The First Complete Plastid Genome from Joinvilleaceae (J. ascendens; Poales) Shows Unique and Unpredicted Rearrangements

Joinvilleaceae is a family of tropical grass-like monocots that comprises only the genus Joinvillea. Previous studies have placed Joinvilleaceae in close phylogenetic proximity to the well-studied grass family. A full plastome sequence was determined and characterized for J. ascendens. The plastome was sequenced with next generation methods, fully assembled de novo and annotated. The assembly revealed two novel inversions specific to the Joinvilleaceae lineage and at least one novel plastid inversion in the Joinvilleaceae-Poaceae lineage. Two previously documented inversions in the Joinvilleaceae-Poaceae lineage and one previously documented inversion in the Poaceae lineage were also verified. Inversion events were identified visually and verified computationally by simulation mutations. Additionally, the loss and subsequent degradation of the accD gene in order Poales was explored extensively in Poaceae and J. ascendens. The two novel inversions along with changes in gene composition between families better delimited lineages in the Poales. The presence of large inversions and subsequent reversals in this small family suggested a high potential for large-scale rearrangements to occur in plastid genomes.     

Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex

Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation.     

Molecules and morphology suggest cryptic species diversity and an overall complex taxonomy of fish scale geckos, genus Geckolepis

The current classification of the Malagasy-Comoroan geckos of the genus Geckolepis recognizes three valid species and is based on morphological differences only. Species allocation of individuals is difficult, mainly because of the insufficiently known degree of variation and the frequent partial loss of the integument in preserved specimens. Here we study Geckolepis specimens from almost their entire known range. We combine molecular and morphological data to estimate species richness in the genus, and to assess the taxonomic validity of the morphological differences proposed. Analyses of mitochondrial (12S, ND4) and nuclear (RAG1, CMOS) gene sequences support three major clades in addition to the morphologically distinct G. polylepis (included for 12S only), and the presence of various divergent lineages within these clades, some occurring in sympatry. Among lineages, the external morphology seems to be comparatively conservative, and differences are faint in many cases. For each major lineage, we summarize the most diagnostic morphological characters that distinguish it from other lineages. The combined molecular and morphological data strongly indicate the presence of highly divergent lineages, three of which are tentatively referred to the names Geckolepis maculata, G. polylepis and G. typica, whereas three other major lineages are considered Confirmed Candidate Species. Among the remaining lineages, differentiation is shallower, and these may qualify for Deep Conspecific Lineages. In conclusion, our analysis provides evidence for an underestimation of species richness in the genus and a complex evolutionary history, not reflected by current Geckolepis species-level taxonomy.     

Tracing plant Mitochondrial DNA evolution: rearrangements of the ancient mitochondrial gene cluster trnA-trnT-nad7 in liverwort phylogeny

Whereas frequent recombination characterizes flowering plant mitochondrial genomes, some mitochondrial gene arrangements may, in contrast, be conserved between streptophyte algae and early land plant clades (bryophytes). Here we explore the evolutionary fate of the mitochondrial gene arrangement trnA-trnT-nad7, which is conserved among the alga Chara, the moss Physcomitrella, and the liverwort Marchantia, although trnT is inverted in orientation in the latter. Surprisingly, we now find that the Chara-type gene arrangement is generally conserved in mosses, but that trnT is lacking between trnA and nad7 in all simple-thalloid and leafy (jungermanniid) liverworts. The ancient gene continuity trnA-trnT-nad7 is, however, conserved in Blasia, representing the sister lineage to all other complex-thalloid (marchantiid) liverworts. The recombinogenic insertion of short sequence stretches, including nad5 and rps7 pseudogene fragments copied from elsewhere in the liverwort mtDNA, likely mediated a subsequent inversion of trnT and flanking sequences in a basal grade of marchantiid liverworts, which was then followed by an independent secondary loss of trnT in derived marchantiid taxa later in evolution. In contrast to the previously observed extreme degree of coding sequence conservation and the assumed absence of active recombination in Marchantia mtDNA, this now reveals a surprisingly dynamic evolution of marchantiid liverwort mitochondrial genomes.     

