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species_definitions
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species_definitions
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# This file is where you can define species for particular RefSeq assemblies,
# overriding the RefSeq species labels. Simply add lines to this file which
# have the RefSeq assembly accession (starts with GCF) followed by a tab and
# then the binomial species name. The version number (e.g. final .1) does not
need to be included in the accession.
# Example:
# GCF_000000000 Genus species
# What follows are my species redefinitions of assemblies in Enterobacterales.
# Some species assignments are clear based on the tree structure, and I was
# able to assign names without checking the literature.
GCF_001281565 Proteus mirabilis
GCF_001808035 Proteus mirabilis
GCF_000512315 Morganella morganii
GCF_001807955 Morganella morganii
GCF_900075225 Klebsiella aerogenes
GCF_900077035 Klebsiella aerogenes
GCF_900083685 Raoultella ornithinolytica
GCF_900083755 Raoultella planticola
GCF_000648315 Raoultella planticola
GCF_001049875 Raoultella planticola
GCF_002108615 Raoultella planticola
GCF_900083925 Serratia marcescens
GCF_900083935 Escherichia coli
GCF_001286085 Escherichia albertii
GCF_002035305 Salmonella enterica
GCF_000408845 Escherichia coli
GCF_000157115 Escherichia coli
GCF_000159895 Escherichia coli
GCF_000158415 Escherichia coli
GCF_000336365 Serratia plymuthica
GCF_000214195 Serratia plymuthica
GCF_000214805 Serratia plymuthica
GCF_000800945 Plesiomonas shigelloides
GCF_000611875 Tatumella ptyseos
GCF_002843235 Providencia rettgeri
GCF_002215245 Pantoea ananatis
GCF_001537385 Serratia marcescens
GCF_001537265 Serratia marcescens
GCF_001808215 Serratia marcescens
GCF_001011075 Serratia marcescens
GCF_000747565 Serratia marcescens
GCF_001714765 Serratia marcescens
GCF_900215455 Serratia marcescens
GCF_001642805 Serratia marcescens
GCF_002752455 Serratia marcescens
GCF_002752475 Serratia marcescens
GCF_000695995 Serratia marcescens
GCF_900215445 Serratia marcescens
GCF_002797215 Serratia marcescens
GCF_001060475 Serratia marcescens
GCF_001060695 Serratia marcescens
GCF_001062045 Serratia marcescens
GCF_001984565 Serratia marcescens
GCF_001066285 Serratia marcescens
GCF_002751955 Serratia marcescens
GCF_002751935 Serratia marcescens
GCF_002752085 Serratia marcescens
GCF_002752255 Serratia marcescens
GCF_002752235 Serratia marcescens
GCF_002752095 Serratia marcescens
GCF_002752135 Serratia marcescens
GCF_002752155 Serratia marcescens
GCF_002752265 Serratia marcescens
GCF_002752195 Serratia marcescens
GCF_002752535 Serratia marcescens
GCF_002752435 Serratia marcescens
GCF_002752495 Serratia marcescens
GCF_001076875 Serratia marcescens
GCF_000330865 Serratia rubidaea
GCF_001692375 Serratia fonticola
GCF_001808015 Citrobacter koseri
GCF_001275405 Xenorhabdus griffiniae
GCF_001422565 Rouxiella silvae
# This assembly was labelled 'Enterobacter sp. CC120223-11' but it isn't
# particularly close to other species in Enterobacter. It's closest relatives
# are Pluralibacter, but it's sufficiently distant that it might deserve a
# genus name of its own.
GCF_900215375 Unknown unknown
# These seven isolates were sequenced in Chen 2017. In this paper they were
# described as 'Erwiniaceae-like' and were therefore labelled with the genus
# Erwinia. However, their closest named relatives are in the genus Izhakiella,
# so that's were I'm putting them.
GCF_002751995 Izhakiella unknown
GCF_002752015 Izhakiella unknown
GCF_002752025 Izhakiella unknown
GCF_002752055 Izhakiella unknown
GCF_002752075 Izhakiella unknown
GCF_002752165 Izhakiella unknown
GCF_002752595 Izhakiella unknown
# This assembly was labelled 'Klebsiella sp. RIT-PI-d', but it is nowhere near
# other Klebsiella, so I think it deserves its own genus.
GCF_001187865 Unknown unknown
# This genome was introduced by Su 2012. It certainly deserves a new species
# name, probably a new genus too, but they didn't propose one in the paper,
# just calling it strain LSJC7.
GCF_000302695 Unknown unknown
# This assembly was labelled 'Enterobacteriaceae bacterium B14', but the paper
# which introduced it (Park 2012) proposed a genus and species name for it,
# which I've used here.
GCF_000307305 Galloisinimonas intestini
# These two assemblies were labelled as Serratia, but are nowhere near the
# rest of Serratia. Their closest relatives are in the genus Dickeya, but they
# are an outgroup and so maybe deserve their own genus.
GCF_000463345 Unknown unknown
GCF_002847015 Unknown unknown
