title: Genomic exaptation enables Lasius niger adaptation to urban environments.
abstract: The world is rapidly urbanizing, and only a subset of species are able to succeed in stressful city environments. Efficient genome-enabled stress response appears to be a likely prerequisite for urban adaptation. Despite the important role ants play in the ecosytem, only the genomes of ~13 have been sequenced so far. Here, we present the draft genome assembly of the black garden ant Lasius niger - the most successful urban inhabitant of all ants - and we compare it with the genomes of other ant species, including the closely related Camponotus floridanus.
  
  
  
  Sequences from 272 M Illumina reads were assembled into 41,406 contigs with total length of 245 MB, and N50 of 16,382 bp, similar to other ant genome assemblies enabling comparative genomic analysis. Remarkably, the predicted proteome of L. niger is significantly enriched relative to other ant genomes in terms of abundance of domains involved in nucleic acid binding, DNA repair, and nucleotidyl transferase activity, reflecting transposable element proliferation and a likely genomic response. With respect to environmental stress, we note a proliferation of various detoxification genes, including glutatione-S-transferases and those in the cytochrome P450 families. Notably, the CYP9 family is highly expanded with 19 complete and 21 nearly complete members - over twice as many compared to other ants. This family exhibits the signatures of strong directional selection, with eleven positively selected positions in ligand-binding pockets of enzymes. Gene family contraction was detected for several components of the olfactory system, accompanied by instances of both directional selection and relaxation.
  
  
  
  Our results suggest that the success of L. niger in urbanized areas may be the result of fortuitous coincidence of several factors, including the expansion of the CYP9 cytochrome family due to coevolution with parasitic fungi, the diversification of DNA repair systems as an answer to proliferation of retroelements, and the reduction of olfactory system and behavioral preadaptations from non-territorial subdominant life strategies found in natural environments. Diversification of cytochromes and DNA repair systems along with reduced odorant communication are the basis of L. niger pollutant resistance and polyphagy, while non-territorial and mobilization strategies allows more efficient exploitation of large but patchy food sources.
authors.affiliation: Faculty of Biology, Department of Evolution, Lomonosov Moscow State University, Moscow, Russian Federation.
authors.forename: Evgenii A
authors.initials: EA
authors.lastname: Konorov
authors.affiliation: Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation.|Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.
authors.forename: Mikhail A
authors.initials: MA
authors.lastname: Nikitin
authors.affiliation: Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation.|Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation.
authors.forename: Kirill V
authors.initials: KV
authors.lastname: Mikhailov
authors.affiliation: Faculty of Biology, Department of Evolution, Lomonosov Moscow State University, Moscow, Russian Federation.
authors.forename: Sergey N
authors.initials: SN
authors.lastname: Lysenkov
authors.affiliation: Faculty of Biology, Department of Evolution, Lomonosov Moscow State University, Moscow, Russian Federation.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Belenky
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA.
authors.forename: Peter L
authors.initials: PL
authors.lastname: Chang
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA.|Department of Applied Mathematics & Mathematical Biology and Bioinformatics Laboratory, St.Petersburg State Polytechnical University, St.Petersburg, 195251, Russia.
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Nuzhdin
authors.affiliation: Faculty of Biology, Department of Evolution, Lomonosov Moscow State University, Moscow, Russian Federation. skobei-khanum@yandex.ru.
authors.forename: Victoria A
authors.initials: VA
authors.lastname: Scobeyeva
mesh_terms: D000064:Acclimatization; D000222:Adaptation, Physiological; D000818:Animals; D001000:Ants / Q000201:enzymology / Q000235:genetics* / Q000382:microbiology / Q000502:physiology; D001483:Base Sequence; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000072472:Cytochrome P450 Family 6 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004251:DNA Transposable Elements; D005658:Fungi / Q000235:genetics; D049750:Genome, Insect; D023281:Genomics; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D018035:Receptors, Odorant / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D018035:Receptors, Odorant; D003577:Cytochrome P-450 Enzyme System; D000072472:Cytochrome P450 Family 6
keywords: Detoxification; Directional selection; Draft genome; Lasius niger; Transposable element; Urban environment