Ho izon al Gene T ans e in Asga d A chaea
Saioa Manzano-Mo ales∗†, Toni Gabald´
on∗†‡
∗Ba celona Supe compu ing Cen e , Ba celona, Spain
†Ins i u e o Resea ch in Biomedicine (IRB Ba celona), The Ba celona Ins i u e o Science and Technology, Ba celona, Spain
‡Ins i uci´
on Ca alana de In es igaci´
on y Es udios A anzados, Ba celona, Spain
E-mail: [email p o ec ed], [email p o ec ed]
Keywo ds—Ho izon al Gene T ans e , Asga d A chaea, Re icu-
la e e olu ion, euka yogenesis.
I. EXTENDED ABSTRACT
Asga d a chaea a e conside ed o be he closes p oka yo ic
ela i e o euka yo es [1]. They ha bo many o wha we e
p e iously hough o be euka yo e-exclusi e p o eins [1],
including ac in and ac in- ela ed p o eins [2], and he p esence
o an ac in cy oskele on in pa icula has been p o en in an
isola ed Lokia chaeum [3]. As such, hey a e a key playe
in he deba e su ounding he o igin o euka yo es (a p ocess
called euka yogenesis) [4].
Being p oka yo es, he genome e olu ion o he Asga d
A chaea is likely o ha e been shaped in no small pa by
Ho izon al Gene T ans e (HGT), ha is, he ans e o gene ic
ma e ial be ween o ganisms ha a e no bound by a pa en -
o sp ing ela ionship [5]. These ans e ed genes o en encode
o p o eins ha a e bene icial o he cell and allow o
adap a ion o new niches [6].
In his wo k, we aim o un eil he ac ion o he Asga d
p o ein epe oi e ha s ems om ho izon al ans e e en s, by
applying a HGT de ec ion pipeline ha combines homology-
based and phylogeny-based me hods. By analyzing he unc-
ional ca ego ies and pu a i e dono s o hese genes, we hope
o unde s and mo e abou he e olu ion o Asga d a chaeal
genomes, so ha we can employ his knowledge o shed
ligh on he pu a i e ecology and ela ionships o he a chaeal
pa ne o he symbiosis ha would gi e ise o euka yo ic
cells.
A. HGT de ec ion pipeline
The genomic sequences and p o ein p edic ions o he
cul u ed isola es Candida us P ome heoa chaeum syn oph-
icum MK-D1 [7] (assembly accession GCF-008000775.1) and
Candida us Lokia chaeum ossi e um/Lokia chaeum sp. B-35
[3] (GenBank code CP104013.1) we e downloaded om NCBI
Assembly and NCBI Nucleo ide/P o ein, espec i ely.
We pe o med a simila i y sea ch wi h BLAST 2.11.0 [8]
o he p o eomes agains a cus om-made da abase comp ised
o all he species ep esen a i es o he Genome Taxonomy
Da abase [9] species ep esen a i es and p o eomes om a
cu a ed se o euka yo es, o ob ain a su icien ly ep esen a i e
sampling o p o ein sequences ac oss he T ee o Li e.
We pa sed he BLAST esul s wi h HGTec o [10], which
sys ema ically analyzes BLAST esul s looking o hi dis ibu-
ion pa e ns incong uen wi h a e ical e olu ion, gi en a se-
ies o hie a chically de ined e olu iona y ca ego ies. This s ep
Fig. 1. HGT de ec ion pipeline
iden i ied pu a i e ho izon ally- ans e ed genes: o hose,
we e ie ed he bes 150 hi s and econs uc ed a gene ee
ollowing he algo i hm implemen ed o PhylomeDB [11]. We
u he analyzed he esul ing gene ees wi h Abaccus [12],
which iden i ies axonomical “jumps” in gene ees ha do
no ollow he species ee and he e o e u he helps disce n
pu a i e HGT e en s. Las ly, we pe o med a manual cu a ion
wi h an e e3-based in-house sc ip [13] o u he il e ou
alse posi i es and o assess he accep o and dono clades.
B. Resul s
Table I displays he numbe o pu a i ely ans e ed genes
pe s ep in he pipeline and o ganism. 9.39% and 6.94% o
he p o ein con en o Ca. Lokia chaeum ossi e um and Ca.