Identification of tammar wallaby SIRH12, derived from a marsupial-specific retrotransposition event

In humans and mice, there are 11 genes derived from sushi-ichi related retrotransposons, some of which are known to play essential roles in placental development. Interestingly, this family of retrotransposons was thought to exist only in eutherian mammals, indicating their significant contributions to the eutherian evolution, but at least one, PEG10, is conserved between marsupials and eutherians. Here we report a novel sushi-ichi retrotransposon-derived gene, SIRH12, in the tammar wallaby, an Australian marsupial species of the kangaroo family. SIRH12 encodes a protein highly homologous to the sushi-ichi retrotransposon Gag protein in the tammar wallaby, while SIRH12 in the South American short-tailed grey opossum is a pseudogene degenerated by accumulation of multiple nonsense mutations. This suggests that SIRH12 retrotransposition occurred only in the marsupial lineage but acquired and retained some as yet unidentified novel function, at least in the lineage of the tammar wallaby.     

Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism

Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals’ classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores.     

Cryptic diversity and unexpected evolutionary patterns in the meadow lizard,Darevskia praticola (Eversmann, 1834)

Darevskia praticola differs from the other species of the genus in having a large but disjunct distribution, covering the Balkan and the Caucasus regions. Furthermore, most Darevskia species occupy saxicolous habitats, whereas D. praticola inhabits meadows and forest environments. Here we determine the phylogeographic and phylogenetic relationships of Darevskia praticola sensu lato and evaluate the current, morphology-based taxonomy. We sequenced two mtDNA genes (Cyt-b and ND4) and two nuclear loci (MC1R and RELN) for samples collected across the species range. Because our sequences amplified with the Cyt-b primers appear to represent a nuclear pseudogene we excluded this marker from the final analysis. Our results support monophyly of D. praticola and show its division into three clades. The first divergence, dated to the Late Pliocene, is between the Balkans and the Caucasus. The Caucasus lineage is further subdivided in a western Greater Caucasus and a Transcaucasia clade, likely due to subsequent differentiation during the Pleistocene. Our findings do not support the current taxonomic arrangement within D. praticola. The main geographic divergence likely happened due to a vicariance event associated with Plio-Pleistocene climatic and vegetation oscillations.     

Diversification of Lupine Bradyrhizobium Strains: Evidence from Nodulation Gene Trees

Bradyrhizobium strains isolated in Europe from Genisteae and serradella legumes form a distinct lineage, designated clade II, on nodulation gene trees. Clade II bradyrhizobia appear to prevail also in the soils of Western Australia and South Africa following probably accidental introduction with seeds of their lupine and serradella hosts. Given this potential for dispersal, we investigated Bradyrhizobium isolates originating from a range of native New World lupines, based on phylogenetic analyses of nodulation (nodA, nodZ, noeI) and housekeeping (atpD, dnaK, glnII, recA) genes. The housekeeping gene trees revealed considerable diversity among lupine bradyrhizobia, with most isolates placed in the Bradyrhizobium japonicum lineage, while some European strains were closely related to Bradyrhizobium canariense. The nodA gene tree resolved seven strongly supported groups (clades I to VII) that correlated with strain geographical origins and to some extent with major Lupinus clades. All European strains were placed in clade II, whereas only a minority of New World strains was placed in this clade. This work, as well as our previous studies, suggests that clade II diversified predominately in the Old World, possibly in the Mediterranean. Most New World isolates formed subclade III.2, nested in a large “pantropical” clade III, which appears to be New World in origin, although it also includes strains originating from nonlupine legumes. Trees generated using nodZ and noeI gene sequences accorded well with the nodA tree, but evidence is presented that the noeI gene may not be required for nodulation of lupine and that loss of this gene is occurring.     