# This assembly was labelled as 'Serratia sp. M24T3', but it is clearly
# nestled amongst Rouxiella, so I've named it as such.
GCF_000257645 Rouxiella unknown
# Pseudocitrobacter is a new genus introduced in Kämpfer 2014, were they
# defined two species, faecalis and anthropi. This assembly (which was
# labelled as Enterobacter) is moderately and equally close to both of those
# species, and so I've put it in that genus but left its species as 'unknown'.
GCF_000330845 Pseudocitrobacter unknown
# Klebsiella pneumoniae and related species are defined well in Brisse 2014
# and Holt 2015. Many isolates are misnamed because previously the entire
# group was called K. pneumoniae. More recently, Long 2017 defined a new
# species, quasivariicola. A significant clade without a species name remains,
# which I currently call Kp5 (Blin 2017). This may end up being a subspecies
# of K. variicola or perhaps its own species.
GCF_000349245 Klebsiella quasipneumoniae
GCF_000367165 Klebsiella quasipneumoniae
GCF_000827665 Klebsiella quasipneumoniae
GCF_001033805 Klebsiella quasipneumoniae
GCF_001033915 Klebsiella quasipneumoniae
GCF_001034125 Klebsiella quasipneumoniae
GCF_001278905 Klebsiella quasipneumoniae
GCF_001280925 Klebsiella quasipneumoniae
GCF_900113365 Klebsiella quasipneumoniae
GCF_900119505 Klebsiella quasipneumoniae
GCF_900119585 Klebsiella quasipneumoniae
GCF_900176555 Klebsiella quasipneumoniae
GCF_900100145 Klebsiella quasipneumoniae
GCF_900102285 Klebsiella quasipneumoniae
GCF_900102775 Klebsiella quasipneumoniae
GCF_900104465 Klebsiella quasipneumoniae
GCF_900107525 Klebsiella quasipneumoniae
GCF_900109625 Klebsiella quasipneumoniae
GCF_900114145 Klebsiella quasipneumoniae
GCF_900119545 Klebsiella quasipneumoniae
GCF_900119605 Klebsiella quasipneumoniae
GCF_900099865 Klebsiella quasipneumoniae
GCF_900101145 Klebsiella quasipneumoniae
GCF_900101155 Klebsiella quasipneumoniae
GCF_900101255 Klebsiella quasipneumoniae
GCF_900101775 Klebsiella quasipneumoniae
GCF_900103095 Klebsiella quasipneumoniae
GCF_900103465 Klebsiella quasipneumoniae
GCF_900107085 Klebsiella quasipneumoniae
GCF_900107425 Klebsiella quasipneumoniae
GCF_900107805 Klebsiella quasipneumoniae
GCF_900108445 Klebsiella quasipneumoniae
GCF_900109975 Klebsiella quasipneumoniae
GCF_900110325 Klebsiella quasipneumoniae
GCF_900110725 Klebsiella quasipneumoniae
GCF_900111335 Klebsiella quasipneumoniae
GCF_900113165 Klebsiella quasipneumoniae
GCF_900113475 Klebsiella quasipneumoniae
GCF_900114985 Klebsiella quasipneumoniae
GCF_900115525 Klebsiella quasipneumoniae
GCF_900119465 Klebsiella quasipneumoniae
GCF_002288845 Klebsiella quasipneumoniae
GCF_002752865 Klebsiella quasipneumoniae
GCF_900093045 Klebsiella quasipneumoniae
GCF_900093195 Klebsiella quasipneumoniae
GCF_900093365 Klebsiella quasipneumoniae
GCF_900093375 Klebsiella quasipneumoniae
GCF_900093395 Klebsiella quasipneumoniae
GCF_900093405 Klebsiella quasipneumoniae
GCF_900173195 Klebsiella quasipneumoniae
GCF_900173205 Klebsiella quasipneumoniae
GCF_900173215 Klebsiella quasipneumoniae
GCF_900173225 Klebsiella quasipneumoniae
GCF_900173255 Klebsiella quasipneumoniae
GCF_900173535 Klebsiella quasipneumoniae
GCF_900173555 Klebsiella quasipneumoniae
GCF_900174385 Klebsiella quasipneumoniae
GCF_900174395 Klebsiella quasipneumoniae
GCF_900174425 Klebsiella quasipneumoniae
GCF_900173815 Klebsiella quasipneumoniae
GCF_900173845 Klebsiella quasipneumoniae
GCF_900173855 Klebsiella quasipneumoniae
GCF_900173865 Klebsiella quasipneumoniae
GCF_900173875 Klebsiella quasipneumoniae
GCF_900174325 Klebsiella quasipneumoniae
GCF_001373075 Klebsiella quasipneumoniae
GCF_001463185 Klebsiella quasipneumoniae
GCF_001466765 Klebsiella quasipneumoniae
GCF_900084845 Klebsiella quasipneumoniae
GCF_900084875 Klebsiella quasipneumoniae
GCF_900084895 Klebsiella quasipneumoniae
GCF_900085235 Klebsiella quasipneumoniae
GCF_900085435 Klebsiella quasipneumoniae
GCF_900086305 Klebsiella quasipneumoniae
GCF_900086455 Klebsiella quasipneumoniae
GCF_900092845 Klebsiella quasipneumoniae
GCF_900093305 Klebsiella quasipneumoniae
GCF_900171795 Klebsiella quasipneumoniae
GCF_900172505 Klebsiella quasipneumoniae
GCF_900172515 Klebsiella quasipneumoniae
GCF_900172535 Klebsiella quasipneumoniae
GCF_900172595 Klebsiella quasipneumoniae
GCF_900172635 Klebsiella quasipneumoniae
GCF_001052595 Klebsiella pneumoniae
GCF_001054225 Klebsiella pneumoniae
GCF_900092915 Klebsiella pneumoniae
GCF_900093145 Klebsiella pneumoniae
GCF_000195655 Klebsiella pneumoniae
GCF_001308905 Klebsiella pneumoniae
