Two new cytotypes reinforce that <Emphasis Type="Italic">Micronycteris hirsuta</Emphasis> Peters, 1869 does not represent a monotypic taxon

Background

The genus Micronycteris is a diverse group of phyllostomid bats currently comprising 11 species, with diploid number (2n) ranging from 26 to 40 chromosomes. The karyotypic relationships within Micronycteris and between Micronycteris and other phyllostomids remain poorly understood. The karyotype of Micronycteris hirsuta is of particular interest: three different diploid numbers were reported for this species in South and Central Americas with 2n?=?26, 28 and 30 chromosomes. Although current evidence suggests some geographic differentiation among populations of M. hirsuta based on chromosomal, morphological, and nuclear and mitochondrial DNA markers, the recognition of new species or subspecies has been avoided due to the need for additional data, mainly chromosomal data.

Results

We describe two new cytotypes for Micronycteris hirsuta (MHI) (2n?=?26 and 25, NF?=?32), whose differences in diploid number are interpreted as the products of Robertsonian rearrangements. C-banding revealed a small amount of constitutive heterochromatin at the centromere and the NOR was located in the interstitial portion of the short arm of a second pair, confirmed by FISH. Telomeric probes hybridized to the centromeric regions and weakly to telomeric regions of most chromosomes. The G-banding analysis and chromosome painting with whole chromosome probes from Carollia brevicauda (CBR) and Phyllostomus hastatus (PHA) enabled the establishment of genome-wide homologies between MHI, CBR and PHA.

Conclusions

The karyotypes of Brazilian specimens of Micronycteris hirsuta described here are new to Micronycteris and reinforce that M. hirsuta does not represent a monotypic taxon. Our results corroborate the hypothesis of karyotypic megaevolution within Micronycteris, and strong evidence for this is that the entire chromosome complement of M. hirsuta was shown to be derivative with respect to species compared in this study.

     

Cytogenetic evidences on the evolutionary relationships between the tetraploids of the section <Emphasis Type="Italic">Rhizomatosae</Emphasis> and related diploid species (<Emphasis Type="Italic">Arachis</Emphasis>, Leguminosae)

Rhizomatosae is a taxonomic section of the South American genus Arachis, whose diagnostic character is the presence of rhizomes in all its species. This section is of particular evolutionary interest because it has three polyploid (A. pseudovillosa, A. nitida and A. glabrata, 2n?=?4x?=?40) and only one diploid (A. burkartii, 2n?=?2x?=?20) species. The phylogenetic relationships of these species as well as the polyploidy nature and the origin of the tetraploids are still controversial. The present study provides an exhaustive analysis of the karyotypes of all rhizomatous species and six closely related diploid species of the sections Erectoides and Procumbentes by cytogenetic mapping of DAPI/CMA heterochromatin bands and 5S and 18–26S rDNA loci. Chromosome banding showed variation in the DAPI heterochromatin distribution pattern, which, together with the number and distribution of rDNA loci, allowed the characterization of all species studied here. The bulk of chromosomal markers suggest that the three rhizomatous tetraploid species constitute a natural group and may have at least one common diploid ancestor. The cytogenetic data of the diploid species analyzed evidenced that the only rhizomatous diploid species—A. burkartii—has a karyotype pattern different from those of the rhizomatous tetraploids, showing that it is not likely the genome donor of the tetraploids and the non-monophyletic nature of the section Rhizomatosae. Thus, the tetraploid species should be excluded from the R genome, which should remain exclusively for A. burkartii. Instead, the karyotype features of these tetraploids are compatible with those of different species of the sections Erectoides and Procumbentes (E genome species), suggesting the hypothesis of multiple origins of these tetraploids. In addition, the polyploid nature and the group of diploid species closer to the tetraploids are discussed.     

Chromosomal polymorphism in the populations of malaria mosquito <Emphasis Type="Italic">Anopheles messeae</Emphasis> (Diptera,Culicidae) in the Volga region

We studied the species composition and chromosomal variability of malaria mosquitoes in the Volga Basin (Upper, Middle, and Lower Volga regions). We investigated larvae karyotypes of sibling species of the Anopheles maculipennis group. We calculated the frequencies of chromosomal inversions in the local populations of the dominant species An. messeae. We discovered that karyotypic structure of An. messeae populations depends on landscape-climatic zones. Populations of the Upper, Middle and Lower Volga differ in frequency of chromosome inversions XL, 2R, 3R, and 3L.     

