DATA NOTE
ERGA-BGE genome o S igma o eu his a c u i Robson, 1948: he
jewelled squid
[ e sion 1; pee e iew: 2 app o ed]
Fe nando Ángel Fe nández-Ál a ez 1,2, Ainhoa Be nal-Bajo3, Nu ia Escude o4,
Ma ía Coneje o5, Ana Riesgo5, Rosa Fe nández4, Ri a Mon ei o 6,
As id Böhne 6, Lau a Aguile a 7,8, Ma a Gu 7,8, Tyle S Alio o 7,8,
F ancisco Câma a Fe ei a7,8, Fe nando C uz 7,8, Jèssica Gómez-Ga ido 7,8,
Leanne Hagge y 9, Fe gal Ma in9, Tom B own 10,11
1Ins i u de Ciencies del Ma (ICM-CSIC), CSIC, Ba celona, Spain
2Ins i u o Español de Oceanog a ía, Cen o Oceanog á ico de Gijón (IEO, CSIC), A . del P íncipe de As u ias, 70 Bis, Gijón, 33212,
Spain
3Cen o Oceanog á ico de Balea es, Ins i u o Español de Oceanog a ía (IEO-CSIC), Palma, Spain
4Ins i u de Biologia E olu i a (UPF-CSIC), Ba celona, Spain
5Museo Nacional de Ciencias Na u ales- CSIC, Mad id, Spain
6Leibniz Ins i u e o he Analysis o Biodi e si y Change - Museum Koenig Bonn, Bonn, Ge many
7Cen o Nacional de Análisis Genómico (CNAG), Ba celona, Spain
8Uni e si a de Ba celona (UB), Ba celona, Spain
9Eu opean Molecula Biology Labo a o y, Eu opean Bioin o ma ics Ins i u e, Wellcome Genome Campus, Camb idge, UK
10Leibniz Ins i u e o Zoo and Wildli e Resea ch, Be lin, Ge many
11Be lin Cen e o Genomics in Biodi e si y Resea ch (BeGenDi ), Be lin, Ge many
Fi s published: 04 Sep 2025, 5:270
h ps://doi.o g/10.12688/open eseu ope.20439.1
La es published: 04 Sep 2025, 5:270
h ps://doi.o g/10.12688/open eseu ope.20439.1
1
Abs ac
The S igma o eu his a c u i e e ence genome o e s a aluable
esou ce o unde s anding he e olu iona y pa e ns o oceanic
squids, who pe o m impo an ecological oles as bo h p eda o s and
p ey in mesopelagic and deep-sea en i onmen s, while hei genomes
emain unde s udied. The en i e y o he genome sequence was
assembled in o 46 con iguous ch omosomal pseudomolecules. This
ch omosome-le el assembly encompasses 3.25 Gb, composed o
1,268 con igs and 497 sca olds, wi h con ig and sca old N50 alues o
11.0 Mb and 74.6 Mb, espec i ely.
Keywo ds
S igma o eu his a c u i, genome assembly, Eu opean Re e ence
Genome A las, Biodi e si y Genomics Eu ope, Ea h Biogenome
P ojec , jewelled squid
Open Pee Re iew
App o al S a us
1 2
e sion 1
04 Sep 2025 iew iew
Masa-Aki Yoshida , Shimane Uni e si y,
Shiman, Japan
1.
José M Ma ín-Du án , Queen Ma y
Uni e si y o London, London, UK
2.
Any epo s and esponses o commen s on he
a icle can be ound a he end o he a icle.
