New Insight into Taxonomy of European Mountain Pines, Pinus mugo Complex, Based on Complete Chloroplast Genomes Sequencing

Comparative and Phylogenetic Analyses of Complete Chloroplast Genomes of Scrophularia incisa Complex (Scrophulariaceae)

The Scrophularia incisa complex is a group of closely related desert and steppe subshrubs that includes S. incisa, S. kiriloviana and S. dentata, which are the only S. sect. Caninae components found in Northwest China. Based on earlier molecular evidence, the species boundaries and phylogenetic relationships within this complex remain poorly resolved. Here, we characterized seven complete chloroplast genomes encompassing the representatives of the three taxa in the complex and one closely related species, S. integrifolia, as well as three other species of Scrophularia. Comparative genomic analyses indicated that the genomic structure, gene order and content were highly conserved among these eleven plastomes. Highly variable plastid regions and simple sequence repeats (SSRs) were identified. The robust and consistent phylogenetic relationships of the S. incisa complex were firstly constructed based on a total of 26 plastid genomes from Scrophulariaceae. Within the monophyletic complex, a S. kiriloviana individual from Pamirs Plateau was identified as the earliest diverging clade, followed by S. dentata from Tibet, while the remaining individuals of S. kiriloviana from the Tianshan Mountains and S. incisa from Qinghai-Gansu were clustered into sister clades. Our results evidently demonstrate the capability of plastid genomes to improve phylogenetic resolution and species delimitation, particularly among closely related species, and will promote the understanding of plastome evolution in Scrophularia.

Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of ‘Saccharum Complex’

High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ‘Saccharum Complex’, and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species.

Characterization of the Complete Chloroplast Genome Sequence of the Socotra Dragon`s Blood Tree (Dracaena cinnabari Balf.)

The Socotra dragon`s blood tree (Dracaena cinnabari Balf.) is endemic to the island of Socotra in Yemen. This iconic species plays an essential role in the survival of associated organisms, acting as an umbrella tree. Overexploitation, overgrazing by livestock, global climate change, and insufficient regeneration mean that the populations of this valuable species are declining in the wild. Although there are many studies on the morphology, anatomy, and physiology of D. cinnabari, no genomic analysis of this endangered species has been performed so far. Therefore, the main aim of this study was to characterize the complete chloroplast sequence genome of D. cinnabari for conservation purposes. The D. cinnabari chloroplast genome is 155,371 bp with a total GC content of 37.5%. It has a quadripartite plastid genome structure composed of one large single-copy region of 83,870 bp, one small single-copy region of 18,471 bp, and two inverted repeat regions of 26,515 bp each. One hundred and thirty-two genes were annotated, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Forty simple sequence repeats have also been identified in this chloroplast genome. Comparative analysis of complete sequences of D. cinnabari chloroplast genomes with other species of the genus Dracaena showed a very high conservativeness of their structure and organization. Phylogenetic inference showed that D. cinnabari is much closer to D. draco, D. cochinchinensis, and D. cambodiana than to D. terniflora, D. angustifolia, D. hokouensis, and D. elliptica. The results obtained in this study provide new and valuable omics data for further phylogenetic studies of the genus Dracaena as well as enable the protection of genetic resources of highly endangered D. cinnabari.

Assessment of ITS2 Region Relevance for Taxa Discrimination and Phylogenetic Inference among Pinaceae

The internal transcribed spacer 2 (ITS2) is one of the best-known universal DNA barcode regions. This short nuclear region is commonly used not only to discriminate taxa, but also to reconstruct phylogenetic relationships. However, the efficiency of using ITS2 in these applications depends on many factors, including the family under study. Pinaceae represents the largest family of extant gymnosperms, with many species of great ecological, economic, and medical importance. Moreover, many members of this family are representatives of rare, protected, or endangered species. A simple method for the identification of Pinaceae species based on DNA is necessary for their effective protection, authentication of products containing Pinaceae representatives, or phylogenetic inference. In this study, for the first time, we conducted a comprehensive study summarizing the legitimacy of using the ITS2 region for these purposes. A total of 368 sequences representing 71 closely and distantly related taxa of the seven genera and three subfamilies of Pinaceae were characterized for genetic variability and divergence. Intra- and interspecies distances of ITS2 sequences as well as rates of sequence identification and taxa discrimination among Pinaceae at various taxonomic levels, i.e., the species complex, genus, subfamily, and family, were also determined. Our study provides a critical assessment of the suitability of the ITS2 nuclear DNA region for taxa discrimination among Pinaceae. The obtained results clearly show that its usefulness for this purpose is limited.

Phylogeny of Maleae (Rosaceae) Based on Complete Chloroplast Genomes Supports the Distinction of Aria, Chamaemespilus and Torminalis as Separate Genera, Different from Sorbus sp

Several genera formerly contained within the genus Sorbus L. sensu lato have been proposed as separate taxa, including Aria, Chamaemespilus and Torminalis. However, molecular evidence for such distinctions are rather scarce. We assembled the complete chloroplast genome of Sorbus aucuparia, another representative of Sorbus s.s., and performed detailed comparisons with the available genomes of Aria edulis, Chamaemespilus alpina and Torminalis glaberrima. Additionally, using 110 complete chloroplast genomes of the Maleae representatives, we constructed the phylogenetic tree of the tribe using Maximum Likelihood methods. The chloroplast genome of S. aucuparia was found to be similar to other species within Maleae. The phylogenetic tree of the Maleae tribe indicated that A. edulis, C. alpina and T. glaberrima formed a concise group belonging to a different clade (related to Malus) than the one including Sorbus s.s. (related to Pyrus). However, Aria and Chamaemespilus appeared to be more closely related to each other than to Torminalis. Our results provide additional support for considering Aria, Chamaemespilus and Torminalis as separate genera different from Sorbus s.s.

On the Edge of Dispensability, the Chloroplast ndh Genes

The polypeptides encoded by the chloroplast ndh genes and some nuclear genes form the thylakoid NADH dehydrogenase (Ndh) complex, homologous to the mitochondrial complex I. Except for Charophyceae (algae related to higher plants) and a few Prasinophyceae, all eukaryotic algae lack ndh genes. Among vascular plants, the ndh genes are absent in epiphytic and in some species scattered among different genera, families, and orders. The recent identification of many plants lacking plastid ndh genes allows comparison on phylogenetic trees and functional investigations of the ndh genes. The ndh genes protect Angiosperms under various terrestrial stresses, maintaining efficient photosynthesis. On the edge of dispensability, ndh genes provide a test for the natural selection of photosynthesis-related genes in evolution. Variable evolutionary environments place Angiosperms without ndh genes at risk of extinction and, probably, most extant ones may have lost ndh genes recently. Therefore, they are evolutionary endpoints in phylogenetic trees. The low number of sequenced plastid DNA and the long lifespan of some Gymnosperms lacking ndh genes challenge models about the role of ndh genes protecting against stress and promoting leaf senescence. Additional DNA sequencing in Gymnosperms and investigations into the molecular mechanisms of their response to stress will provide a unified model of the evolutionary and functional consequences of the lack of ndh genes.