GCF_000238715 Klebsiella pneumoniae
GCF_001030715 Klebsiella pneumoniae
GCF_001030745 Klebsiella pneumoniae
GCF_900084675 Klebsiella pneumoniae
GCF_001443245 Klebsiella pneumoniae
GCF_001717795 Klebsiella pneumoniae
GCF_001808265 Klebsiella pneumoniae
GCF_900084925 Klebsiella pneumoniae
GCF_002850275 Klebsiella pneumoniae
GCF_900083665 Klebsiella pneumoniae
GCF_900084005 Klebsiella pneumoniae
GCF_900084685 Klebsiella pneumoniae
GCF_900085055 Klebsiella pneumoniae
GCF_001052475 Klebsiella pneumoniae
GCF_001557575 Klebsiella pneumoniae
GCF_001006625 Klebsiella variicola
GCF_000019565 Klebsiella variicola
GCF_000163075 Klebsiella variicola
GCF_000398905 Klebsiella variicola
GCF_000786375 Klebsiella variicola
GCF_000986855 Klebsiella variicola
GCF_001006575 Klebsiella variicola
GCF_001033825 Klebsiella variicola
GCF_001317095 Klebsiella variicola
GCF_001463685 Klebsiella variicola
GCF_001549975 Klebsiella variicola
GCF_001620885 Klebsiella variicola
GCF_001807645 Klebsiella variicola
GCF_001807705 Klebsiella variicola
GCF_001808325 Klebsiella variicola
GCF_002156765 Klebsiella variicola
GCF_002724035 Klebsiella variicola
GCF_002810575 Klebsiella variicola
GCF_002810595 Klebsiella variicola
GCF_002837625 Klebsiella variicola
GCF_900084135 Klebsiella variicola
GCF_900085165 Klebsiella variicola
GCF_900084205 Klebsiella variicola
GCF_900084295 Klebsiella variicola
GCF_900084765 Klebsiella variicola
GCF_900084775 Klebsiella variicola
GCF_900084795 Klebsiella variicola
GCF_900084995 Klebsiella variicola
GCF_900085015 Klebsiella variicola
GCF_900085175 Klebsiella variicola
GCF_900085185 Klebsiella variicola
GCF_900085825 Klebsiella variicola
GCF_900086175 Klebsiella variicola
GCF_900086385 Klebsiella variicola
GCF_900171785 Klebsiella variicola
GCF_900171975 Klebsiella variicola
GCF_900171985 Klebsiella variicola
GCF_900173285 Klebsiella variicola
GCF_900173315 Klebsiella variicola
GCF_900174165 Klebsiella variicola
GCF_900174175 Klebsiella variicola
GCF_900173385 Klebsiella variicola
GCF_900173565 Klebsiella variicola
GCF_900174345 Klebsiella variicola
GCF_900174355 Klebsiella variicola
GCF_900174375 Klebsiella variicola
GCF_900173705 Klebsiella variicola
GCF_900173715 Klebsiella variicola
GCF_900174035 Klebsiella variicola
GCF_900174115 Klebsiella variicola
GCF_900175105 Klebsiella variicola
GCF_002837615 Klebsiella variicola
GCF_001548315 Klebsiella Kp5
GCF_002806645 Klebsiella Kp5
GCF_002806655 Klebsiella Kp5
GCF_002806695 Klebsiella Kp5
GCF_002810615 Klebsiella Kp5
GCF_002810635 Klebsiella Kp5
GCF_002837655 Klebsiella Kp5
GCF_002810475 Klebsiella Kp5
GCF_002810535 Klebsiella Kp5
GCF_002810545 Klebsiella Kp5
GCF_002810495 Klebsiella Kp5
GCF_002810515 Klebsiella Kp5
GCF_900087855 Klebsiella Kp5
GCF_000523395 Klebsiella quasivariicola
GCF_002186515 Klebsiella quasivariicola
GCF_900172085 Klebsiella quasivariicola
GCF_900174015 Klebsiella quasivariicola
# Klebsiella oxytoca and its related species were recently defined in Passet
# 2017. One unnamed clade remains, which here I have left as 'unknown'.
# The remaining clade I called Ko4 based on the sequences from the
# phylogenetic groups given in Fevre 2005. It may become either a subspecies
# of grimontii or its own species.
# FYI: phylogroup Ko1 is now michiganensis, Ko2 is now oxytoca and Ko6 is now
# grimontii. I haven't seen Ko3 in full genomes, and I don't have a reference
# sequence for Ko5.
GCF_001809025 Klebsiella oxytoca
GCF_001808475 Klebsiella oxytoca
GCF_000427015 Klebsiella grimontii
GCF_000733495 Klebsiella grimontii
GCF_001052235 Klebsiella grimontii
GCF_001052825 Klebsiella grimontii
GCF_001053665 Klebsiella grimontii
GCF_001060405 Klebsiella grimontii
GCF_001054995 Klebsiella grimontii
GCF_001070955 Klebsiella grimontii
GCF_001072735 Klebsiella grimontii
GCF_001072835 Klebsiella grimontii
GCF_001076805 Klebsiella grimontii
GCF_001065765 Klebsiella grimontii
GCF_001066775 Klebsiella grimontii
GCF_001548355 Klebsiella grimontii
GCF_001633115 Klebsiella grimontii
GCF_002090195 Klebsiella grimontii
GCF_002080105 Klebsiella grimontii
GCF_002556465 Klebsiella grimontii
GCF_002559635 Klebsiella grimontii
GCF_002856195 Klebsiella grimontii
GCF_002880715 Klebsiella grimontii
GCF_900083595 Klebsiella grimontii
GCF_900083605 Klebsiella grimontii
GCF_900200035 Klebsiella grimontii
GCF_900083805 Klebsiella michiganensis
GCF_900083835 Klebsiella michiganensis
GCF_900083695 Klebsiella michiganensis
GCF_000293135 Klebsiella michiganensis
GCF_000524315 Klebsiella michiganensis
GCF_000714655 Klebsiella michiganensis
GCF_001022195 Klebsiella michiganensis