The Motilin Gene Evolved a New Function in Kangaroo Rats and Kangaroo Mice (Dipodomyinae)

The motilin receptor gene was lost in the ancestral lineage of rodents. Subsequently, the gene encoding its ligand, motilin, has experienced different evolutionary fates. Previous genomic analyses had shown that the motilin gene (MLN) became a pseudogene independently in the lineages leading to the guinea pig and the common ancestor of the mouse and rat, yet an intact, and thus potentially functional, open reading frame for the MLN was preserved in the Dipodomys ordii genome. As only a single MLN haplotype from D. ordii was available, and this sequence is from a low coverage draft genome, it is possible that the intact MLN found in the draft kangaroo rat genome is an artifact, or represents an intermediate in the process of becoming a pseudogene. In order to establish whether an intact MLN is retained in kangaroo rats despite the loss of its specific receptor, and to investigate the evolutionary mechanisms underlying the retention of this gene sequence, we isolated MLN sequences from species that represent the diversity of the Dipodomyinae [the monophyletic Dipodomyinae subfamily consists of two genera: Dipodomys (kangaroo rats) and Microdipodops (kangaroo mice)]. The results demonstrate that the MLN sequence is well conserved in Dipodomyinae, and it codes for a predicted motilin peptide sequence possessing a conserved N-terminal pharmacophore and the potential to be processed and secreted as a hormone. The observations that the MLN evolved as a functional gene during the radiation of the Dipodomyinae, species that have lost their original motilin receptor, suggest that the MLN has undergone a lineage-specific physiological adaptation to a new function.     

Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?

Background  

Phylogenies reconstructed with only one or a few independently inherited loci may be unresolved or incongruent due to taxon and gene sampling, horizontal gene transfer, or differential selection and lineage sorting at individual loci. In an effort to remedy this situation, we examined the utility of conserved orthologous set (COSII) nuclear loci to elucidate the phylogenetic relationships among 29 diploid Solanum species in the sister clades that include tomato and potato, and in Datura inoxia as a far outgroup. We screened 40 COSII markers with intron content over 60% that are mapped in different chromosomes; selected a subset of 19 by the presence of single band amplification of size mostly between 600 and 1200 bp; sequenced these 19 COSII markers, and performed phylogenetic analyses with individual and concatenated datasets. The present study attempts to provide a fully resolved phylogeny among the main clades in potato and tomato that can help to identify the appropriate markers for future studies using additional species.     

Conservation Genetics of Kangaroo Mice, Genus Microdipodops

The two currently recognized species of kangaroo mice, Microdipodops megacephalus and M. pallidus, inhabit sandy soils of the Great Basin Desert in western North America. Given their habitat specificity and the fluctuating climate throughout the Pleistocene, kangaroo mice likely endured a turbulent biogeographic history that resulted in disjunct distributions and isolation of genetic lineages. Recent phylogenetic investigations using mitochondrial data have revealed several mitochondrial clades within this genus that may represent cryptic species. These mitochondrial clades are genetically unique, occupy relatively small distributions, and, as such, may be at an increased risk of extinction due to climate change and extensive recent habitat alteration. Herein, we apply haplotype network, population genetic, and historical demographic analyses to mitochondrial data of each Micropdipodops species and mitochondrial clade to assess conservation genetics within kangaroo mice. Results indicate that each mitochondrial clade is a distinct lineage with little to no gene flow occurring among clades. Additionally, historical demographic analyses support past population expansions and identify locations of past refugium for each distinct lineage. Although mitochondrial data indicate that the clades appear to be in approximate genetic equilibrium and have not suffered any extreme bottlenecks over time, there is still concern for the survival of smaller and more vulnerable Microdipodops subpopulations due to impending habitat threats in the Great Basin Desert.     

Genomic and gene regulatory signatures of cryptozoic adaptation: Loss of blue sensitive photoreceptors through expansion of long wavelength-opsin expression in the red flour beetle Tribolium castaneum

Background

Hox genes are expressed in specific domains along the anterior posterior body axis and define the regional identity. In most animals these genes are organized in a single cluster in the genome and the order of the genes in the cluster is correlated with the anterior to posterior expression of the genes in the embryo. The conserved order of the various Hox gene orthologs in the cluster among most bilaterians implies that such a Hox cluster was present in their last common ancestor. Vertebrates are the only metazoans so far that have been shown to contain duplicated Hox clusters, while all other bilaterians seem to possess only a single cluster.

