The genetic and phylogenetic relationships for strains of Mesorhizobium tianshanense and its relatives were compared by an analysis of the results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins, DNA-DNA hybridization, and full 16s rRNA gene sequencing. The strains of M. tianshanense formed a cluster which was distinct from those of other rhizobium species in the clustering analysis of SDS-PAGE. DNA-DNA relatedness between A-1BS (type strain of M. tianshanense) and the type or reference strains for Mesorhizobium loti, M. huakuii, M. ciceri, M. mediterraneum, and cluster U, an unnamed rhizobial group, ranged from 4.4 to 43.8%. The phylogenetic analysis based on the 16s rRNA gene sequences showed that M. tianshunense was closely related to the Mesorhizobium phylogenetic branch and could be distinguished from the other four species in this branch. These results further confirmed that these bacteria constitute a distinct rhizobial species. ~ ~~The genetic approaches now widely applied to the taxonomy of root nodule bacteria have opened the possibility to infer their phylogenies and to correctly define the species and genera of these bacteria. The improved methods for identifying bacteria and a growing interest in characterization of new rhizobial isolates have brought about many changes in the taxonomy of rhizobia since 1984; a revised taxonomic system for these bacteria was proposed in "Bergey's Manual of Systematic Bacteriology" (16). Several reviews on the development of rhizobial taxonomy and phylogeny have been published recently (20,33). The main developments include the descriptions of the genera Azorhizobium (S), Sinorhizobium (4, 6 ) , and Mesorhizobium (14, IS), as well as many new species. Up to now, six distinct phylogenetic branches, Azorhizobium, Bradyrhizobium, the Rhizobium-Agrobacterium rhizogenes branch, Mesorhizobium (14), the Rhizobium galegae-Agrobacterium branch, and Sinorhizobium, have been identified, and all of them were located in the alpha subclass of Proteobacteria (6, 31-33). Mesorhizobium has been proposed recently by Jarvis et al. (14), and five species, M. loti (15), M. huakuii (3), M. ciceri (23), M. mediterraneum (22), and M. tianshanense (2) were included on the basis of the data from full sequences of 16s rRNA genes. A group of rhizobia named cluster U has been classified in this genus by 16s ribosomal DNA (rDNA) sequencing (6). Some isolates from nodules of Amolpha fruticosa also belong to it, as indicated by the PCR-based restriction fragment length polymorphism patterns of their 16s rDNA (unpublished data). M. tianshanense was described in our previous paper dealing with a group of rhizobia isolated from saline and arid soils in the Xinjiang region of China (2). Some of the strains in this species grow as slowly as Bradyrhizobium spp. Other strains grow faster than Bradyrhizobium but slower than Rhizobium leguminosarum. According to the data from the partial 16s rDNA sequence, this species belongs to the M. loti-M. huakuii branch ...

The chloroplast genome (plastome) of angiosperms (particularly photosynthetic members) is generally highly conserved, although structural rearrangements have been reported in a few lineages. In this study, we revealed Corydalis to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced Corydalis plastomes that represent all the three subgenera of Corydalis, we detected (1) two independent relocations of the same five genes (trnV-UAC-rbcL) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the atpH gene in Corydalis saxicola or the trnK-UUU gene in both Corydalis davidii and Corydalis hsiaowutaishanensis; (2) relocation of the rps16 gene from the LSC region to the inverted repeat (IR) region in Corydalis adunca; (3) uniform inversion of an 11–14 kb segment (ndhB-trnR-ACG) in the IR region of all the four Corydalis species (the same below); (4) expansions (>10 kb) of IR into the small single-copy (SSC) region and corresponding contractions of SSC region; and (5) extensive pseudogenizations or losses of 13 genes (accD, clpP, and 11 ndh genes). In addition, we also found that the four Corydalis plastomes exhibited elevated GC content in both gene and intergenic regions and high number of dispersed repeats. Phylogenomic analyses generated a well-supported topology that was consistent with the result of previous studies based on a few DNA markers but contradicted with the morphological character-based taxonomy to some extent. This study provided insights into the evolution of plastomes throughout the three Corydalis subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of Corydalis.

The complete mitochondrial genome of Choroterpides apiculata (Ephemeroptera: Leptophlebiidae) is typically a circular molecule of 15,199 bp in length, containing 37 genes (13 protein-coding genes, 22 tRNAs, and two rRNAs) and one control region. The overall A þ T content of the whole genome is 74% and the A þ T content of the control region is 79.7%. In Bayesian inference and maximum-likelihood phylogenetic trees using 24 species from 13 families of Ephemeroptera, the monophyly of the families Isonychiidae, Heptageniidae, Vietnamellidae, Leptophlebiidae, Caenidae, and Baetidae were highly supported and C. apiculata was a sister group to Habrophlebiodes zijinensis.

A robust backbone phylogeny is fundamental for developing a stable classification and is instructive for further research. However, it was still not available for Corydalis DC., a species-rich (> 500 species), ecologically and medically important, but taxonomically notoriously difficult genus. Here, we constructed backbone phylogeny and estimated the divergence of Corydalis based on the plastome data from 39 Corydalis species (32 newly sequenced), which represent ca. 80% of sections and series across this genus. Our phylogenetic analyses recovered six fully supported main clades (I–VI) and provided full support for the majority of lineages within Corydalis. Section Archaeocapnos was unexpectedly turned out to be sister to the rest of the subg. Corydalis s. l. (clades IV–VI), thus treating as a distinct clade (clade III) to render all the main clades monophyletic. Additionally, some unusual plastome structural rearrangements were constantly detected within Corydalis and were proven to be lineage-specific in this study, which, in turn, provided further support to our phylogeny. A segment containing five genes (trnV-UAC–rbcL) in the plastome's LSC region was either normally located downstream of the ndhC gene in clade I species or translocated downstream of the atpH gene in clade II species or translocated to downstream of the trnK-UUU gene in clade III–VI species. The unique large inversion (ca. 50 kb) in the plastome LSC region of clade III species, representing an intermediate stage of the above translocation in clades IV–VI, firmly supported clade III as a distinct and early diverged clade within this large lineage (clades III–VI). Our phylogeny contradicted substantially with the morphology-based taxonomy, rejected the treatment of tuberous species as an independent evolutionary group, and proved that some commonly used diagnostic characters (e.g., root and rhizome) were results of convergent evolution, suggestive of unreliability in Corydalis. We dated the origin of crown Corydalis to the early Eocene (crown age 49.08 Ma) and revealed possible explosive radiation around 25 Ma, coinciding with the drastic uplift of the Qinghai-Tibetan Plateau in Oligocene and Miocene. This study provided the most reliable and robust backbone phylogeny of Corydalis to date and shed some new insights on the evolution of Corydalis.

The complete chloroplast genome of Corydalis inopinata Prain ex Fedde was assembled and characterized in this study. The chloroplast genome was 181,335 bp in length, consisting of a large single-copy (LSC) region of 91,727 bp, a small single-copy (SSC) region of 1502 bp, and a pair of inverted repeat (IR) regions of 44,053 bp. It encoded 110 unique genes, including 68 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 9 pseudogenes. Phylogenetic analyses by maximum likelihood (ML) and Bayesian inference (BI) revealed that C. inopinata was closely related to C. conspersa Maxim. with full support in the present sampling. The complete plastid genome provided in this work would be useful for elucidating the taxonomy, phylogeny, and evolution of C. inopinata and other related species.