GCF_001753185 Klebsiella michiganensis
GCF_001970835 Klebsiella michiganensis
GCF_002072655 Klebsiella michiganensis
GCF_002111445 Klebsiella michiganensis
GCF_002906395 Klebsiella michiganensis
GCF_002906415 Klebsiella michiganensis
GCF_002906435 Klebsiella michiganensis
GCF_900083565 Klebsiella michiganensis
GCF_900083575 Klebsiella michiganensis
GCF_900083635 Klebsiella michiganensis
GCF_900083825 Klebsiella michiganensis
GCF_900083885 Klebsiella michiganensis
GCF_900083915 Klebsiella michiganensis
GCF_900084035 Klebsiella michiganensis
GCF_001807845 Klebsiella michiganensis
GCF_000247915 Klebsiella Ko4
GCF_001057685 Klebsiella Ko4
GCF_002186735 Klebsiella Ko4
GCF_001065705 Klebsiella Ko4
# Raoultella terrigena (sometimes called Klebsiella terrigena) is a bit
# unclear, though Drancount 2001 sheds some light on its relationship to other
# Raoultella species. There is an outgroup to the rest of terrigena
# (GCF_002270295) which I've here called 'unknown', but should perhaps be
# included with terrigena.
GCF_000829965 Raoultella terrigena
GCF_002270295 Raoultella unknown
# This assembly was a decent but not perfect match for the 1GB strain of
# Raoultella electrica (Kimura 2014). Due to the assembly's lack of any close
# neighbours in the tree, I decided it was close enough and labelled it as
# electrica.
GCF_002806725 Raoultella electrica
# Kluyvera georgiana doesn't have many representatives, but based on the
# phylogeny in Pavan 2005, I'm confident in renaming this one ascorbata
# assembly as georgiana.
GCF_001682915 Kluyvera georgiana
# This assembly, named Klebsiella aerogenes in NCBI, is very close to an
# Atlantibacter hermannii assembly. Based on the relationships in Hata 2016,
# I think this assembly should also be hermannii, as the other Atlantibacter
# species (subterranea) is much more distantly related.
GCF_000878365 Atlantibacter hermannii
# Cedecea davisae and Cedeceaneteri form a clade, but the third species
# (lapagei) was only only applied to a mislabelled Lelliottia, What I've
# currently defined as neteri has some very deep branches, so I wonder if the
# real lapagei is in there.
GCF_900177785 Cedecea neteri
GCF_000277545 Cedecea neteri
GCF_000963575 Cedecea neteri
# Walk 2009 and Luo 2011 described five 'crytic' lineages of E. coli, which
# aren't part of E. coli, called clades I-V. Liu 2015 named clade-5 as
# Escherichia marmotae, which I've gone with here.
GCF_000190955 Escherichia clade-1
GCF_001650555 Escherichia clade-1
GCF_002133995 Escherichia clade-1
GCF_002134215 Escherichia clade-1
GCF_002531355 Escherichia clade-1
GCF_000190995 Escherichia clade-1
GCF_000208545 Escherichia clade-1
GCF_001910995 Escherichia clade-1
GCF_001911065 Escherichia clade-1
GCF_001911405 Escherichia clade-1
GCF_001912385 Escherichia clade-1
GCF_001912565 Escherichia clade-1
GCF_000194175 Escherichia clade-1
GCF_000194575 Escherichia clade-1
GCF_002133425 Escherichia clade-1
GCF_000208485 Escherichia clade-1
GCF_000687125 Escherichia clade-1
GCF_000703725 Escherichia clade-1
GCF_000812765 Escherichia clade-1
GCF_001264195 Escherichia clade-1
GCF_001911145 Escherichia clade-1
GCF_001912235 Escherichia clade-1
GCF_001912525 Escherichia clade-1
GCF_002207125 Escherichia clade-1
GCF_002810695 Escherichia clade-1
GCF_002901325 Escherichia clade-1
GCF_001660175 Escherichia clade-2
GCF_000208445 Escherichia clade-3
GCF_000208465 Escherichia clade-3
GCF_000398885 Escherichia clade-3
GCF_000407925 Escherichia clade-3
GCF_000407765 Escherichia clade-3
GCF_000459855 Escherichia clade-3
GCF_000208525 Escherichia clade-4
GCF_000601195 Escherichia clade-4
GCF_002110245 Escherichia clade-4
GCF_000208565 Escherichia marmotae
GCF_000350705 Escherichia marmotae
GCF_000408525 Escherichia marmotae
GCF_002573245 Escherichia marmotae
GCF_002573255 Escherichia marmotae
GCF_000408325 Escherichia marmotae
GCF_000408805 Escherichia marmotae
GCF_001561675 Escherichia marmotae
GCF_002109985 Escherichia marmotae
# The Buttiauxella genus doesn't have many representatives, but I think that
# GCF_000737905 is misnamed based on the trees in Alnajar 2017.
GCF_000737905 Buttiauxella noackiae
# These changes are pretty straightforward and are backed by the phylogeny in
# Jackson 2015.
GCF_000485925 Siccibacter turicensis
GCF_000486025 Siccibacter turicensis
# Walterson 2015 provides a nice overview of Pantoea, which I used to guide
# renaming of this genus. Some of the species in that paper were not in the
# tree: wallisii, gavinae and deleyi. Some species were in the tree in two
# incompatible locations (e.g. rodasii was in two very separate branches), so
# I've renamed the ones incompatible with the type strains as 'unknown'.
GCF_001641135 Pantoea allii