P ome heoa chaeum syn ophicum, espec i ely, is o bac e ial
o igin.
The ans e e en s ha e occu ed o e a se ies o ime-
poin s ac oss he Asga d lineage 2: om genus-le el o
ans e s ha p ecede he di e si ica ion o he Loki lineage.
In e es ingly, he e is a high deg ee o pa aphyly, wi h many
ins ances o he Asga d lineage o ming wo (o mo e) clades:
one ha b anches close o A chaea ( he e o e, likely a copy o
e ical inhe i ance) and one ha b anches close o a bac e ial
clade ( he e o e, a likely ans e ). This implies some deg ee
TABLE I. NUMBER OF HORIZONTALLY TRANSFERRED GENES)
O ganism P o . HGTec o Abaccus HGTs
Ca. L. ossi e um 5119 717 513 481 (442)
Ca. P. syn ophicum 3890 432 359 270 (256)
ossi e um
syn ophicum
Lokia chaeum AMARA-1 CR-4 Lokia chaeia Asga da chaeo a P ome heoa chaeum AMARA-1 CR-4 Lokia chaeia Asga da chaeo a
0
30
60
90
120
T ans e pa ne
Numbe o HGT ees
monophyly_lineage
False
T ue
A
ossi e um
syn ophicum
Lokia chaeum AMARA-1 CR-4 Lokia chaeia Asga da chaeo a P ome heoa chaeum AMARA-1 CR-4 Lokia chaeia Asga da chaeo a
0
30
60
90
120
T ans e pa ne
Numbe o HGT ees
monophyly_Asga d
False
T ue
B
Fig. 2. Ba plo displaying he numbe o ees pe ans e accep o . (A) Monophyly o he accep o lineage. (B) Monophyly o he Asga d a chaea.
o subs i u ion o e ically-inhe i ed copies by ans e ed
ones, and a co-exis ence o bo h sou ces ac oss he Asga d
clade. Independen ans e e en s also canno be uled ou .
These ans e s come om a wide a ange o dono phyla,
wi h p ominen dono s being Fi micu es and Chlo o lexo a,
ollowed by P o eobac e ia, Spi ochaeo a, Desul obac e io a
and Bac e oido a. The con ibu ion o Desul obac e o a is
pa icula ly in e es ing, as sul a e- educing bac e ia a e known
syn ophic pa ne s o hese Asga d a chaea. The con ibu ion
o Anae olineae wi hin Chlo o lexo a is also non- i ial, since
his lineage is known o inhabi ma ine sedimen s, a habi a
whe e hese Lokia chaeia ha e been sampled.
We ound ins ances o bo h Bac e ia- o-Asga d and Asga d-
o-Bac e ia ans e , implying bidi ec ional low be ween ans-
e pa ne s.
T ans e ed genes seem o be en iched in me abolic unc-
ions, mainly ela ed o lipid and amino acid me abolism, unc-
ions ha seem cen al o he unc ions o he cell. They seem
o mainly be componen s o he memb ane (GO:0016021), and
he e is a high deg ee o o e lap be ween bo h Lokia chaeia.
C. Conclusion
In his s udy, we obse e HGT e en s o be widesp ead
ac oss Asga d e olu ion, cons i u ing a con inuous low o
ans e ed genes a di e en poin s in he di e si ica ion o
hese a chaea, and coming om a a ie y o dono s, some o
which can be linked by a me abolic o ecologic ela ionship.
II. ACKNOWLEDGMENT
This esea ch was suppo ed by Go don and Be y Moo e
Founda ion (G an GBMF9742).
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Saioa Manzano-Mo ales ecei ed his BSc deg ee
in Biochemis y and Molecula Biology om he
Uni e si y o he Basque Coun y (UPV-EHU), Spain
in 2019. She hen comple ed he MSc deg ee in
Compu a ional Biology om he Poli echnical Uni-
e si y o Mad id, Spain in 2021. A e a b ie
in e nship in he CIB Ma ga i a Salas (CSIC), she
has been wi h he Compa a i e Genomics g oup o
Ba celona Supe compu ing Cen e (BSC), whe e she
is de eloping he PhD.