Molecular cytogenetic characterization of natural hybrids of Roegneria stricta and Roegneria turczaninovii (Triticeae: Poaceae)

Hybridization is an important part of species evolution. The hybrid progeny population had rich genetic and phenotypic variation, which made the boundaries between them and their parents blurred and difficult to distinguish. There was little research on the origin of natural hybrids of Triticeae. In this study, we found a large number of putative hybrids of Roegneria in West Sichuan Plateau, China. The hybrid plants showed strong heterosis in plant height, tiller number and floret number. Morphologically, the putative hybrids showed intermediate of Roegneria stricta Keng and Roegneria turczaninovii (Drob.) Nevski. Hybrids had 28 chromosomes corresponding to that of R. stricta and R. turczaninovii (2n=4x=28). Meiotic pairing in hybrids were less regular than those of R. stricta and R. turczaninovii. GISH analysis showed that the hybrid plants had the same genome as that of R. stricta and R. turczaninovii (StY). Phylogenetic analysis based on the single copy nuclear gene DMC1 and chloroplast gene rps16 showed the plants were closely related to R. stricta and R. turczaninovii. This study indicated that the plants were hybrids of R. stricta and R. turczaninovii. The results provided data for the utilization of hybrid. This study provided a case study of natural hybrids.

Shotgun sequencing decades-old lichen specimens to resolve phylogenomic placement of type material

Natural history collections, including name-bearing type specimens, are an important source of genetic information. These data can be critical for appropriate taxonomic revisions in cases where the phylogenetic position of name-bearing type specimens needs to be identified, including morphologically cryptic lichen-forming fungal species. Here, we use high-throughput metagenomic shotgun sequencing to generate genome-scale data from decades-old (i.e., more than 30 years old) isotype specimens representing three vagrant taxa in the lichen-forming fungal genus Rhizoplaca, including one species and two subspecies. We also use data from high-throughput metagenomic shotgun sequencing to infer the phylogenetic position of an enigmatic collection, originally identified as R. haydenii, that failed to yield genetic data via Sanger sequencing. We were able to construct a 1.64 Mb alignment from over 1200 single-copy nuclear gene regions for the Rhizoplaca specimens. Phylogenomic reconstructions recovered an isotype representing Rhizoplaca haydenii subsp. arbuscula within a clade comprising other specimens identified as Rhizoplaca haydenii subsp. arbuscula, while an isotype of R. idahoensis was recovered within a clade with substantial phylogenetic substructure comprising Rhizoplaca haydenii subsp. haydenii and other specimens. Based on these data and morphological differences, Rhizoplaca haydenii subsp. arbuscula is elevated to specific rank as Rhizoplaca arbuscula. For the enigmatic collection, we were able to assemble the nearly complete nrDNA cistron and over 50 Mb of the mitochondrial genome. Using these data, we identified this specimen as a morphologically deviant form representing Xanthoparmelia aff. subcumberlandia. This study highlights the power of high-throughput metagenomic shotgun sequencing in generating larger and more comprehensive genetic data from taxonomically important herbarium specimens.

Molecular phylogeny of Juniperus in Iran with special reference to the J. excelsa complex, focusing on J. seravschanica

A total of over 100 accessions representing 11 species of Juniperus in Iran using multiple DNA regions were included in phylogenetic analyses. Analyses of four plastid intergenic spacers (petN-psbM, trnD-trnT, trnL-trnF, trnS-trnG) and nrDNA ITS sequences retrieved Juniperus in Iran as a monophyletic group with two clades corresponding to sections Juniperus and Sabina. Our data support the recognition of J. communis, J. deltoides, J. foetidissima, J. polycarpos var. polycarpos and var. turcomanica, J. sabina and J. seravschanica in Iran. Based on sequences from nrDNA ITS, plastid petN-psbM and single copy nuclear gene LHCA, specimens from the SE Iran that were previously considered to be a part of the J. excelsa complex were shown to be J. seravschanica. Samples from NE Iran were found to be J. polycarpos var. turcomanica and specimens from NW Iran were shown to be J. polycarpos var. polycarpos. Plants belonging to the J. excelsa complex from SW Iran appear to be of hybrid origin between J. polycarpos from N Iran and J. seravschanica from SE Iran. None of the Juniperus samples from Iran were found to be J. excelsa s str., as compared with typical samples from Greece. The sequence data from nrDNA ITS, plastid petN-psbM, trnD-trnT, trnL-trnF, trnS-trnG and single copy nuclear genes (LHCA4, maldehy, myb, CnAIP3 and 4CL) were utilized in this study to identify Iranian samples R, U, K as J. seravschanica.

Identification of nuclear low-copy genes and their phylogenetic utility in rosids

By far, the interordinal relationships in rosids remain poorly resolved. Previous studies based on chloroplast, mitochondrial, and nuclear DNA has produced conflicting phylogenetic resolutions that has become a widely concerned problem in recent phylogenetic studies. Here, a total of 96 single-copy nuclear gene loci were identified from the KOG (eukaryotic orthologous groups) database, most of which were first used for phylogenetic analysis of angiosperms. The orthologous sequence datasets from completely sequenced genomes of rosids were assembled for the resolution of the position of the COM (Celastrales–Oxalidales–Malpighiales) clade in rosids. Our analysis revealed strong and consistent support for CM topology (the COM clade as sister to the malvids). Our results will contribute to further exploring the underlying cause of conflict between chloroplast, mitochondrial, and nuclear data. In addition, our study identified a few novel nuclear molecular markers with potential to investigate the deep phylogenetic relationship of plants or other eukaryotic taxonomical groups.