GCF_000731025 Pantoea brenneri
GCF_001743465 Pantoea brenneri
GCF_002233725 Pantoea brenneri
GCF_000255315 Pantoea anthophila
GCF_000784875 Pantoea eucrina
GCF_001881025 Pantoea eucrina
GCF_002207995 Pantoea dispersa
GCF_000220605 Pantoea agglomerans
GCF_000952095 Pantoea agglomerans
GCF_001238615 Pantoea agglomerans
GCF_001264395 Pantoea agglomerans
GCF_900068865 Pantoea agglomerans
GCF_002082355 Pantoea agglomerans
GCF_000745295 Pantoea vagans
GCF_001558735 Pantoea vagans
GCF_002554555 Pantoea vagans
GCF_000179655 Pantoea eucalypti
GCF_000330765 Pantoea eucalypti
GCF_000816655 Pantoea eucalypti
GCF_900167425 Pantoea eucalypti
GCF_000784965 Pantoea calida
GCF_000738765 Pantoea septica
GCF_001067555 Pantoea septica
GCF_002313185 Pantoea septica
GCF_000759475 Pantoea unknown
GCF_000773965 Pantoea unknown
GCF_000801085 Pantoea unknown
GCF_001506165 Pantoea unknown
GCF_002749715 Pantoea unknown
GCF_900215435 Pantoea unknown
GCF_900068835 Pantoea unknown
GCF_900068855 Pantoea unknown
GCF_900068845 Pantoea unknown
# These two assemblies are very distant from everything else (and from each
# other). While they were labelled as Enterobacter/Pantoea, I judged them to
# be sufficiently unique to not belong to either of those genera.
GCF_001922585 Unknown unknown
GCF_002837195 Unknown unknown
# GCF_001691555.1 is interesting - it was labelled as Pantoea eucrina, and it
# does form a clade with the rest of eucrina, but it is quite separate from
# the others. I left it as eucrina, but wouldn't be surprised if it gets a
# separate species name in the future.
# There were a couple odd Serratia species in the tree: ureilytica and
# nematodiphila. These were both clearly within the marcescens clade, so I've
# renamed them to marcescens.
GCF_000988045 Serratia marcescens
GCF_000738675 Serratia marcescens
GCF_900101535 Serratia marcescens
GCF_002082115 Serratia marcescens
GCF_002185265 Serratia marcescens
GCF_900005125 Serratia marcescens
# Ribeiro 2015 and Ribeiro 2017 (2 papers) provided nice phylogenies of
# Citrobacter.
# Strain A316 was odd - in one of the papers, Riberio put it as an outgroup
# of freundii, but in my tree it looked like an outgroup of portucalensis
# instead, so I've left it as unknown.
# Citrobacter youngae was also a problem. The strain ATCC 29220 which was
# labelled as youngae was very different from the youngae defined in Ribeiro's
# papers. I went with Ribeiro's and changed ATCC 29220 to Citrobacter unknown.
GCF_000208765 Citrobacter braakii
GCF_000398845 Citrobacter braakii
GCF_000398865 Citrobacter braakii
GCF_000972645 Citrobacter braakii
GCF_001273815 Citrobacter braakii
GCF_001689745 Citrobacter braakii
GCF_002289385 Citrobacter braakii
GCF_002850715 Citrobacter braakii
GCF_002903215 Citrobacter braakii
GCF_900169625 Citrobacter braakii
GCF_900169695 Citrobacter braakii
GCF_001022685 Citrobacter braakii
GCF_000692115 Citrobacter europaeus
GCF_000783995 Citrobacter europaeus
GCF_001922445 Citrobacter europaeus
GCF_002073755 Citrobacter europaeus
GCF_002786865 Citrobacter europaeus
GCF_000692135 Citrobacter amalonaticus
GCF_000809165 Citrobacter amalonaticus
GCF_001297795 Citrobacter amalonaticus
GCF_900112055 Citrobacter amalonaticus
GCF_000158355 Citrobacter portucalensis
GCF_000521945 Citrobacter portucalensis
GCF_001037485 Citrobacter portucalensis
GCF_001037515 Citrobacter portucalensis
GCF_001037585 Citrobacter portucalensis
GCF_001281005 Citrobacter portucalensis
GCF_001317135 Citrobacter portucalensis
GCF_001317155 Citrobacter portucalensis
GCF_001867255 Citrobacter portucalensis
GCF_001880775 Citrobacter portucalensis
GCF_002796485 Citrobacter portucalensis
GCF_002903305 Citrobacter portucalensis
GCF_000648515 Citrobacter werkmanii
GCF_001721255 Citrobacter werkmanii
GCF_001570325 Citrobacter werkmanii
GCF_001570345 Citrobacter werkmanii
GCF_000277565 Citrobacter freundii
GCF_000313895 Citrobacter freundii
GCF_000398825 Citrobacter freundii
GCF_001034445 Citrobacter freundii
GCF_001034475 Citrobacter freundii
GCF_001034485 Citrobacter freundii
GCF_001037505 Citrobacter freundii
GCF_001037575 Citrobacter freundii
GCF_001586835 Citrobacter freundii
GCF_001586845 Citrobacter freundii
GCF_000739675 Citrobacter murliniae
GCF_001037495 Citrobacter murliniae
GCF_002386385 Citrobacter gillenii
GCF_001034465 Citrobacter youngae
GCF_001559235 Citrobacter youngae
GCF_002151815 Citrobacter youngae
GCF_002863945 Citrobacter youngae
GCF_001463265 Citrobacter sedlakii