Open Resea ch Eu ope
Page 1 o 9
Open Resea ch Eu ope 2025, 5:270 Las upda ed: 27 SEP 2025
Co esponding au ho : Tom B own ([email p o ec ed])
Au ho oles: Fe nández-Ál a ez FÁ: In es iga ion, Me hodology, Resou ces, W i ing – O iginal D a P epa a ion, W i ing – Re iew &
Edi ing; Be nal-Bajo A: In es iga ion, Resou ces, W i ing – Re iew & Edi ing; Escude o N: Me hodology, Supe ision, Valida ion, W i ing
– Re iew & Edi ing; Coneje o M: In es iga ion, Resou ces, W i ing – Re iew & Edi ing; Riesgo A: In es iga ion, Resou ces, W i ing –
Re iew & Edi ing; Fe nández R: Funding Acquisi ion, Me hodology, Supe ision, Valida ion, W i ing – Re iew & Edi ing; Mon ei o R:
Me hodology, Supe ision, Valida ion, W i ing – Re iew & Edi ing; Böhne A: Funding Acquisi ion, Me hodology, Supe ision, Valida ion,
W i ing – Re iew & Edi ing; Aguile a L: In es iga ion, W i ing – Re iew & Edi ing; Gu M: Funding Acquisi ion, In es iga ion, Supe ision,
W i ing – Re iew & Edi ing; Alio o TS: Da a Cu a ion, Fo mal Analysis, Funding Acquisi ion, Supe ision, W i ing – Re iew & Edi ing;
Câma a Fe ei a F: Da a Cu a ion, Fo mal Analysis, W i ing – Re iew & Edi ing; C uz F: Da a Cu a ion, Fo mal Analysis, W i ing – Re iew
& Edi ing; Gómez-Ga ido J: Da a Cu a ion, Fo mal Analysis, W i ing – Re iew & Edi ing; Hagge y L: Da a Cu a ion, Fo mal Analysis,
W i ing – Re iew & Edi ing; Ma in F: Da a Cu a ion, Fo mal Analysis, Funding Acquisi ion, Supe ision, W i ing – Re iew & Edi ing;
B own T: Visualiza ion, W i ing – O iginal D a P epa a ion
Compe ing in e es s: No compe ing in e es s we e disclosed.
G an in o ma ion: This p ojec has ecei ed unding om he Eu opean Union’s Ho izon Eu ope esea ch and inno a ion p og amme
unde g an ag eemen No 101059492 (Biodi e si y Genomics Eu ope [BGE]). This p ojec ecei ed unding om Ho izon Eu ope unde
he Biodi e si y, Ci cula Economy and En i onmen (REA.B.3); co- unded by he Swiss S a e Sec e a ia o Educa ion, Resea ch and
Inno a ion (SERI) unde con ac numbe s 22.00173 and 24.00054; and by he UK Resea ch and Inno a ion (UKRI) unde he Depa men
o Business, Ene gy and Indus ial S a egy’s Ho izon Eu ope Gua an ee Scheme. Funding was p o ided by he Spanish Minis y o
Science, Inno a ion and Uni e si ies (OCTOSET, Re . RTI2018-097908-B-I00; ECOPHYN, Re . PID2021-126824NB-C32; MCIU/AEI/FEDER,
EU), and he Spanish go e nmen h ough he “Se e o Ochoa Cen e o Excellence” acc edi a ion (CEX2019-000928-S). F.Á.F.-Á. was
suppo ed by a Bea iu de Pinós ellowship om Sec e a ia d Uni e si a s i Rece ca del Depa amen de Rece ca i Uni e si a s o he
Gene ali a de Ca alunya (Re . BP 2021 00035) and a Ramón y Cajal ellowship (Re . RYC2023-043494-I) unded by MCIN/AEI
/10.13039/501100011033 and FSE+.
The unde s had no ole in s udy design, da a collec ion and analysis, decision o publish, o p epa a ion o he manusc ip .
Copy igh : © 2025 Fe nández-Ál a ez FÁ e al. This is an open access a icle dis ibu ed unde he e ms o he C ea i e Commons
A ibu ion License, which pe mi s un es ic ed use, dis ibu ion, and ep oduc ion in any medium, p o ided he o iginal wo k is p ope ly
ci ed.
How o ci e his a icle: Fe nández-Ál a ez FÁ, Be nal-Bajo A, Escude o N e al. ERGA-BGE genome o S igma o eu his a c u i Robson,
1948: he jewelled squid [ e sion 1; pee e iew: 2 app o ed] Open Resea ch Eu ope 2025, 5:270
h ps://doi.o g/10.12688/open eseu ope.20439.1
Fi s published: 04 Sep 2025, 5:270 h ps://doi.o g/10.12688/open eseu ope.20439.1
This a icle is included in he Ho izon Eu ope
ga eway.
This a icle is included in he Genome Repo s
om he Biodi e si y Genomics Eu ope P ojec
collec ion.
