10695-023-01264-8
pubmed: 37943346
Homaei, A. A. et al. Purification and characterization of a novel thermostable luciferase from Benthosema pterotum. J Photoch Photobio B 125, 131–136 (2013).
doi: 10.1016/j.jphotobiol.2013.05.015
Paxton, J. R. Osteology and Relationships of the Lanternfishes (Family Myctophidae). Bull. Nat. Hist. Mus. Los Angel. Cty. 13, 1–81 (1972).
Chen, S. Fauna Sinica Osteichthyes: Myctophiformes Cetomimiformes Osteoglossiformes. (Beijing: Science Press, 2002).
Poulsen, J. Y. et al. Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei). BMC Evol Biol 13, 111 (2013).
doi: 10.1186/1471-2148-13-111
pubmed: 23731841
pmcid: 3682873
D’elia, M. et al. Diel variation in the vertical distribution of deep-water scattering layers in the Gulf of Mexico. Deep Sea Research Part I: Oceanographic Research Papers 115, 91–102 (2016).
doi: 10.1016/j.dsr.2016.05.014
Ariza, A. et al. Vertical distribution, composition and migratory patterns of acoustic scattering layers in the Canary Islands. J Marine Syst 157, 82–91 (2016).
doi: 10.1016/j.jmarsys.2016.01.004
Irigoien, X. et al. Large mesopelagic fishes biomass and trophic efficiency in the open ocean. Nat Commun 5, 3271 (2014).
doi: 10.1038/ncomms4271
pubmed: 24509953
Cherel, Y., Fontaine, C., Richard, P. & Labatc, J.-P. Isotopic niches and trophic levels of myctophid fishes and their predators in the Southern Ocean. Limnol. Oceanogr. 55, 324–332 (2010).
doi: 10.4319/lo.2010.55.1.0324
Hudson, J. M., Steinberg, D. K., Sutton, T. T., Graves, J. E. & Latour, R. J. Myctophid feeding ecology and carbon transport along the northern Mid-Atlantic Ridge. Deep Sea Research Part I: Oceanographic Research Papers 93, 104–116 (2014).
doi: 10.1016/j.dsr.2014.07.002
FAOSTAT. Food and Agriculture Organization of the United Nations. https://www.fao.org/fishery/en/fishstat (2023).
Dypvik, E. & Kaartvedt, S. Vertical migration and diel feeding periodicity of the skinnycheek lanternfish (Benthosema pterotum) in the Red Sea. Deep Sea Research Part I: Oceanographic Research Papers 72, 9–16 (2013).
doi: 10.1016/j.dsr.2012.10.012
Wisner, R. L. The Taxonomy and Distribution of Lanternfishes (Family Myctophidae) of the Eastern Pacific Ocean. (Bay St. Louis, Miss: Navy Ocean Research and Development Activity, 1974).
Zahuranec, B. et al. Cryptic speciation in the mesopelagic environment: Molecular phylogenetics of the lanternfish genus Benthosema. Mar Genom 7, 7–10 (2012).
doi: 10.1016/j.margen.2012.05.001
Musilova, Z., Cortesi, F. & Matschiner, M. Vision using multiple distinct rod opsins in deep-sea fishes. Science 364, 588–592 (2019).
doi: 10.1126/science.aav4632
pubmed: 31073066
pmcid: 6628886
Martin, P. R., Olson, E. E., Girard, M. G., Smith, W. L. & Davis, M. P. Light in the darkness: New perspective on lanternfish relationships and classification using genomic and morphological data. Mol Phylogenet Evol 121, 71–85 (2018).
doi: 10.1016/j.ympev.2017.12.029
pubmed: 29305244
Malmstrøm, M., Matschiner, M., Tørresen, O. K., Jakobsen, K. S. & Jentoft, S. Whole genome sequencing data and de novo draft assemblies for 66 teleost species. Sci Data 4, 160132 (2017).
doi: 10.1038/sdata.2016.132
pubmed: 28094797
pmcid: 5240625
Chen, Y. et al. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience 7, 1–6 (2018).
doi: 10.1093/gigascience/gix120
pubmed: 29659813
pmcid: 5827348
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J Mol Biol 215, 403–410 (1990).
doi: 10.1016/S0022-2836(05)80360-2
pubmed: 2231712
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
doi: 10.1093/bioinformatics/btr011
pubmed: 21217122
pmcid: 3051319
Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202–2204 (2017).
doi: 10.1093/bioinformatics/btx153
pubmed: 28369201
pmcid: 5870704
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).
doi: 10.1101/gr.215087.116
pubmed: 28298431
pmcid: 5411767
Huang, S., Kang, M. & Xu, A. HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly. Bioinformatics 33, 2577–2579 (2017).
doi: 10.1093/bioinformatics/btx220
pubmed: 28407147
pmcid: 5870766
Walker, B. J. et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 9, e112963 (2014).
doi: 10.1371/journal.pone.0112963
pubmed: 25409509
pmcid: 4237348
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16, 259 (2015).
doi: 10.1186/s13059-015-0831-x
pubmed: 26619908
pmcid: 4665391
Durand, N. C. et al. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 3, 95–98 (2016).
doi: 10.1016/j.cels.2016.07.002
pubmed: 27467249
pmcid: 5846465
Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).
doi: 10.1126/science.aal3327
pubmed: 28336562
pmcid: 5635820
Tarailo‐Graovac, M. & Chen, N. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences. Curr Protoc Bioinformatics 25 (2009).
Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res 35, W265–W268 (2007).
doi: 10.1093/nar/gkm286
pubmed: 17485477
pmcid: 1933203
Bao, W., Kojima, K. K. & Kohany, O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA 6, 11 (2015).
doi: 10.1186/s13100-015-0041-9
pubmed: 26045719
pmcid: 4455052
Stanke, M., Diekhans, M., Baertsch, R. & Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637–644 (2008).
doi: 10.1093/bioinformatics/btn013
pubmed: 18218656
Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004).
doi: 10.1101/gr.1865504
pubmed: 15123596
pmcid: 479130
Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11, 1650–1667 (2016).
doi: 10.1038/nprot.2016.095
pubmed: 27560171
pmcid: 5032908
Elsik, C. G. et al. Creating a honey bee consensus gene set. Genome Biol 8, R13 (2007).
doi: 10.1186/gb-2007-8-1-r13
pubmed: 17241472
pmcid: 1839126
Liu, Q., Ding, S. & Liu, S. NCBI GenBank https://identifiers.org/ncbi/insdc.gca:GCA_039105355.1 (2024).
Liu, Q., Liu, S. & Ding, S. NCBI Sequence Read Archive https://identifiers.org/ncbi/insdc.sra:SRP500492 (2024).
Liu, Q. Chromosome-level genome assembly of the skinnycheek lanternfish Benthosema ptertum. figshare https://doi.org/10.6084/m9.figshare.25710927 (2024).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
doi: 10.1093/bioinformatics/btp324
pubmed: 19451168
pmcid: 2705234
Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol 21, 245 (2020).
doi: 10.1186/s13059-020-02134-9
pubmed: 32928274
pmcid: 7488777
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
doi: 10.1093/bioinformatics/btv351
pubmed: 26059717