# This strain of Citrobacter (Y19) was labelled as amalonaticus but seems to
# be its own species, slightly closer to Citrobacter farmeri.
GCF_000981805 Citrobacter unknown
# These two Citrobacters are relatively close and belong in the same species.
# They probably deserve their own species name, but could possibly be included
# with amalonaticus, the closest named group.
GCF_001559075 Citrobacter unknown
GCF_002880615 Citrobacter unknown
# These three assemblies were labelled Citrobacter freundii, Enterobacter
# cloacae and Citrobacter sp. A316. I've decided to group them in with
# portucalensis, with which they form a clade. However, they may deserve their
# own species name, especially GCF_002042945.1 which is the outgroup of the
# rest.
GCF_000238735 Citrobacter portucalensis
GCF_900077125 Citrobacter portucalensis
GCF_002042945 Citrobacter portucalensis
# This assembly was labelled Citrobacter youngae but is an outgroup to
# Citrobacter werkmanii. It wasn't close enough for me to include with
# werkmanii, however, so I've left it unknown.
GCF_000155975 Citrobacter unknown
# For Hafnia, the genus seems to originally have had one species, alvei, but
# this was later split into two species: alvei and paralvei (Huys 2010).
# 'Obesumbacterium proteus' appeared within the alvei clade, but based on
# The phylogeny and comments seen on some websites, I've reclassified it as
# Hafnia alvei:
# http://www.tgw1916.net/Enterobacteria/Obesumbacterium.html
# http://www.bacterio.net/obesumbacterium.html
GCF_000185685 Hafnia paralvei
GCF_000239255 Hafnia paralvei
GCF_001559255 Hafnia paralvei
GCF_001816025 Hafnia paralvei
GCF_002355555 Hafnia alvei
GCF_001586165 Hafnia alvei
GCF_001655035 Hafnia alvei
# The Proteus genus was quite messy. Proteus mirabilis was clear, but
# vulgaris/hauseri/columbiae were all mixed up. I used O’Hara 2000 to sort out
# some of the classifications. Hyun 2016 and Dai 2018 helped with some of the
# more recently named species. Proteus terrae and inconstans weren't present
# in the assemblies, and many unnamed clades remain.
GCF_002184635 Proteus vulgaris
GCF_001049955 Proteus penneri
GCF_001939795 Proteus cibarius
GCF_002749905 Proteus cibarius
GCF_002607735 Proteus alimentorum
GCF_001722135 Proteus unknown
GCF_001742985 Proteus unknown
GCF_001049975 Proteus unknown
GCF_000497855 Proteus unknown
GCF_002206145 Proteus unknown
GCF_002591155 Proteus unknown
# Providencia was mostly straightforward, except for one odd assembly:
# GCF_001853385. This was labelled as 'stuartii' and there is a paper
# describing its genome sequence: Yuan 2017. However, it is very distant from
# the other stuartii genomes, sufficiently so to be a different species, so
# here I label it as 'unknown'.
GCF_001853385 Providencia unknown
# Xenorhabdus has a lot of species, but there was relatively little conflict
# to sort out. The assembly of 'Xenorhabdus stockiae' had two moderately close
# relatives, which I've relabelled as stockiae here. However, the more distant
# of the two (GCF_002632765) might be considered a different species, so this
# could change. Only one assembly (GCF_000798625, strain NBAII XenSa04)
# remains unnamed.
GCF_002632865 Xenorhabdus stockiae
GCF_002632765 Xenorhabdus stockiae
# Edwardsiella had some recent species definitions. I went with the ones given
# in Bujan 2017.
GCF_000020865 Edwardsiella piscicida
GCF_000146305 Edwardsiella piscicida
GCF_000804515 Edwardsiella piscicida
GCF_001186215 Edwardsiella anguillarum
GCF_000711175 Edwardsiella anguillarum
GCF_000800725 Edwardsiella anguillarum
# There are only two species in Trabulsiella, but it still proved difficult.
# Trabulsiella odontotermitis was first described in Chou 2007. Then in 2015,
# Sapountzis sequenced two more isolates that they called odontotermitis, but
# these are quite distinct from other odontotermitis isolates. There appears
# to be three species: guamensis and two separate groups both named
# odontotermitis. I have left the name odontotermitis on the assemblies which
# match the Chou 2007 odontotermitis and changed the more recently described
# Sapountzis 2015 isolates to 'unknown' - they probably deserve a species
# name of their own.
GCF_001188485 Trabulsiella unknown
GCF_001188495 Trabulsiella unknown