Mechanisms of karyotype evolution in the Brazilian scorpions of the subfamily Centruroidinae (Buthidae)

The recently-revised subfamily Centruroidinae is part of the New World clade of buthid scorpions. In this study, we analyzed the cytogenetic characteristics of nine of the 10 Brazilian centruroidines, and one undescribed species of the genus Ischnotelson, using a phylogenetic approach to determine the chromosomal rearrangements responsible for the differentiation of karyotypes among the species. The cytogenetic data recorded in the present study supported the new taxonomic arrangement of the Centruroidinae, with all the species of the same genus sharing the same or similar diploid numbers, i.e., 2n?=?20 or 22 in Troglorhopalurus lacrau and T. translucidus, 2n?=?25 or 26 in Ischnotelson sp., I. guanambiensis and I. peruassu, and 2n?=?28 in Jaguajir agamemnon, J. pintoi and J. rochae. The karyotype modelling in the ChromEvol software indicated 2n?=?18 as the ancestral diploid number of the Centruroidinae. The differentiation of karyotypes among the centruroidine genera was based on increasing chromosome numbers resulting from progressive fission events. These changes probably occurred prior to the diversification of the genera Ischnotelson, Jaguajir, Physoctonus and Rhopalurus, and appear to have played a more important role in karyotype evolution at the intergeneric level than the interspecific one. However, the observed increase in diploid numbers was not accompanied by changes in the number or location of ribosomal genes or telomeric sequences. The identification of meiotic cells in female specimens also allowed us to discuss the mechanisms of achiasmatic meiosis in scorpions.     

Chromosomal studies in <Emphasis Type="Italic">Crenicichla lepidota</Emphasis> and <Emphasis Type="Italic">Australoheros facetus</Emphasis> (Cichlidae,Perciformes) from extreme Southern Brazil

Fishes of the family Cichlidae generally show low karyotype variability. Nevertheless, karyotype variants have been identified within some genera, providing information about their evolutionary history. In the present study, karyotype characteristics of Crenicichla lepidota and Australoheros facetus, two sympatric species found in the São Gonçalo-Mangueira basin, were studied. Besides conventional procedures, double fluorochromes staining chromomycin A₃/DAPI and fluorescent in situ hybridization (FISH) with rDNA probes were also used. Both species presented 2n = 48 chromosomes, but karyotypes were differentiated by fundamental number, which was equal to 70 in A. facetus and 56 in C. lepidota. Similar heterochromatin distribution patterns were also observed on the pericentromeric region of most chromosomes, although C. lepidota presented an additional heterochromatic block in the first pair. The Ag-NORs, 18S rDNA probe and CMA₃/DAPI were coincident in location on the first and second pairs of C. lepidota and A. facetus, respectively. The minor rDNA loci (5S rDNA) were found in four sites located on two distinct chromosomal pairs in C. lepidota. Although the data obtained here to C. lepidota and to A. facetus show chromosomal characteristics considered ancestral to the family, new data are presented to both species. Additionally, this study corroborates the hypothesis in which evolutionary processes like non-Robertsonian rearrangements are involved in the diversification of the major groups of Neotropical Cichlidae. Thus, the karyotype diversification observed in A. facetus have the high fundamental number pathway while C. lepidota has others evolutionary chromosomal mechanisms.     

Molecular cytogenetic analysis of DNA from pericentric heterochromatin of chromosome 2L of malaria mosquito <Emphasis Type="Italic">Anopheles beklemishevi</Emphasis> (culicidae,Diptera)

Using the method of microdissection of polytene chromosomes, followed by in situ hybridization, chromosomal localization of region-specific DNA probe from pericentic heterochromatin of chromosome 2L of Anopheles beklemishevi Stegnii et Kabanova was examined on polytene chromosomes of Anopheles atroparvus van Thiel, An. messeae Fall, and An. beklemishevi. DNA sequences homologous to the probe used were found in all species examined on chromosomes 2 and 3 in pericentric regions and in attachment regions. The exclusion were the attachment regions of chromosome XL in An. beklemishevi and An. messeae, and pericentric region of arm 2R in An. messeae. Pericentric α -heterochromatin of arm 2L in An. messeae and arm 3R in An. atroparvus also contained no sequences homologous to the DNA probe. The data obtained were compared with the earlier obtained data on localization of species-specific probe from the segment of chromosome 2R of An. atroparvus on chromosomes of An. artoparvus, An. messeae, and An. beklemishevi. The differences between the species in the sites of probes localization and fluorescence intensity revealed pointed to the existence of individual sequence associations in the regions of chromosomes attachment.     

