Root nodules of Genista germanica harbor Bradyrhizobium and Rhizobium bacteria exchanging nodC and nodZ genes

A collection of 18 previously unstudied strains isolated from root nodules of Genista germanica (German greenweed) grown in southeast Poland was evaluated for the level of genetic diversity using the BOX-PCR technique and the phylogenetic relationship based on both core (16S rRNA, dnaK, ftsA, glnII, gyrB, recA, rpoB) and nodulation (nodC and nodZ) gene sequences. Each of the 18 G. germanica root nodule isolates displayed unique BOX-PCR patterns, indicating their high level of genomic heterogeneity. Based on the comparative 16S rDNA sequence analysis, 12 isolates were affiliated to the Bradyrhizobium genus and the other strains were most similar to Rhizobium species. Phylogenetic analysis of the core gene sequences indicated that the studied Bradyrhizobium bacteria were most closely related to Bradyrhizobium japonicum, whereas Rhizobium isolates were most closely related to Rhizobium lusitanum and R. leguminosarum. The phylogenies of nodC and nodZ for the Rhizobium strains were incongruent with each other and with the phylogenies inferred from the core gene sequences. All Rhizobium nodZ gene sequences acquired in this study were grouped with the sequences of Bradyrhizobium strains. Some of the studied Rhizobium isolates were placed in the nodC phylogenetic tree together with reference Rhizobium species, while the others were closely related to Bradyrhizobium bacteria. The results provided evidence for horizontal transfer of nodulation genes between Bradyrhizobium and Rhizobium. However, the horizontal transfer of nod genes was not sufficient for Rhizobium strains to form nodules on G. germanica roots, suggesting that symbiotic genes have to be adapted to the bacterial genome.     

A new clade of Mesorhizobium nodulating Alhagi sparsifolia

We isolated 33 nodule bacteria from the legume Alhagi sparsifolia growing in the desert of northwest China. They fell into three groups by restriction analysis of their rrs (small subunit ribosomal RNA) genes, and these, together with dnaK and dnaJ genes, were sequenced from representative isolates to assess their taxonomic position by phylogenetic analysis. The bacteria in each group belonged to different lineages that might represent three different new Mesorhizobium species, two of which form a novel clade very distinct from other species in the genus. Most A. sparsifolia symbionts harboured closely related nodA and nodC genes forming new lineages. The presence of these closely related symbiosis genes in various genomic backgrounds and the incongruence observed between the different gene phylogenies indicate a history of horizontal gene transfer of symbiosis genes between the A. sparsifolia symbionts.     

Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus

In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89^T and Bradyrhizobium valentinum LmjM3^T. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887^T in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89^T, Bradyrhizobium valentinum LmjM3^T and Bradyrhizobium retamae Ro19^T belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.     

Lotus endemic to the Canary Islands are nodulated by diverse and novel rhizobial species and symbiotypes

Genetic and symbiotic characterization of 34 isolates from several Lotus species endemic to the Canary Islands showed extraordinary diversity, with bacteria belonging to different species of the genera Mesorhizobium (17 isolates), Sinorhizobium (12 isolates) and Rhizobium/Agrobacterium (5 isolates). In a previous report, we showed that the Sinorhizobium isolates mostly belonged to S. meliloti. Here, we focused on the remaining isolates. The Lotus mesorhizobial strains were distributed in the rrs tree within six poorly resolved branches. Partial sequences from atpD and recA genes produced much better resolved phylogenies that were, with some exceptions, congruent with the ribosomal phylogeny. Thus, up to six different mesorhizobial species were detected, which matched with or were sister species of M. ciceri, M. alhagi, M. plurifarium or M. caraganae, and two represented new lineages that did not correspond to any of the currently recognized species. Neither M. loti nor Bradyrhizobium sp. (Lotus), recognized as the typical Lotus-symbionts, were identified among the Canarian Lotus isolates, although their nodulation genes were closely related to M. loti. However, several subbranches of mesorhizobia nodulating Lotus spp. could be differentiated in a nodC tree, with the isolates from the islands distributed in two of them (A1 and A3). Subbranch A1 included reference strains of M. loti and a group of isolates with a host range compatible with biovar loti, whereas A3 represented a more divergent exclusive subbranch of isolates with a host range almost restricted to endemic Lotus and it could represent a new biovar among the Lotus rhizobia.     