Results

We here show that at least three Hox genes of the spider Cupiennius salei are present as two copies in this spider. In addition to the previously described duplicated Ultrabithorax gene, we here present sequence and expression data of a second Deformed gene, and of two Sex comb reduced genes. In addition, we describe the sequence and expression of the Cupiennius proboscipedia gene. The spider Cupiennius salei is the first chelicerate for which orthologs of all ten classes of arthropod Hox genes have been described. The posterior expression boundary of all anterior Hox genes is at the tagma border of the prosoma and opisthosoma, while the posterior boundary of the posterior Hox genes is at the posterior end of the embryo.

Conclusion

The presence of at least three duplicated Hox genes points to a major duplication event in the lineage to this spider, perhaps even of the complete Hox cluster as has taken place in the lineage to the vertebrates. The combined data of all Cupiennius Hox genes reveal the existence of two distinct posterior expression boundaries that correspond to morphological tagmata boundaries.     

Knockdown of the plastid-encoded acetyl-CoA carboxylase gene uncovers functions in metabolism and development

De novo fatty acid biosynthesis in plants relies on a prokaryotic-type acetyl-CoA carboxylase (ACCase) that resides in the plastid compartment. The enzyme is composed of four subunits, one of which is encoded in the plastid genome, whereas the other three subunits are encoded by nuclear genes. The plastid gene (accD) encodes the β-carboxyltransferase subunit of ACCase and is essential for cell viability. To facilitate the functional analysis of accD, we pursued a transplastomic knockdown strategy in tobacco (Nicotiana tabacum). By introducing point mutations into the translational start codon of accD, we obtained stable transplastomic lines with altered ACCase activity. Replacement of the standard initiator codon AUG with UUG strongly reduced AccD expression, whereas replacement with GUG had no detectable effects. AccD knockdown mutants displayed reduced ACCase activity, which resulted in changes in the levels of many but not all species of cellular lipids. Limiting fatty acid availability caused a wide range of macroscopic, microscopic, and biochemical phenotypes, including impaired chloroplast division, reduced seed set, and altered storage metabolism. Finally, while the mutants displayed reduced growth under photoautotrophic conditions, they showed exaggerated growth under heterotrophic conditions, thus uncovering an unexpected antagonistic role of AccD activity in autotrophic and heterotrophic growth.

Analysis of the only plastid genome-encoded fatty acid biosynthesis gene reveals functions in plastid division and seed development, and antagonistic roles in autotrophic and heterotrophic growth.     

“Candidatus Accumulibacter” Population Structure in Enhanced Biological Phosphorus Removal Sludges as Revealed by Polyphosphate Kinase Genes

We investigated the fine-scale population structure of the “Candidatus Accumulibacter” lineage in enhanced biological phosphorus removal (EBPR) systems using the polyphosphate kinase 1 gene (ppk1) as a genetic marker. We retrieved fragments of “Candidatus Accumulibacter” 16S rRNA and ppk1 genes from one laboratory-scale and several full-scale EBPR systems. Phylogenies reconstructed using 16S rRNA genes and ppk1 were largely congruent, with ppk1 granting higher phylogenetic resolution and clearer tree topology and thus serving as a better genetic marker than 16S rRNA for revealing population structure within the “Candidatus Accumulibacter” lineage. Sequences from at least five clades of “Candidatus Accumulibacter” were recovered by ppk1-targeted PCR, and subsequently, specific primer sets were designed to target the ppk1 gene for each clade. Quantitative real-time PCR (qPCR) assays using “Candidatus Accumulibacter”-specific 16S rRNA and “Candidatus Accumulibacter” clade-specific ppk1 primers were developed and conducted on three laboratory-scale and nine full-scale EBPR samples and two full-scale non-EBPR samples to determine the abundance of the total “Candidatus Accumulibacter” lineage and the relative distributions and abundances of the five “Candidatus Accumulibacter” clades. The qPCR-based estimation of the total “Candidatus Accumulibacter” fraction as a proportion of the bacterial community as measured using 16S rRNA genes was not significantly different from the estimation measured using ppk1, demonstrating the power of ppk1 as a genetic marker for detection of all currently defined “Candidatus Accumulibacter” clades. The relative distributions of “Candidatus Accumulibacter” clades varied among different EBPR systems and also temporally within a system. Our results suggest that the “Candidatus Accumulibacter” lineage is more diverse than previously realized and that different clades within the lineage are ecologically distinct.     

Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species

Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.