Open Resea ch Eu ope
Page 2 o 9
Open Resea ch Eu ope 2025, 5:270 Las upda ed: 27 SEP 2025
In oduc ion
S igma o eu his a c u i Robson, 1948 belongs o he amily
His io eu hidae Ve ill, 1880–1881, known as he jewelled
squids, which a e one o he mos impo an componen s o he
die o endange ed mega auna, such as spe m whales (Cla ke,
2006). Jewelled squids a e cha ac e ised by a unique mo phol-
ogy wi h a numbe o pho opho es on hei skin o b eak i s
shadow and decei e p eda o s om deepe wa e s. They also
possess high le els o asymme y in hei bodies, peaking in
a la ge di e ence in size, mo phology and pigmen a ion o
hei eyes, hemsel es specialised o di e en asks (Thomas
e al., 2017). While he la ge le eye looks a he dim ligh
coming om he su ace o spo hei mega aunal p eda o s, he
smalle igh eye looks owa ds he bo om looking o biolumi-
nescence o hei mic onek on p ey. S. a c u i is one o he h ee
allopa ic species o he genus S igma o eu his P e e , 1900,
which a e cha ac e ised by duplica ed e minal pa s o he
male ep oduc i e sys em and wi h sub le mo phological di -
e ences among hem, which can only be ecognised in ma u e
males (Young & Vecchione, 2016). I dis ibu es in opical
and sub opical A lan ic o sho e mesopelagic wa e s and as
wi h any o he cephalopod, S. a c u i is as g owing, ueled
by a e y in ense p eda o y ac i i y. Jewelled squids a e
pa a enic hos s o pa asi ic asca id helmin hs, such as Anysakis
Duja din, 1845 and o he nema odes (Palomba e al., 2021).
They ans e hese pa asi es o highe ophic le el hos s,
such as comme cially impo an swo d ishes and endange ed
oo hed whales, whe e hese pa asi es inish hei li e cycles.
Jewelled squids a e he la ges componen o spe m whales
die s in many a eas (Cla ke, 2006) and an impo an p ey i em
o many o he mega aunal species, such as dolphins, sha ks
and swo d ishes. Thus, hey ep esen an impo an ene gy
and biomass link among lowe and uppe ophic le els in
pelagic oceanic ood webs. Jewelled squids ha e an unse led
posi ion in he phylogeny o oceanic squids (Fe nández-Ál a ez
e al., 2022). The genome o S. a c u i is a aluable ool o
sol e he phylogene ic posi ion o jewelled squids wi hin
oceanic squids.
The gene a ion o his e e ence esou ce was coo dina ed by
he Eu opean Re e ence Genome A las (ERGA) ini ia i e’s
Biodi e si y Genomics Eu ope (BGE) p ojec , suppo ing
ERGA’s aims o p omo ing ansna ional coope a ion o p o-
mo e ad ances in he applica ion o genomics echnologies o
p o ec and es o e biodi e si y (Mazzoni e al., 2023).
Ma e ials & me hods
ERGA’s sequencing s a egy includes Ox o d Nanopo e Tech-
nology (ONT) and/o Paci ic Biosciences (PacBio) o long- ead
sequencing, along wi h Hi-C sequencing o ch omosomal
a chi ec u e, Illumina Pai ed-End (PE) o polishing (i.e. ec-
ommended o ONT-only assemblies), and RNA sequencing
o ansc ip omic p o iling, o acili a e genome assembly
and anno a ion.
Sample and sampling in o ma ion
Ainhoa Be nal-Bajo sampled one specimen o S igma o-
eu his a c u i, which was iden i ied based on mo phology by
Fe nando Ángel Fe nández-Ál a ez, om in e na ional A lan ic
wa e s nea Azo es and he Cana y Islands on 28 h Feb ua y
2023. As sampling was pe o med in in e na ional wa e s, no
pe mi is equi ed. As he squid is no conside ed an expe i-
men al animal acco ding o he Spanish di ec i e RD 53/2013,
he e is no need o an app o al by an e hical commi ee.
Sampling was pe o med using a Mesopelagos ne .
The specimen was eu hanized by eezing a -80 °C. Un il DNA
and RNA ex ac ions, samples we e p ese ed a -80 °C.