Comparative morphology and molecular phylogeny of aplanochytrids (Labyrinthulomycota)

Aplanochytrids comprise one of three major subgroups within the Labyrinthulomycota. We have surveyed the diversity of aplanochytrids and have discovered that most isolates are difficult to identify to species because of character plasticity and ambiguity. Ten isolates were studied using molecular phylogenies based on small subunit ribosomal gene sequences (SSU rDNA) and morphological characters derived from light microscopy, SEM and TEM (e.g., colony size, colony shape, colony pattern, agar penetration, cell shape, cell surface patterns, cell inclusion characteristics and ectoplasmic net morphology). Of these isolates, we could positively identify two of them to species, namely Aplanochytrium yorkensis (Perkins, 1973) Leander and Porter, 2000 and A. minuta (Watson and Raper, 1957) Leander and Porter, 2000. We used standardized conditions for growing aplanochytrid isolates in order to minimize environmentally induced phenotypic plasticity in our comparative studies of morphology. By mapping the morphological characters listed above onto a conservative phylogenetic topology derived from SSU rDNA sequences, we were able to identify several synapomorphies (e.g., gross colony characteristics and cell surface patterns) that serve as valuable taxonomic characters for the identification of species and specific clades of aplanochytrids.     

Herbarium phylogenomics: Resolving the generic status of the enigmatic Pseudobartsia (Orobanchaceae)

The millions of herbarium specimens in collections around the world provide historical resources for phylogenomics and evolutionary studies. Many rare and endangered species exist only as historical specimens. Here, we report a case study of the monotypic Pseudobartsia yunnanensis D. Y. Hong (=Pseudobartsia glandulosa[Bentham] W. B. Yu & D. Z. Li: Orobanchaceae) known from a single Chinese collection taken in 1940. We obtained genomic data of Pseudobartsia glandulosa using high-throughput short-read sequencing, and then assembled a complete chloroplast genome and nuclear ribosome DNA region in this study. We found that the newly assembled three plastid DNA regions (atpB-rbcL, rpl16, and trnS-G) and nuclear ribosomal internal transcribed spacer (nrITS) of Pseudobartsia glandulosa were more than 99.98% similar to published sequences obtained by target sequencing. Phylogenies of Orobanchaceae using 30 plastomes (including 10 new plastomes), using both supermatrix and multispecies coalescent approaches following a novel plastid phylogenomic workflow, recovered seven recognized tribes and two unranked groups, both of which were proposed as new tribes, that is, Brandisieae and Pterygielleae. Within Pterygielleae, all analyses strongly supported Xizangia D. Y. Hong as the first diverging genus, with Pseudobartsia D. Y. Hong as sister to Pterygiella Oliver + Phtheirospermum Bunge (excluding Phtheirospermum japonicum [Thunberg] Kanitz); this supports reinstatement of Pseudobartsia and Xizangia. Although elements of Buchnereae-Cymbarieae-Orobancheae and Brandisieae-Pterygielleae-Rhinantheae showed incongruence among gene trees, the topology of the supermatrix tree was congruent with the majority of gene trees and functional-group trees. Therefore, most plastid genes are evolving as a linkage group, allowing the supermatrix tree approach to yield internally consistent phylogenies for Orobanchaceae.     

Is 16S rDNA a Reliable Phylogenetic Marker to Characterize Relationships Below the Family Level in the Enterobacteriaceae?

The phylogenetic relationships of multiple enterobacterial species were reconstructed based on 16S rDNA gene sequences to evaluate the robustness of this housekeeping gene in the taxonomic placement of the enteric plant pathogens Erwinia, Brenneria, Pectobacterium, and Pantoea. Four data sets were compiled, two of which consisted of previously published data. The data sets were designed in order to evaluate how 16S rDNA gene phylogenies are affected by the use of different plant pathogen accessions and varying numbers of animal pathogen and outgroup sequences. DNA data matrices were analyzed using maximum likelihood (ML) algorithms, and character support was determined by ML bootstrap and Bayesian analyses. As additional animal pathogen sequences were added to the phylogenetic analyses, taxon placement changed. Further, the phylogenies varied in their placement of the plant pathogen species, and only the genus Pantoea was monophyletic in all four trees. Finally, bootstrap and Bayesian support values were low for most of the nodes, and all nonterminal branches collapsed in strict consensus trees. Inspection of 16S rDNA nucleotide alignments revealed several highly variable blocks punctuated by regions of conserved sequence. These data suggest that 16S rDNA, while effective for both species-level and family-level phylogenetic reconstruction, may underperform for genus-level phylogenetic analyses in the Enterobacteriaceae.     