# Enterobacter is a particularly messy genus. I used Paauw 2008 to guide my
# species assignments for the Enterobacter cloacae complex. E roggenkapii was
# a newer name I got from Sutton 2018.
#
# Paauw Hoffmann
# cluster clusters species
# -----------------------------------
# 1 3 E. hormaechei
# 2 6, 8 E. hormaechei
# 3 11, 12 E. cloacae
# 4 5 E. ludwigii
# 5 1 E. asburiae
# 6 2 E. kobei
# 7 4 E. roggenkampii
#
# These are the Hoffmann groups not represented in Paauw 2008:
#
# ? 7 E. hormaechei
# ? 9 E. bugandensis
# ? 10 Lelliottia nimipressuralis
#
# So according to this scheme, the 'real' E. cloacae are Hoffmann groups 11
# and 12.
# cluster 1 -> hormaechei
# cluster 2 -> hormaechei
# cluster 4 -> ludwigii
# cluster 5 -> asburiae
# cluster 6 -> kobei
# The remaining clusters (3 and 7) as well as other unnamed clades in the
# cloacae complex were left as Enterobacter cloacae, making that a
# polyphyletic group.
# I found assemblies labelled as 'Enterobacter xiangfangensis' to be scattered
# throughout the cloacae complex, so I did not use that species name.
# 'Enterobacter nickellidurans' best matched to within the asburiae clade, so
# I didn't use that name either.
GCF_000315775 Enterobacter hormaechei
GCF_000492455 Enterobacter hormaechei
GCF_001469415 Enterobacter hormaechei
GCF_900076045 Enterobacter hormaechei
GCF_000492495 Enterobacter hormaechei
GCF_000492575 Enterobacter hormaechei
GCF_000492615 Enterobacter hormaechei
GCF_000492715 Enterobacter hormaechei
GCF_000492855 Enterobacter hormaechei
GCF_000534035 Enterobacter hormaechei
GCF_000534175 Enterobacter hormaechei
GCF_000534195 Enterobacter hormaechei
GCF_000534215 Enterobacter hormaechei
GCF_000534295 Enterobacter hormaechei
GCF_000534455 Enterobacter hormaechei
GCF_000534635 Enterobacter hormaechei
GCF_000724505 Enterobacter hormaechei
GCF_000750225 Enterobacter hormaechei
GCF_000750275 Enterobacter hormaechei
GCF_000784905 Enterobacter hormaechei
GCF_000783855 Enterobacter hormaechei
GCF_000952315 Enterobacter hormaechei
GCF_000958805 Enterobacter hormaechei
GCF_001022435 Enterobacter hormaechei
GCF_001030145 Enterobacter hormaechei
GCF_001030195 Enterobacter hormaechei
GCF_001037565 Enterobacter hormaechei
GCF_000478345 Enterobacter hormaechei
GCF_002151865 Enterobacter hormaechei
GCF_000534755 Enterobacter hormaechei
GCF_000474785 Enterobacter hormaechei
GCF_001037845 Enterobacter hormaechei
GCF_002201815 Enterobacter hormaechei
GCF_900075045 Enterobacter hormaechei
GCF_900075525 Enterobacter hormaechei
GCF_900075905 Enterobacter hormaechei
GCF_900075925 Enterobacter hormaechei
GCF_900076095 Enterobacter hormaechei
GCF_900076425 Enterobacter hormaechei
GCF_900076505 Enterobacter hormaechei
GCF_900076655 Enterobacter hormaechei
GCF_900076665 Enterobacter hormaechei
GCF_900076685 Enterobacter hormaechei
GCF_900077635 Enterobacter hormaechei
GCF_900077965 Enterobacter hormaechei
GCF_900078125 Enterobacter hormaechei
GCF_900078135 Enterobacter hormaechei
GCF_000474805 Enterobacter hormaechei
GCF_000492975 Enterobacter hormaechei
GCF_000534475 Enterobacter hormaechei
GCF_000534595 Enterobacter hormaechei
GCF_000534615 Enterobacter hormaechei
GCF_000534655 Enterobacter hormaechei
GCF_000534715 Enterobacter hormaechei
GCF_000534775 Enterobacter hormaechei
GCF_000633795 Enterobacter hormaechei
GCF_001037735 Enterobacter hormaechei
GCF_002204935 Enterobacter hormaechei
GCF_002204945 Enterobacter hormaechei
GCF_002204955 Enterobacter hormaechei
GCF_002204965 Enterobacter hormaechei
GCF_000692315 Enterobacter hormaechei
GCF_900074995 Enterobacter hormaechei
GCF_900075055 Enterobacter hormaechei
GCF_900075115 Enterobacter hormaechei
GCF_900075155 Enterobacter hormaechei
GCF_900075275 Enterobacter hormaechei
GCF_900075325 Enterobacter hormaechei
GCF_900075675 Enterobacter hormaechei
GCF_900075835 Enterobacter hormaechei
GCF_900075865 Enterobacter hormaechei
GCF_900076195 Enterobacter hormaechei
GCF_900076215 Enterobacter hormaechei
GCF_900076315 Enterobacter hormaechei
GCF_900076705 Enterobacter hormaechei
GCF_900076965 Enterobacter hormaechei
GCF_900077255 Enterobacter hormaechei
GCF_900077415 Enterobacter hormaechei
GCF_900077435 Enterobacter hormaechei
GCF_900077445 Enterobacter hormaechei
GCF_900077565 Enterobacter hormaechei
GCF_900077595 Enterobacter hormaechei
GCF_900077825 Enterobacter hormaechei
GCF_900077865 Enterobacter hormaechei
GCF_900077915 Enterobacter hormaechei
GCF_900078035 Enterobacter hormaechei
GCF_900078095 Enterobacter hormaechei
GCF_000534395 Enterobacter hormaechei
GCF_001037665 Enterobacter hormaechei
GCF_000747015 Enterobacter hormaechei
GCF_002055735 Enterobacter hormaechei
GCF_002087625 Enterobacter hormaechei
GCF_900075345 Enterobacter hormaechei
GCF_900075355 Enterobacter hormaechei
GCF_900075665 Enterobacter hormaechei
GCF_900076005 Enterobacter hormaechei
GCF_900076065 Enterobacter hormaechei