Centromeric and non-centromeric satellite DNA organisation differs in holocentric <Emphasis Type="Italic">Rhynchospora</Emphasis> species

Satellite DNA repeats (or satDNA) are fast-evolving sequences usually associated with condensed heterochromatin. To test whether the chromosomal organisation of centromeric and non-centromeric satDNA differs in species with holocentric chromosomes, we identified and characterised the major satDNA families in the holocentric Cyperaceae species Rhynchospora ciliata (2n = 10), R. globosa (2n = 50) and R. tenuis (2n = 2x = 4 and 2n = 4x = 8). While conserved centromeric repeats (present in R. ciliata and R. tenuis) revealed linear signals at both chromatids, non-centromeric, species-specific satDNAs formed distinct clusters along the chromosomes. Colocalisation of both repeat types resulted in a ladder-like hybridisation pattern at mitotic chromosomes. In interphase, the centromeric satDNA was dispersed while non-centromeric satDNA clustered and partly colocalised to chromocentres. Despite the banding-like hybridisation patterns of the clustered satDNA, the identification of chromosome pairs was impaired due to the irregular hybridisation patterns of the homologues in R. tenuis and R. ciliata. These differences are probably caused by restricted or impaired meiotic recombination as reported for R. tenuis, or alternatively by complex chromosome rearrangements or unequal condensation of homologous metaphase chromosomes. Thus, holocentricity influences the chromosomal organisation leading to differences in the distribution patterns and condensation dynamics of centromeric and non-centromeric satDNA.     

Evolution of blue-flowered species of genus <Emphasis Type="Italic">Linum</Emphasis> based on high-throughput sequencing of ribosomal RNA genes

Background

The species relationships within the genus Linum have already been studied several times by means of different molecular and phylogenetic approaches. Nevertheless, a number of ambiguities in phylogeny of Linum still remain unresolved. In particular, the species relationships within the sections Stellerolinum and Dasylinum need further clarification. Also, the question of independence of the species of the section Adenolinum still remains unanswered. Moreover, the relationships of L. narbonense and other species of the section Linum require further clarification. Additionally, the origin of tetraploid species of the section Linum (2n?=?30) including the cultivated species L. usitatissimum has not been explored. The present study examines the phylogeny of blue-flowered species of Linum by comparisons of 5S rRNA gene sequences as well as ITS1 and ITS2 sequences of 35S rRNA genes.

Results

High-throughput sequencing has been used for analysis of multicopy rRNA gene families. In addition to the molecular phylogenetic analysis, the number and chromosomal localization of 5S and 35S rDNA sites has been determined by FISH.Our findings confirm that L. stelleroides forms a basal branch from the clade of blue-flowered flaxes which is independent of the branch formed by species of the sect. Dasylinum. The current molecular phylogenetic approaches, the cytogenetic analysis as well as different genomic DNA fingerprinting methods applied previously did not discriminate certain species within the sect. Adenolinum. The allotetraploid cultivated species L. usitatissimum and its wild ancestor L. angustifolium (2n?=?30) could originate either as the result of hybridization of two diploid species (2n?=?16) related to the modern L. gandiflorum and L. decumbens, or hybridization of a diploid species (2n?=?16) and a diploid ancestor of modern L. narbonense (2n?=?14).

Conclusions

High-throughput sequencing of multicopy rRNA gene families allowed us to make several adjustments to the phylogeny of blue-flowered flax species and also reveal intra- and interspecific divergence of the rRNA gene sequences.

     

Chromosomal locations of U2 snDNA clusters in <Emphasis Type="Italic">Megaleporinus</Emphasis>, <Emphasis Type="Italic">Leporinus</Emphasis> and <Emphasis Type="Italic">Schizodon</Emphasis> (Characiformes: Anostomidae)

The U small nuclear RNA (U snRNA) genes comprise a multigene family and are required for splicing of pre-mRNA. In this paper, we aimed to study the chromosomal location of the U2 snRNA gene in Megaleporinus, Leporinus and Schizodon species, which constitute interesting models for the study of repetitive DNA and genomic evolution in fish once the group comprises species with and without heteromorphic sex chromosomes. The all six species showed 2n?=?54 chromosomes: Megaleporinus elongatus, Megaleporinus macrocephalus, Leporinus striatus, Leporinus friderici, Schizodon borelli and Schizodon isognathus. The U2 snDNA clusters were evident in only one medium-sized submetracentric pair in all analyzed species and this may represent a condition shared by Anostomidae family.     