Evaluation of ribosomal RNA gene restriction patterns for the classification of Bacillus species and related genera

AIMS: To identify Bacillus species and related genera by fingerprinting based on ribosomal RNA gene restriction patterns; to compare ribosomal RNA gene restriction patterns-based phylogenetic trees with trees based on 16S rRNA gene sequences; to evaluate the usefulness of ribosomal RNA gene restriction patterns as a taxonomic tool for the classification of Bacillus species and related genera. METHODS AND RESULTS: Seventy-eight bacterial species which include 42 Bacillus species, 31 species from five newly created Bacillus-related genera, and five species from five phenotypically related genera were tested. A total of 77 distinct 16S rRNA gene hybridization banding patterns were obtained. The dendrogram resulting from UPGMA analysis showed three distinct main genetic clusters at the 75% banding pattern similarity. A total of 77 distinct 23S and 5S rRNA genes hybridization banding patterns were obtained, and the dendrogram showed four distinct genetic clusters at the 75% banding pattern similarity. A third dendrogram was constructed using a combination of the data from the 16S rRNA gene fingerprinting and the 23S and 5S rRNA genes fingerprinting. It revealed three distinct main phylogenetic clusters at the 75% banding pattern similarity. CONCLUSIONS: The Bacillus species along with the species from related genera were identified successfully and differentiated by ribosomal RNA gene restriction patterns, and most were distributed with no apparent order in various clusters on each of the three dendrograms. SIGNIFICANCE AND IMPACT OF THE STUDY: Our data indicate that ribosomal RNA gene restriction patterns can be used to reconstruct the phylogeny of the Bacillus species and derived-genera that approximates, but does not duplicate, phylogenies based on 16S rRNA gene sequences.     

Isolation of a new vahlkampfiid amoeba from soil: Paravahlkampfia lenta n. sp.

When the genus Paravahlkampfia was distinguished from the genus Vahlkampfia on the basis of significant differences in small subunit ribosomal DNA sequences, Paravahlkampfia ustiana was the only described species of this new genus. More recently, a vahlkampfiid strain has been isolated (from soil from an upland farm in Scotland) which has trophozoite and cyst morphology more similar to P. ustiana than to other non-flagellating vahlkampfiid species. Also, it clusters with P. ustiana in phylogenetic trees derived from 5.8S ribosomal DNA sequences. However, it is significantly different from P. ustiana in both phenotype and internal transcribed spacer sequence. Consequently, a new species, Paravahlkampfia lenta, is proposed.     

Speciation and host-parasite relationships in the parasite genus Gyrodactylus (Monogenea, Platyhelminthes) infecting gobies of the genus Pomatoschistus (Gobiidae, Teleostei)

Using species-level phylogenies, the speciation mode of Gyrodactylus species infecting a single host genus was evaluated. Eighteen Gyrodactylus species were collected from gobies of the genus Pomatoschistus and sympatric fish species across the distribution range of the hosts. The V4 region of the ssrRNA and the internal transcribed spacers encompassing the 5.8S rRNA gene were sequenced; by including published sequences a total of 30 species representing all subgenera were used in the data analyses. The molecular phylogeny did not support the morphological groupings into subgenera as based on the excretory system, suggesting that the genus needs systematic revisions. Paraphyly of the total Gyrodactylus fauna of the gobies indicates that at least two independent colonisation events were involved, giving rise to two separate groups, belonging to the subgenus Mesonephrotus and Paranephrotus, respectively. The most recent association probably originated from a host switching event from Gyrodactylus arcuatus, which parasitises three-spined stickleback, onto Pomatoschistus gobies. These species are highly host-specific and form a monophyletic group, two possible ‘signatures’ of co-speciation. Host specificity was lower in the second group. The colonising capacity of these species is illustrated by a host jump from gobiids to another fish order (Anguilliformes), supporting the hypothesis of a European origin of Gyrodactylus anguillae and its intercontinental introduction by the eel trade. Thus, allopatric speciation seems to be the dominant mode of speciation in this host–parasite system, with a possible case of sympatric speciation.     

Horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plants Astragalus luteolus and Astragalus ernestii in Sichuan, China

Thirty-three rhizobial strains isolated from the root nodules of Astragalus luteolus and Astragalus ernestii growing on the west plateau at two different altitudes in Sichuan province, China, were characterized by amplified rDNA restriction analysis (ARDRA), amplified fragment length polymorphism (AFLP), and by sequencing of rrs, glnA, glnII and nifH . The ARDRA analysis revealed considerable genomic diversity. In AFLP analysis, 20 of 33 Astragalus rhizobia formed three distinct clades, with others dispersed into different groups with the reference strains. Phylogenetic analysis of the rrs gene of six representative strains showed that the isolates were members of the genus Mesorhizobium . Three of the isolates formed a sister clade to Mesorhizobium loti and Mesorhizobium ciceri , whereas the other three formed a sister clade to a clade harboring the species Mesorhizobium huakuii, Mesorhizobium plurifarum, Mesorhizobium septentrionale and Mesorhizobium amorphae , indicating the existence of two new species. Phylogenetic analysis of glnA and glnII confirmed the rrs phylogenies for four strains, but the trees were incongruent. The nifH sequences of the strains formed a monophyletic clade and were typical of those of mesorhizobia forming symbioses with inverted repeat lacking clade legume species. The incongruent phylogenies of the genes studied suggest that horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plants.     

Phylogenetic validation of the genera Angomonas and Strigomonas of trypanosomatids harboring bacterial endosymbionts with the description of new species of trypanosomatids and of proteobacterial symbionts

We comparatively examined the nutritional, molecular and optical and electron microscopical characteristics of reference species and new isolates of trypanosomatids harboring bacterial endosymbionts. Sequencing of the V7V8 region of the small subunit of the ribosomal RNA (SSU rRNA) gene distinguished six major genotypes among the 13 isolates examined. The entire sequences of the SSU rRNA and glycosomal glyceraldehyde phosphate dehydrogenase (gGAPDH) genes were obtained for phylogenetic analyses. In the resulting phylogenetic trees, the symbiont-harboring species clustered as a major clade comprising two subclades that corresponded to the proposed genera Angomonas and Strigomonas. The genus Angomonas comprised 10 flagellates including former Crithidia deanei and C. desouzai plus a new species. The genus Strigomonas included former Crithidia oncopelti and Blastocrithidia culicis plus a new species. Sequences from the internal transcribed spacer of ribosomal DNA (ITS rDNA) and size polymorphism of kinetoplast DNA (kDNA) minicircles revealed considerable genetic heterogeneity within the genera Angomonas and Strigomonas. Phylogenetic analyses based on 16S rDNA and ITS rDNA sequences demonstrated that all of the endosymbionts belonged to the Betaproteobacteria and revealed three new species. The congruence of the phylogenetic trees of trypanosomatids and their symbionts support a co-divergent host-symbiont evolutionary history.     

Molecular phylogeny of Bradyrhizobium bacteria isolated from root nodules of tribe Genisteae plants growing in southeast Poland

The phylogeny of 16 isolates from root nodules of Genista germanica, Genista tinctoria, Cytisus ratisbonensis, and Cytisus scoparius growing in southeast Poland was estimated by comparative sequence analysis of core (16S rDNA, atpD, glnII, recA) and symbiosis-related (nodC, nodZ, nifH) genes. All the sequences analyzed placed the studied rhizobia in the genus Bradyrhizobium. Phylogenetic analysis of individual and concatenated housekeeping genes showed that the Genisteae microsymbionts form a homogeneous group with Bradyrhizobium japonicum strains. The phylogeny of nodulation and nitrogen fixation genes indicated a close relationship of the examined rhizobia with B. japonicum, Bradyrhizobium canariense, Bradyrhizobium cytisi, Bradyrhizobium rifense and Bradyrhizobium lupini strains infecting other plants of the tribe Genisteae. For the first time, the taxonomic position of G. germanica and C. ratisbonensis rhizobia, inferred from multigenic analysis, is described. The results of the phylogenetic analysis based on the protein-coding gene sequences presented in this study also indicate potential pitfalls concerning the choice of marker and reference strains, which may lead to conflicting conclusions in species delineation.     

