Straight From the Plastome: Molecular Phylogeny and Morphological Evolution of Fargesia (Bambusoideae: Poaceae)

The complete chloroplast genome of Fargesia angustissima T. P. Yi: a panda dietary bamboo species

Fargesia angustissima T. P. Yi, categorized into Arundinarieae (Poaceae: Bambusoideae), is a critical species endemic to Minshan Mountain, China. F. angustissima provides shelter and food sources for the giant panda and other endangered animals (e.g. red panda and snub-nosed monkey). This study assembled the complete chloroplast (cp) genome of F. angustissima using the high-throughput sequencing technique. The total cp length was 139,706 bp, containing 130 annotated genes with predicted GC content at 38.87%. The cp genome comprises two single-copy (LSC and SSC) regions, harboring 83,282 bp and 12,830 bp, respectively. The SSC regions were located between two inverted repeats (IR) regions (21,797 bp). Reconstruction of the phylogenetic tree illustrated that F. angustissima clustered F. canaliculata in Fargesia II. The study provides theoretical clues to explore the geographical distribution and species-level identification of the Fargesia genus.

Comparative plastomes of Pueraria montana var. lobata (Leguminosae: Phaseoleae) and closely related taxa: insights into phylogenomic implications and evolutionary divergence

BACKGROUND

Pueraria montana var. lobata (kudzu) is an important food and medicinal crop in Asia. However, the phylogenetic relationships between Pueraria montana var. lobata and the other two varieties (P. montana var. thomsonii and P. montana var. montana) remain debated. Although there is increasing evidence showing that P. montana var. lobata adapts to various environments and is an invasive species in America, few studies have systematically investigated the role of the phylogenetic relationships and evolutionary patterns of plastomes between P. montana var. lobata and its closely related taxa.

RESULTS

26 newly sequenced chloroplast genomes of Pueraria accessions resulted in assembled plastomes with sizes ranging from 153,360 bp to 153,551 bp. Each chloroplast genome contained 130 genes, including eight rRNA genes, 37 tRNA genes, and 85 protein-coding genes. For 24 newly sequenced accessions of these three varieties of P. montana, we detected three genes and ten noncoding regions with higher nucleotide diversity (π). After incorporated publically available chloroplast genomes of Pueraria and other legumes, 47 chloroplast genomes were used to construct phylogenetic trees, including seven P. montana var. lobata, 14 P. montana var. thomsonii and six P. montana var. montana. Phylogenetic analysis revealed that P. montana var. lobata and P. montana var. thomsonii formed a clade, while all sampled P. montana var. montana formed another cluster based on cp genomes, LSC, SSC and protein-coding genes. Twenty-six amino acid residues were identified under positive selection with the site model. We also detected six genes (accD, ndhB, ndhC, rpl2, rpoC2, and rps2) that account for among-site variation in selective constraint under the clade model between accessions of the Pueraria montana var. lobata clade and the Pueraria montana var. montana clade.

CONCLUSION

Our data provide novel comparative plastid genomic insights into conservative gene content and structure of cp genomes pertaining to P. montana var. lobata and the other two varieties, and reveal an important phylogenetic clue and plastid divergence among related taxa of P. montana come from loci that own moderate variation and underwent modest selection.

Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia

Fargesia, the largest genus within the temperate bamboo tribe Arundinarieae, has more than 90 species mainly distributed in the mountains of Southwest China. The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals, including the giant panda. However, species-level identification of Fargesia is difficult. Moreover, the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes (rbcL, matK, and ITS) in bamboos. With progress in the sequencing technologies, complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) sequences have been proposed as organelle barcodes for species identification; however, these have not been tested in bamboos. We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes. Our analysis indicates that complete plastomes have substantially higher discriminatory power (28.6%) than standard barcodes (5.7%), whereas nrDNA sequences show a moderate improvement (65.4%) compared to ITS (47.2%). We also found that nuclear markers performed better than plastid markers, and ITS alone had higher discriminatory power than complete plastomes. The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia. However, neither of these sequences were able to discriminate all the sampled species, and therefore, more nuclear markers need to be identified.