Vouche ing in o ma ion
Physical e e ence ma e ial o he he e sequenced speci-
men has been deposi ed in he Na ional Museum o Na u al
His o y o Mad id (MNCN-CSIC) h ps://www.mncn.csic.es/es/
colecciones unde he accession numbe MNCN 15.06/521.
F ozen e e ence issue ma e ial o skin is a ailable om he
same indi idual a he Biobank Na ional Museum o Na u al
His o y o Mad id (MNCN-CSIC) h ps://www.mncn.csic.es/es/
colecciones unde he ID MNCN-ADN-151723.
An elec onic ouche image o he sequenced indi idual is
a ailable om ERGA’s EBI BioImageA chi e da ase h ps://
www.ebi.ac.uk/bios udies/bioimages/s udies/S-BIAD1012?
que y=ERGA unde accession IDs SAMEA114541340_1.jpg,
SAMEA114541340_2.jpg, and SAMEA114541340_3.jpg.
Gene ic in o ma ion
The es ima ed genome size, based on ances al axa, is 3.2 Gb.
This is a diploid genome wi h a haploid numbe o 46
ch omosomes (2n=92). All in o ma ion o his species
was e ie ed om Genomes on a T ee (Challis e al., 2023).
DNA/RNA p ocessing
DNA was ex ac ed om a m issue using he Blood & Cell
Cul u e DNA Midi Ki (Qiagen) ollowing he manu ac u e ’s
ins uc ions. DNA quan i ica ion was pe o med using a
Qubi dsDNA BR Assay Ki (The mo Fishe Scien i ic),
and DNA in eg i y was assessed using a Genomic DNA 165 Kb
Ki (Agilen ) on he Fem o Pulse sys em (Agilen ). The
DNA was s o ed a +4°C un il used.
RNA was ex ac ed using an RNeasy Mini Ki (Qiagen)
acco ding o he manu ac u e ’s ins uc ions. RNA was ex ac ed
om ou di e en specimen pa s: muscle, skin, a m issue
and en acle s alk. RNA quan i ica ion was pe o med using
Page 3 o 9
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he Qubi RNA BR ki and RNA in eg i y was assessed using
a Bioanalyze 2100 sys em (Agilen ) RNA 6000 Nano Ki
(Agilen ). RNA was equimola ly pooled o he lib a y
p epa a ion and s o ed a -80°C un il used.
Lib a y p epa a ion and sequencing
Fo long- ead whole genome sequencing, a lib a y was p e-
pa ed using he SQK-LSK114 Ki (Ox o d Nanopo e Technolo-
gies, ONT) and was sequenced on a P ome hION 24 A Se ies
ins umen (ONT). A sho - ead whole genome sequencing
lib a y was p epa ed using he KAPA Hype P ep Ki (Roche).
A Hi-C lib a y was p epa ed om a m issue using he Do e-
ail Omni-C ki (Can a a Bio), ollowed by he KAPA Hype
P ep ki o Illumina sequencing (Roche). The RNA lib a y om
he pooled sample was p epa ed using he KAPA mRNA Hype
p ep ki o Illumina sequencing (Roche). The sho - ead
sequencing lib a ies we e p ocessed on a No aSeq 6000
ins umen (Illumina). In o al, 180.5 Gb Ox o d Nanopo e,
203.5 Gb Illumina WGS sho gun, and 195.3 Gb HiC da a we e
sequenced o gene a e he assembly.
Genome assembly me hods
The genome was assembled using he CNAG CLAWS pipe-
line (Gomez-Ga ido, 2024). B ie ly, eads we e p ep oc-
essed o quali y and leng h using T im Galo e 0.6.7 and
Fil long 0.2.1, and ini ial con igs we e assembled using
Nex Deno o 2.5.0, ollowed by polishing o he assembled
con igs using HyPo 1.0.3, emo al o e ained haplo igs using
pu ge-dups 1.2.6 and sca olding wi h YaHS 1.2a. Finally,
assembled sca olds we e cu a ed ia manual inspec ion using
P e ex 0.2.5 wi h he Rapid Cu a ion Toolki (h ps://gi -
lab.com/w si-g i / apid-cu a ion) o emo e any alse joins
and inco po a e any sequences no au oma ically sca -
olded in o hei espec i e loca ions in he ch omosomal
pseudomolecules (o supe -sca olds). Summa y analysis o
he eleased assembly was pe o med using he ERGA-BGE
Genome Repo ASM Galaxy wo k low (h ps://doi.o g/10.48546/
wo k lowhub.wo k low.1103.2).