Retama species growing in different ecological–climatic areas of northeastern Algeria have a narrow range of rhizobia that form a novel phylogenetic clade within the Bradyrhizobium genus

Sixty-seven isolates were isolated from nodules collected on roots of Mediterranean shrubby legumes Retama raetam and Retama sphaerocarpa growing in seven ecological–climatic areas of northeastern Algeria. Genetic diversity of the Retama isolates was analyzed based on genotyping by restriction fragment length polymorphism of PCR-amplified fragments of the 16S rRNA gene, the intergenic spacer (IGS) region between the 16S and 23S rRNA genes (IGS), and the symbiotic genes nifH and nodC. Eleven haplotypes assigned to the Bradyrhizobium genus were identified. Significant biogeographical differentiation of the rhizobial populations was found, but one haplotype was predominant and conserved across the sites. All isolates were able to cross-nodulate the two Retama species. Accordingly, no significant genetic differentiation of the rhizobial populations was found in relation to the host species of origin. Sequence analysis of the 16S rRNA gene grouped the isolates with Bradyrhizobium elkanii, but sequence analyses of IGS, the housekeeping genes (dnaK, glnII, recA), nifH, and nodC yielded convergent results showing that the Retama nodule isolates from the northeast of Algeria formed a single evolutionary lineage, which was well differentiated from the currently named species or well-delineated unnamed genospecies of bradyrhizobia. Therefore, this study showed that the Retama species native to northeastern Algeria were associated with a specific clade of bradyrhizobia. The Retama isolates formed three sub-groups based on IGS and housekeeping gene phylogenies, which might form three sister species within a novel bradyrhizobial clade.     

Characterization of bacterial pectinolytic strains involved in the water retting process

Pectinolytic microorganisms involved in the water retting process were characterized. Cultivable mesophilic anaerobic and aerobic bacteria were isolated from unretted and water-retted material. A total of 104 anaerobic and 23 aerobic pectinolytic strains were identified. Polygalacturonase activity was measured in the supernatant of cell cultures; 24 anaerobic and nine aerobic isolates showed an enzymatic activity higher than the reference strains Clostridium felsineum and Bacillus subtilis respectively. We performed the first genotypic characterization of the retting microflora by a 16S amplified ribosomal DNA restriction analysis (ARDRA). Anaerobic isolates were divided into five different groups, and the aerobic isolates were clustered into three groups. 84.6% of the anaerobic and 82.6% of the aerobic isolates consisted of two main haplotypes. Partial 16S rRNA gene sequences were determined for 12 strains, representative of each haplotype. All anaerobic strains were assigned to the Clostridium genus, whereas the aerobic isolates were assigned to either the Bacillus or the Paenibacillus genus. Anaerobic isolates with high polygalacturonase (PG) activity belong to two clearly distinct phylogenetic clusters related to C. acetobutylicum-C. felsineum and C. saccharobutylicum species. Aerobic isolates with high PG activity belong to two clearly distinct phylogenetic clusters related to B. subtilisT and B. pumilusT.     

白粉菌交配型位点基因结构及分子系统学关系

白粉菌是一类植物专性寄生真菌,广泛分布于世界各地,可引起多种植物白粉病。开展白粉菌交配型基因研究可以为全面认识白粉菌的生活史循环和系统演化提供证据。本研究以子囊菌中已报道的10种MAT基因和4种侧翼基因的氨基酸序列为种子序列,采用生物信息学方法在21个白粉菌基因组中进行氨基酸同源性分析,探索MAT基因及其侧翼基因的种类和线性排布。结果表明,21个白粉菌基因组中有10个属于MAT1-1型,包含MAT1-1-1和MAT1-1-3两种基因;10个属于MAT1-2型,仅包含MAT1-2-1基因;在Erysiphe pulchra的基因组中同时存在MAT1-1-1、MAT1-1-3、MAT1-2-1;而4种侧翼基因SLA2、APC5、APN2和CoxVia在21个白粉菌基因组中均存在。21个菌株中有两个菌株Blumeria graminis f. sp. hordei RACE1和Golovinomyces orontii的MAT基因和4种侧翼基因分布在同一个scaffold,其余菌株MAT基因和侧翼基因均不在同一scaffold出现。本研究分别分析了具有MAT1-1和MAT1-2的菌株中MAT基因和4种侧翼基因的排列关系,同时根据9个菌株的MAT基因注释信息,推测了其他菌株的MAT基因结构。结果表明,同属白粉菌的MAT基因结构相同,属间MAT基因结构差异明显。以从白粉菌基因组中获得的MAT1-1-1、MAT1-1-3和MAT1-2-1 3种MAT基因序列分别构建系统发育树,发现布氏白粉菌属Blumeria、白粉菌属Erysiphe和戈洛文白粉菌属Golovinomyces分别形成独立分枝,且白粉菌属与戈洛文白粉菌属形成姊妹群,这与前人对白粉菌系统发育关系的研究结果一致。本研究得到的白粉菌MAT基因种类、分布及其结构的相关结果为进一步实验提供了理论依据,为探究白粉菌的系统发育提供了新的思路。     