Karyotype characteristics of <Emphasis Type="Italic">Chironomus fraternus</Emphasis> Wülker and <Emphasis Type="Italic">Ch. beljaninae</Emphasis> Wülker (Diptera,Chironomidae) from Northern Russia

Karyotypes of Chironomus fraternus Wülker (2n = 8) (cytocomplex thummi) and Ch. beljaninae Wülker (2n = 6) (cytocomplex modified thummi) from the aberratus group are described. Both species are recorded for the first time for the Russian fauna. Their karyotypes are similar in the banding sequences of chromosome arms A, C, D, E, and F, which suggests that Ch. fraternus and Ch. beljaninae are sister species. Besides the chromosome number, the two species differ in some karyotype markers, the amount of heterochromatin in the centromeres, and the chromosome arm combinations (AB, CD, EF, G in Ch. fraternus and GAB, CD, EF in Ch. beljaninae).     

Molecular and cytogenic analysis of pericentromeric heterochromatin in ovarian nurse cells of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> subgroup species

Evolutionary rearrangements of pericentromeric heterochromatin among Drosophila melanogaster subgroup species have been investigated. A region-specific DNA library from Drosophila orena ovarian nurse cell chromocenter was obtained by the microdissection of polythene chromosomes. The probe has been localized on chromosomes of ovarian nurse cells of Drosophila melanogaster subgroup species using fluorescent hybridization in situ. Sequences homologous to the sequences of the DNA probe were detected in the chromocenter and pericentromeric regions of D. orena polythene chromosomes, in all pericentromeric regions of other species with several exceptions. There was no labeling on one of the arms of the D. simulans chromosome 2; however, these sequences were present on the telomere of D. erecta chromosome 3 and in regions adjacent to the brightly DAPI-stained heterochromatin blocks of D. yakuba, D. santomea and D. teissieri chromosomes 2 and 3. At the S₆ stage (secondary reticulate nucleus), labeled chromatin can be found mostly within a restricted territory in D. orena nucleus; no such chromatin can be detected throughout the rest of the nucleus. On the contrary, at this stage, in nuclei of other species, labeled DNA is spread diffusely.     

Comparative cytogenetic analysis of four species of <Emphasis Type="Italic">Dendropsophus</Emphasis> (Hylinae) from the Brazilian Atlantic forest

We conducted a cytogenetic study of four hyline frog species (Dendropsophus elegans, D. microps, D. minutus and D. werneri) from southern Brazil. All species had 2n = 30 chromosomes, with interspecific and intraspecific variation in the numbers of metacentric, submetacentric, subtelocentric and telocentric chromosomes. C-banding and fluorochrome staining revealed conservative GC-rich heterochromatin localized in the pericentromeric regions of all species. The location of the nucleolus organizer regions, as confirmed by fluorescent in situ hybridization, differed between species. Telomeric probes detected sites that were restricted to the terminal regions of all chromosomes and no interstitial or centromeric signals were observed. Our study corroborates the generic synapomorphy of 2n = 30 chromosomes for Dendropsophus and adds data that may become useful for future taxonomic revisions and a broader understanding of chromosomal evolution among hylids.     

Multi-approach analysis of the diversity in <Emphasis Type="Italic">Colletotrichum cliviae</Emphasis> sensu lato

Colletotrichum cliviae is a fungal species reported both as pathogen and endophyte with broad geographical distribution. Some purported isolates of this species have been assigned to different taxa, including Colletotrichum aracearum, Colletotrichum orchidearum and Colletotrichum. sichuanensis, for which a preliminary analysis of extensive multilocus (ACT, GAPDH, ITS, TUB2) data in this study revealed high sequence similarity with C. cliviae. We further reassessed the species delineation by using the coalescent method of the generalized mixed Yule-coalescent (GMYC) and Poisson Tree Processes (PTP). Single and multilocus gene trees strongly supported a C. cliviae s. lat. clade including the four species. This clade unfolded eight subclades grouped into three distinct lineages, but no monophyly of any of the four species. GMYC and PTP analyses confidently supported the evolutionary independence of these lineages. C. sichuanensis and C. cliviae, except one isolate, formed the largest lineage. The second lineage was made up of isolates named C. aracearum and some of C. orchidearum sharing the haplotype and the third lineage accommodated two isolates named C. cliviae and C. orchidearum. This finding suggests the synonymization of C. sichuanensis with C. cliviae whereas the taxonomic status of C. aracearum and C. orchidearum still needs clarification. This study lays great stress upon the use of comprehensive data for sequence-based characterisation of species in the C. cliviae s. lat. It also presents the first report of C. cliviae in tropical Africa and on citrus host.     