Genome anno a ion me hods
A gene se was gene a ed using he Ensembl Gene Anno-
a ion sys em (Aken e al., 2016), p ima ily by aligning
publicly a ailable sho - ead RNA-seq da a om BioSam-
ple: SAMEA117648700 o he genome. Gaps in he anno a ion
we e illed ia p o ein- o-genome alignmen s o a selec se o
clade-speci ic p o eins om UniP o (“UniP o : A Wo ldwide
Hub o P o ein Knowledge,” 2019), which had expe imen al
e idence a he p o ein o ansc ip le el. A each locus, da a
we e agg ega ed and consolida ed, p io i ising models de i ed
om RNA-seq da a, esul ing in a inal se o gene models and
associa ed non- edundan ansc ip se s. To dis inguish ue
iso o ms om agmen s, he likelihood o each open ead-
ing ame (ORF) was e alua ed agains known me azoan
p o eins. Low-quali y ansc ip models, such as hose show-
ing e idence o agmen ed ORFs, we e emo ed. In cases
whe e RNA-seq da a we e agmen ed o absen , homology
da a we e p io i ised, a ou ing longe ansc ip s wi h s ong
in on suppo om sho - ead da a. The esul ing gene
models we e classi ied in o wo ca ego ies: p o ein-coding, and
long non-coding. Models ha did no o e lap p o ein-cod-
ing genes, and we e cons uc ed om ansc ip omic da a
we e conside ed po en ial lncRNAs. Po en ial lncRNAs
we e u he il e ed o emo e single-exon loci due o hei
un eliabili y. Pu a i e miRNAs we e p edic ed by pe o m-
ing a BLAST sea ch o miRBase (Kozoma a e al., 2019)
agains he genome, ollowed by RNA old analysis (G ube
e al., 2008). O he small non-coding loci we e iden i ied by
scanning he genome wi h R am (Kal a i e al., 2018) and pass-
ing he esul s h ough In e nal (Naw ocki & Eddy, 2013).
Summa y analysis o he eleased anno a ion was pe o med
using he ERGA-BGE Genome Repo ANNOT Galaxy wo k low
(h ps://doi.o g/10.48546/wo k lowhub.wo k low.1096.1), inco -
po a ing ools such as AGAT 1.2, OMA k 0.3 and BUSCO
( 5.5.0).
Resul s
Genome assembly
The genome assembly has a o al leng h o 3,249,387,216 bp
in 497 sca olds (Figu e 1 & Figu e 2), wi h a GC con en o
34.92%. The assembly has a con ig N50 o 10,980,000 bp and
L50 o 88 and a sca old N50 o 74,550,748 bp and L50 o 19.
The assembly has a o al o 771 gaps, o aling 154.2 kb in
cumula i e size. The single-copy gene con en analysis using
he Me azoa da abase wi h BUSCO (Manni e al., 2021)
esul ed in 94.8% comple eness (94.0% single and 0.8% dupli-
ca ed). 80.5% o eads k-me s we e p esen in he assembly
and he assembly has a base accu acy Quali y Value (QV) o
35.4 as calcula ed by Me qu y (Rhie e al., 2020).
Genome anno a ion
The genome anno a ion consis s o 12,987 p o ein-coding
genes wi h an associa ed 21,447 ansc ip s, in addi ion o
3,561 non-coding genes (Table 1). Using he longes iso o m
pe ansc ip , he single-copy gene con en analysis using he
Me azoa_odb10 da abase wi h BUSCO esul ed in 93.8%
comple eness. Using he OMAme Myomo pha da abase o
OMA k (Ne e s e al., 2025) esul ed in 93.31% comple eness
and 74.74% consis ency (Table 2).
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Figu e 1. Snail plo summa y o assembly s a is ics. The main plo is di ided in o 1,000 size-o de ed bins a ound he ci cum e ence,
wi h each bin ep esen ing 0.1% o he 3,249,387,216 bp assembly including he mi ochond ial genome. The dis ibu ion o sequence
leng hs is shown in da k g ey, wi h he plo adius scaled o he longes sequence p esen in he assembly (99,556,817 bp, shown in ed).