The identification of vahlkampfiid amoebae by ITS sequencing

We have determined the internal transcribed spacer (ITS) sequences (including the 5.8S ribosomal DNA) of 30 strains of 14 species belonging to eight vahlkampfiid genera. Each previously described species has a specific ITS sequence, except for Tetramitus aberdonicus, Tetramitus thorntoni, and Tetramitus jugosus, which have identical ITS sequences. The latter three may therefore constitute a single species despite their apparent phenotypic differences. The ITS sequence appears to be conserved within a species. The species Willaertia magna appears to be ubiquitous. The 5.8S rDNA sequences of Singhamoeba horticola and Learamoeba waccamwensis indicate that they do not represent different genera, but both belong to the genus Tetramitus. The ITS sequences of 16 undescribed vahlkampfiid isolates were determined. Based on these sequences, seven isolates were identified as belonging to described species, while nine probably represent seven new species. Five of these presumed new species belong to the genus Tetramitus, and one each to the genera Vahlkampfia and Paravahlkampfia.     

Invasive Robinia pseudoacacia in China is nodulated by Mesorhizobium and Sinorhizobium species that share similar nodulation genes with native American symbionts

The aim of this work is to describe the diversity of potentially symbiotic bacteria associated with the invasive introduced legume Robinia pseudoacacia in China. Thirty-three isolates from 33 separate trees and nodules were characterized using restriction length fragment polymorphism and sequencing of 16S rRNA, nodA, nodC and nifH genes. Their 16S rRNA gene patterns and sequences placed them in three clades: 85% of isolates were related to the Mesorhizobium mediterraneum/temperatum group, whereas the remaining were similar either to Mesorhizobium amorphae or to Sinorhizobium meliloti . However, despite their diverse taxonomic positions, the nodA, nodC and nifH genes' phylogenies indicated that these R. pseudoacacia symbionts share similar symbiosis genes, implying gene transfers and a degree of host specificity. Comparison of R. pseudoacacia symbiotic diversity in native and other invaded areas suggests that most Chinese symbionts may not have arrived with the seed but were local bacteria that acquired specific symbiotic genes from native American rhizobia.     

Phylogeny,classification, and biogeography of Afrotrichloris,Apochiton, Coelachyrum,Dinebra, Eleusine,Leptochloa, Schoenefeldia,and a new genus,Schoenefeldiella (Poaceae: Chloridoideae: Cynodonteae: Eleusininae)

To investigate the evolutionary relationships among species of Afrotrichloris, Apochiton, Coelachyrum, Dinebra, Eleusine, Leptochloa, and Schoenefeldia of subtribe Eleusininae, a phylogeny based on DNA sequences from nine gene regions (ITS, rps16-trnK, rps3, rps16, rpoC2, rpl32-trnL, ndhF, ndhA, ccsA) is presented. Previous molecular phylogenies indicated that Coelachyrum was polyphyletic and Schoenefeldia was paraphyletic, with Afrotrichloris embedded within it. Apochiton burttii was embedded in the Coelachyrum clade paired with C. longiglume, Coelachyrumpoiflorum was placed outside of Coelachyrum and sister to Eleusine, and Schoenefeldia is paraphyletic, with its two species forming a grade sister to Afrotrichoris. Our molecular phylogeny supports recognition of a new genus, Schoenefeldiella, and a new combination, Schoenfeldiella transiens. In addition, we provide generic emendations for Coelachyrum, which now includes five species including a new combination proposed here, Coelachyrum burttii, and Eleusine, which now includes 11 species.