The contribution of foliar micromorphology and anatomy to the circumscription of species within the <Emphasis Type="Italic">Chusquea ramosissima</Emphasis> informal group (Poaceae,Bambusoideae, Bambuseae)

Chusquea is a diverse but monophyletic genus of Neotropical woody bamboos from primarily montane forests that comprises four well-supported lineages: subg. Magnifoliae, subg. Platonia, subg. Rettbergia, and the Euchusquea clade (comprising subg. Swallenochloa and subg. Chusquea). However, the relationships among clades or taxa within the Euchusquea clade inferred from molecular data are mostly not congruent with those inferred from morphological evidence, consequently limiting our ability to understand species relationships. In this study we generated foliar micromorphological and anatomical data for the Chusquea ramosissima informal group (Chusquea ramosissima, C. tenella, and C. tenuiglumis), and for the putative new species from Bolivia in this group, in order to test the value of these types of data for defining species and to seek potential synapomorphies for this group. Our results demonstrate that epidermal features, mainly with regard to the stomatal apparatus, proved to be more valuable in distinguishing species than anatomical characters. The presence of horizontally elongated silica cells over the veins and adaxial arm cells with invaginations from the abaxial side was shared by all the studied species but is not unique to this group. The type of trichomes, shape of silica bodies, type of arm cells, and midrib structure may be useful to lesser degree. All four species exhibited intraspecific variation in development of the papillae on the long cells. Support for the recognition of the new species from Bolivia is provided by micromorphological characters. An identification key based on leaf blade features is provided for the four studied species.     

A comparative cytogenetic study of the tetraploid oat species with the A and C genomes: <Emphasis Type="Italic">Avena insularis,A. magna</Emphasis>, and <Emphasis Type="Italic">A. murphyi</Emphasis>

C-banding of chromosomes and in situ hybridization with the probes pTa71 and pTa794 were used for a comparative cytogenetic study of the three tetraploid oat species with the A and C genomes: Avena insularis, A. magna, and A. murphyi. These species were similar in the structure and C-banding patterns of several chromosomes as well as in the location of the loci 5S rRNA genes and major NOR sites; however, they differed in the number and localization of minor 45S rDNA loci as well as in the morphology and distribution of heterochromatin in some chromosomes. According to the data obtained, A. insularis is closer to A. magna, whereas A. murphyi is somewhat separated from these two species. Presumably, all the three studied species originated from the same tetraploid ancestor, and their divergence is connected with various species-specific chromosome rearrangements. The evolution of A. murphyi is likely to have occurred independently of the other two species.     

Further progress towards the delimitation of <Emphasis Type="Italic">Cheilanthes</Emphasis> (Cheilanthoideae,Pteridaceae), with emphasis on South American species

Cheilanthoid ferns (Cheilanthoideae sensu PPG 1 2016) constitute an important group within the Pteridaceae and are cosmopolitan in distribution. In South America, there are 155 species distributed in 13 genera, among which the largest are Adiantopsis (35), Cheilanthes (27), and Doryopteris (22). Most of the cheilanthoid species are morphologically adapted to grow in arid to semi-arid conditions and show convergent evolution, which has implied difficulties in defining the genera throughout their taxonomic history (Copeland 1947, Tryon & Tryon 1973, Gastony & Rollo 1995, 1998, Kirkpatrick Systematic Botany, 32: 504–518, 2007, Rothfels et al. Taxon, 57: 712–724, 2008). Here, we sequenced two plastid markers (rbcL?+?trnL-F) of 33 South American cheilanthoid species, most of which have not been included in phylogenetic analyses previously. The South American species were analyzed together with South African and Australasian Cheilanthes and representatives of related cheilanthoid genera. The phylogenetic analysis showed that most Cheilanthes species are related to the genus Hemionitis, constituting different groups according to their distribution; moreover, three species—C. hassleri, C. pantanalensis, and C. obducta—appear as the sister clade of Hemionitis. Cheilanthes micropteris, the type species, is strongly supported in a clade with Australasian Cheilanthes plus five South American Cheilanthes species, all of which show a reduction in the number of spores per sporangium; this feature would be a synapomorphy for core Cheilanthes s.s. We found no support uniting other South American Cheilanthes to either the group of South African Cheilanthes or to core Cheilanthes s.s. On the other hand, C. geraniifolia, C. goyazensis, and C. bradei formed a clade related to Doryopteris that, with further study, could be considered as a new genus. The phylogenetic hypotheses presented here contribute substantially to the delimitation of Cheilanthes s.s. and related groups and provide the basis for re-examining the generic taxonomy.     