GCF_900076225 Enterobacter hormaechei
GCF_900076445 Enterobacter hormaechei
GCF_900077025 Enterobacter hormaechei
GCF_900077375 Enterobacter hormaechei
GCF_900077455 Enterobacter hormaechei
GCF_000534415 Enterobacter hormaechei
GCF_001037835 Enterobacter hormaechei
GCF_000534495 Enterobacter hormaechei
GCF_000692235 Enterobacter hormaechei
GCF_001037595 Enterobacter hormaechei
GCF_001037815 Enterobacter hormaechei
GCF_002152945 Enterobacter hormaechei
GCF_900075015 Enterobacter hormaechei
GCF_900075625 Enterobacter hormaechei
GCF_900075955 Enterobacter hormaechei
GCF_900075965 Enterobacter hormaechei
GCF_900077475 Enterobacter hormaechei
GCF_900077935 Enterobacter hormaechei
GCF_900077945 Enterobacter hormaechei
GCF_000534535 Enterobacter hormaechei
GCF_000534555 Enterobacter hormaechei
GCF_000534575 Enterobacter hormaechei
GCF_000534735 Enterobacter hormaechei
GCF_000949365 Enterobacter hormaechei
GCF_000952195 Enterobacter hormaechei
GCF_000952215 Enterobacter hormaechei
GCF_000952275 Enterobacter hormaechei
GCF_000952285 Enterobacter hormaechei
GCF_000952355 Enterobacter hormaechei
GCF_000952405 Enterobacter hormaechei
GCF_000952415 Enterobacter hormaechei
GCF_000952455 Enterobacter hormaechei
GCF_000952475 Enterobacter hormaechei
GCF_000952495 Enterobacter hormaechei
GCF_000952505 Enterobacter hormaechei
GCF_000952515 Enterobacter hormaechei
GCF_000952555 Enterobacter hormaechei
GCF_000952585 Enterobacter hormaechei
GCF_000952595 Enterobacter hormaechei
GCF_000952655 Enterobacter hormaechei
GCF_000952665 Enterobacter hormaechei
GCF_000952675 Enterobacter hormaechei
GCF_000952755 Enterobacter hormaechei
GCF_000958665 Enterobacter hormaechei
GCF_000958695 Enterobacter hormaechei
GCF_000958725 Enterobacter hormaechei
GCF_000958745 Enterobacter hormaechei
GCF_000958765 Enterobacter hormaechei
GCF_000958815 Enterobacter hormaechei
GCF_000958825 Enterobacter hormaechei
GCF_000958845 Enterobacter hormaechei
GCF_000958925 Enterobacter hormaechei
GCF_001010875 Enterobacter hormaechei
GCF_001025045 Enterobacter hormaechei
GCF_001025055 Enterobacter hormaechei
GCF_001922365 Enterobacter hormaechei
GCF_002192395 Enterobacter hormaechei
GCF_002204775 Enterobacter hormaechei
GCF_900076175 Enterobacter hormaechei
GCF_002161915 Enterobacter hormaechei
GCF_002161935 Enterobacter hormaechei
GCF_000534675 Enterobacter hormaechei
GCF_000534695 Enterobacter hormaechei
GCF_000534795 Enterobacter hormaechei
GCF_001022015 Enterobacter hormaechei
GCF_001022055 Enterobacter hormaechei
GCF_001022075 Enterobacter hormaechei
GCF_001022255 Enterobacter hormaechei
GCF_000770745 Enterobacter hormaechei
GCF_002237465 Enterobacter hormaechei
GCF_000783835 Enterobacter hormaechei
GCF_900077875 Enterobacter hormaechei
GCF_002177145 Enterobacter hormaechei
GCF_002184665 Enterobacter hormaechei
GCF_002185845 Enterobacter hormaechei
GCF_000938355 Enterobacter hormaechei
GCF_900074975 Enterobacter hormaechei
GCF_900076255 Enterobacter hormaechei
GCF_900076265 Enterobacter hormaechei
GCF_900077485 Enterobacter hormaechei
GCF_900077495 Enterobacter hormaechei
GCF_001276405 Enterobacter hormaechei
GCF_001276425 Enterobacter hormaechei
GCF_002151935 Enterobacter hormaechei
GCF_900075985 Enterobacter hormaechei
GCF_900077505 Enterobacter hormaechei
GCF_900076345 Enterobacter hormaechei
GCF_900076375 Enterobacter hormaechei
GCF_900076395 Enterobacter hormaechei
GCF_900076455 Enterobacter hormaechei
GCF_900076865 Enterobacter hormaechei
GCF_002264185 Enterobacter hormaechei
GCF_900075685 Enterobacter hormaechei
GCF_001487035 Enterobacter hormaechei
GCF_002416525 Enterobacter hormaechei
GCF_002416535 Enterobacter hormaechei
GCF_900075105 Enterobacter hormaechei
GCF_900075185 Enterobacter hormaechei
GCF_900075205 Enterobacter hormaechei
GCF_900075215 Enterobacter hormaechei
GCF_900075255 Enterobacter hormaechei
GCF_900075365 Enterobacter hormaechei
GCF_900075415 Enterobacter hormaechei
GCF_900075505 Enterobacter hormaechei
GCF_900075535 Enterobacter hormaechei
GCF_900075635 Enterobacter hormaechei
GCF_900075795 Enterobacter hormaechei
GCF_900076135 Enterobacter hormaechei
GCF_900076155 Enterobacter hormaechei
GCF_900076355 Enterobacter hormaechei
GCF_900076605 Enterobacter hormaechei
GCF_900076745 Enterobacter hormaechei
GCF_900076845 Enterobacter hormaechei
GCF_900076975 Enterobacter hormaechei
GCF_900077185 Enterobacter hormaechei
GCF_900077355 Enterobacter hormaechei
GCF_900077515 Enterobacter hormaechei
GCF_900077815 Enterobacter hormaechei
GCF_900077975 Enterobacter hormaechei
GCF_900078115 Enterobacter hormaechei