O ange and pale-o ange a cs show he sca old N50 and N90 sequence leng hs (74,550,748 and 46,349,533 bp), espec i ely. The pale
g ey spi al shows he cumula i e sequence coun on a log-scale, wi h whi e scale lines showing successi e o de s o magni ude. The blue
and pale-blue a ea a ound he ou side o he plo shows he dis ibu ion o GC, AT, and N pe cen ages in he same bins as he inne plo .
A summa y o comple e, agmen ed, duplica ed, and missing BUSCO genes ound in he assembled genome om he Me azoa da abase
(odb10) is shown in he op igh .
Figu e 2. Hi-C con ac map showing spa ial in e ac ions be ween egions o he genome. The diagonal co esponds o in a-
ch omosomal con ac s, depic ing ch omosome bounda ies. The equency o con ac s is shown on a loga i hmic hea map scale. Hi-C ma ix
bins we e me ged in o a 25 kb bin size o plo ing. Names o al e na e ch omosomes ha e been labelled on x- and y-axes o isualisa ion
pu poses.
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Da a a ailabili y
S. a c u i and he ela ed genomic s udy we e assigned o T ee
o Li e ID (ToLID) ‘xcS iA c 1’ and all sample, sequence,
and assembly in o ma ion a e a ailable unde he umb ella
BioP ojec PRJEB81320. The sample in o ma ion is a ailable
a he ollowing BioSample accessions: SAMEA114541340,
SAMEA114541342, SAMEA114541343, and SAMEA114541354.
The genome assembly is accessible om ENA unde acces-
sion numbe GCA_964276865.1. Sequencing da a p oduced
as pa o his p ojec a e a ailable om ENA a he ollow-
ing accessions: ERX13202607, ERX13202608, ERX13202609
and ERX13202610. Documen a ion ela ed o he genome
assembly and cu a ion can be ound in he ERGA Assembly
Repo (EAR) documen a ailable a h ps://gi hub.com/ERGA-
conso ium/EARs/ ee/main/Assembly_Repo s/S igma o eu-
his_a c u i/xcS iA c 1. Fu he de ails and da a abou he p ojec
a e hos ed on he ERGA po al a h ps://po al.e ga-biodi e si y.
eu/da a_po al/2053936.
Au ho con ibu ions
AB-B collec ed he samples, FÁF-Á iden i ied he species,
FÁF-Á sampled and p ese ed biological ma e ial and p o ided
me ada a, MC and AR p o ided ma e ial and in o ma ion
o ouche ing and ba coding, AsB p o ided sampling and
me ada a suppo and managemen , RM, NE, RF, and AsB p o-
ided suppo in sampling, shipping o biological ma e ial,
me ada a collec ion, and managemen , LA and MG ex ac ed
DNA, p epa ed lib a ies, and pe o med sequencing, FCF, FC
and JGG pe o med genome assembly and cu a ion unde he
supe ision o TSA, LH, and FM pe o med genome anno a ion,
TB gene a ed he analysis and epo . All au ho s con ibu ed
o he w i ing, e iew, and edi ing o his genome no e and ead
and app o ed he inal e sion.
Acknowledgemen s
The specimen was cap u ed du ing he oceanic esea ch
c uise DESAFIO (Re . PID2020-118118RB-I00). We would
like o acknowledge he assembly e iewe , Adama Nda ,
om Genoscope. The au ho s acknowledge he suppo o
he F eibu g Galaxy Team: Saim Momin and Bjö n G üning,
Bioin o ma ics, Uni e si y o F eibu g (Ge many), unded by
he Ge man Fede al Minis y o Educa ion and Resea ch BMBF
g an 031 A538A de.NBI-RBC and he Minis y o Science,
Resea ch and he A s Baden-Wü embe g (MWK) wi hin he
amewo k o LIBIS/de.NBI F eibu g.
Table 1. S a is ics om assembled gene models.
No. genes No.
ansc ip s
Mean gene
leng h (bp)
No. single-
exon genes
Mean exons
pe ansc ip
mRNA 12,987 21,447 42,913 519 9.0
snoRNA 219 219 170 219 1
lncRNA 1,300 1,405 13,735 438 2.0
snRNA 837 837 133 837 1
RNA 1,545 1,545 229 1,545 1
scRNA 5 5 131 5 1
RNA 12,259 12,259 77 12,259 1
Table 2. Anno a ion comple eness and consis ency sco es calcula ed by BUSCO
un in p o ein mode (me azoa_odb10) and OMA k (Lopho ochozoa).