Phylogenetic relationships in southern African Bryde’s whales inferred from mitochondrial DNA: further support for subspecies delineation between the two allopatric populations

Bryde’s whales (Balaenoptera edeni) are medium-sized balaenopterids with tropical and subtropical distribution. There is confusion about the number of species, subspecies and populations of Bryde’s whale found globally. Two eco-types occur off South Africa, the inshore and offshore forms, but with unknown relationship between them. Using the mtDNA control region we investigated the phylogenetic relationship of these populations to each other and other Bryde’s whale populations. Skin, baleen and bone samples were collected from biopsy-sampled individuals, strandings and museum collections. 97 sequences of 674 bp (bp) length were compared with published sequences of Bryde’s whales (n?=?6) and two similar species, Omura’s (B. omurai) and sei (B. borealis) whales (n?=?3). We found eight haplotypes from the study samples: H1–H4 formed a distinct, sister clade to pelagic populations of Bryde’s whales (B. brydei) from the South Pacific, North Pacific and Eastern Indian Ocean. H5–H8 were included in the pelagic clade. H1–H4 represented samples from within the distributional range of the inshore form. Pairwise comparisons of the percentage of nucleotide differences between sequences revealed that inshore haplotypes differed from published sequences of B. edeni by 4.7–5.5% and from B. brydei by 1.8–2.1%. Ten fixed differences between inshore and offshore sequences supported 100% diagnosability as subspecies. Phylogenetic analyses grouped the South African populations within the Bryde’s-sei whale clade and excluded B. edeni. Our data, combined with morphological and ecological evidence from previous studies, support subspecific classification of both South African forms under B. brydei and complete separation from B. edeni.     

Genome sequences and comparative genomics of two <Emphasis Type="Italic">Lactobacillus ruminis</Emphasis> strains from the bovine and human intestinal tracts

Background

The genus Lactobacillus is characterized by an extraordinary degree of phenotypic and genotypic diversity, which recent genomic analyses have further highlighted. However, the choice of species for sequencing has been non-random and unequal in distribution, with only a single representative genome from the L. salivarius clade available to date. Furthermore, there is no data to facilitate a functional genomic analysis of motility in the lactobacilli, a trait that is restricted to the L. salivarius clade.

Results

The 2.06 Mb genome of the bovine isolate Lactobacillus ruminis ATCC 27782 comprises a single circular chromosome, and has a G+C content of 44.4%. In silico analysis identified 1901 coding sequences, including genes for a pediocin-like bacteriocin, a single large exopolysaccharide-related cluster, two sortase enzymes, two CRISPR loci and numerous IS elements and pseudogenes. A cluster of genes related to a putative pilin was identified, and shown to be transcribed in vitro. A high quality draft assembly of the genome of a second L. ruminis strain, ATCC 25644 isolated from humans, suggested a slightly larger genome of 2.138 Mb, that exhibited a high degree of synteny with the ATCC 27782 genome. In contrast, comparative analysis of L. ruminis and L. salivarius identified a lack of long-range synteny between these closely related species. Comparison of the L. salivarius clade core proteins with those of nine other Lactobacillus species distributed across 4 major phylogenetic groups identified the set of shared proteins, and proteins unique to each group.

Conclusions

The genome of L. ruminis provides a comparative tool for directing functional analyses of other members of the L. salivarius clade, and it increases understanding of the divergence of this distinct Lactobacillus lineage from other commensal lactobacilli. The genome sequence provides a definitive resource to facilitate investigation of the genetics, biochemistry and host interactions of these motile intestinal lactobacilli.