Inflorescences of Fargesiaangustissima T.P. Yi and Yushaniapauciramificans T.P. Yi (Poaceae, Bambusoideae) shed light on the taxonomy of the Sino-Himalayan alpine bamboos

The taxonomy of the Sino-Himalayan alpine bamboos is controversial due to their complex evolutionary history and further complicated by the scarcity of inflorescence. Here, we supplement the description of the inflorescence of Fargesiaangustissima T.P. Yi and Yushaniapauciramificans T.P. Yi, which shed light on the taxonomy of Fargesia Franchet, Borinda Stapleton and Yushania Keng. F.angustissima has compressed inflorescence unilateral stretching out from reduced spathe, showing a transitional state between species with condensed inflorescence embraced by spathe-like bracts and species with open inflorescence without bracts. Considering that extensive gene flow existed between several clades of Fargesia found in recent studies, a broadly-defined Fargesia s. l. should be adopted. Meanwhile, the inflorescence of Y.pauciramificans has typical characteristics of Yushania, such as axilla with tuberculate glands, rachilla internodes ciliate and cylindrical florets, supporting the delimitation of Yushania.

Two new species of Fargesia (Poaceae, Bambusoideae) from southwestern China

Two new species of Fargesia, one from Xizang (Tibet) and one from Yunnan, China, are described and illustrated. Fargesia viridis D.Z. Li & X.Y. Ye is characterized by its densely white powder, nearly solid internodes, yellow setose sheath scar and culm sheaths, and 4-6 leaves of large size. Fargesia purpurea D.Z. Li & X.Y. Ye has thinner culms (0.5-1.4 cm in diameter), a ring of 4-5 mm tall brown setae below nodes, fewer branches, glabrous sheath scar and culm sheaths, differentiated from the related species.

Extensive reticulate evolution within Fargesia (s.l.) (Bambusoideae: Poaceae) and its allies: Evidence from multiple nuclear markers

Reticulate evolution resulting from hybridization and introgression has been recognized as a creative source of species and diversification in bamboos. Previous phylogenetic studies revealed that Fargesia (s.l.) (Fargesia and Yushania) was divided into the Fargesia spathe clade and the non-spathe clade. Interestingly, the Fargesia spathe clade may have originated from hybridization among other clades within Fargesia (s.l.). Understanding the hybrid origin of this clade requires a robust phylogenetic framework in which major clades within Fargesia (s.l.) are resolved. Here, we used three nuclear genes to reconstruct the evolutionary history of Fargesia (s.l.) and its allies to identify putative patterns in the origin of the Fargesia spathe clade and to examine the extent to which reticulate evolution has occurred at the interspecific level in bamboos. Bashania species form a clade with Fargesia (s.l.), which is further divided into Group I and Group II. The Fargesia spathe clade, the Alpine Bashania clade, and Fargesia yajiangensis comprise Group I, while the Bashania fargesii clade and the remaining Fargesia (s.l.) species form Group II. Incongruence between the current nuclear-based and previous plastid phylogenies demonstrate several possible hybridization events among Fargesia (s.l.) species and related taxa, which have given rise to the Fargesia spathe clade, the Phyllostachys clade, and the Ampelocalamus clade. We also detected several putative hybrid species of Fargesia (s.l.). Our results show that reticulate evolution has played a prominent role in Fargesia (s.l.) evolution, which could, in part, account for the taxonomic difficulty associated with Fargesia (s.l.) and the alpine bamboos. The study also underscores the importance of hybridization in the evolution of bamboos, at both intergeneric and intrageneric levels.

Two plastomes of Phyllostachys and reconstruction of phylogenic relationship amongst selected Phyllostachys species using genome skimming

The genus Phyllostachys is economically important; however, only a small amount of complete plastid genomes have been reported to date. Here, we characterized two complete chloroplast genomes of Phyllostachys using genome skimming. The chloroplast genomes of Phyllostachys reticulata and Phyllostachys edulis ‘Pachyloen’ were 136,689 bp and 139,678 bp in length, respectively, and their GC contents were 38.8% and 38.9%, respectively. The sequences of each species contained 132 unique genes, including 39 tRNA, eight rRNA, and 85 protein-coding genes. Phylogenetic analysis shows that all selected Phyllostachys species were grouped into one well-supported clade in the Phyllostachys clade (V) of Arundinarieae. Moreover, in terms of chloroplast genome size, structure, and composition, P. edulis ‘Pachyloen’ is identical to P. edulis, further indicating the affinity between them.