Comple e Singula Duplica ed F agmen ed Missing
BUSCO 895 (93.8%) 887 (93.0%) 8 (0.8%) 21 (2.2%) 38 (4.0%)
OMA k 2,009 (93.31%) 1,890 (87.78%) 119 (5.53%) - 144 (6.69%)
Consis en Inconsis en Con aminan s Unknown
OMA k 9,706 (74.74%) 1,163 (8.96%) 0 (0.0%) 2,118 (16.31%)
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Open Pee Re iew
Cu en Pee Re iew S a us:
Ve sion 1
Re iewe Repo 27 Sep embe 2025
h ps://doi.o g/10.21956/open eseu ope.22118. 60078
© 2025 Ma ín-Du án J. This is an open access pee e iew epo dis ibu ed unde he e ms o he C ea i e
Commons A ibu ion License, which pe mi s un es ic ed use, dis ibu ion, and ep oduc ion in any medium,
p o ided he o iginal wo k is p ope ly ci ed.
José M Ma ín-Du án
Queen Ma y Uni e si y o London, London, England, UK
This genome no e epo s he genome assembly and anno a ion o he jewelled squid
S igma o eu his a c u i. This is an impo an da ase and esou ce o he s udy o oceanic
cephalopods ha will bene i mul iple esea ch ields, om phylogenomics and e olu iona y
biology o ecology. S eng hs: This is a gold-s anda d, high-quali y esou ce. The genome
assembly comes wi h an anno a ion, which will allow immedia e e-use o he da a; Weaknesses:
none.
Is he a ionale o c ea ing he da ase (s) clea ly desc ibed?
Yes
A e he p o ocols app op ia e and is he wo k echnically sound?
Yes
A e su icien de ails o me hods and ma e ials p o ided o allow eplica ion by o he s?
Yes
A e he da ase s clea ly p esen ed in a useable and accessible o ma ?
Yes
Compe ing In e es s: No compe ing in e es s we e disclosed.
Re iewe Expe ise: E o-De o, compa a i e genomics and epigenomics
I con i m ha I ha e ead his submission and belie e ha I ha e an app op ia e le el o
expe ise o con i m ha i is o an accep able scien i ic s anda d.
Re iewe Repo 16 Sep embe 2025
Open Resea ch Eu ope
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Open Resea ch Eu ope 2025, 5:270 Las upda ed: 27 SEP 2025
h ps://doi.o g/10.21956/open eseu ope.22118. 60081
© 2025 Yoshida M. This is an open access pee e iew epo dis ibu ed unde he e ms o he C ea i e
Commons A ibu ion License, which pe mi s un es ic ed use, dis ibu ion, and ep oduc ion in any medium,
p o ided he o iginal wo k is p ope ly ci ed.
Masa-Aki Yoshida
Shimane Uni e si y, Shiman, Japan
O e all, he s udy is well documen ed and appea s publishable; howe e , o he bene i o u u e
ela ed esea ch, he ollowing mino poin should be add essed.
As he au ho s hemsel es no e, genomic analysis o pelagic squid emains limi ed and
incomple e. Simply es ima ing genome size by compa ison wi h o he species is no accep able.
Al hough he assembled size appea s consis en , bo h genome size and ch omosome numbe
should be independen ly alida ed using al e na i e me hods.
Is he a ionale o c ea ing he da ase (s) clea ly desc ibed?
Yes
A e he p o ocols app op ia e and is he wo k echnically sound?
Yes
A e su icien de ails o me hods and ma e ials p o ided o allow eplica ion by o he s?
Yes
A e he da ase s clea ly p esen ed in a useable and accessible o ma ?
Yes
Compe ing In e es s: No compe ing in e es s we e disclosed.
Re iewe Expe ise: Bioin o ma ics, Genomics
I con i m ha I ha e ead his submission and belie e ha I ha e an app op ia e le el o
expe ise o con i m ha i is o an accep able scien i ic s anda d.
Open Resea ch Eu ope
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