Diversity and community assembly mechanism of soil ectomycorrhizal fungi in urban parks of Baotou City, China.

Ectomycorrhizal (EM) fungi play an important role in forest ecosystems. However, little is known about the mechanisms driving diversity and community composition of soil EM fungi in urban forest parks which are intensively affected by anthropogenic activities. In this study, we investigated the EM fungal community using Illumina high-throughput sequencing with soil samples collected from three typical forest parks, including Olympic Park, Laodong Park, and Aerding Botanical Garden of Baotou City. The results showed that soil EM fungi richness index followed a pattern of Laodong Park (146.43±25.17) > Aerding Botanical Garden (102.71±15.31) > Olympic Park (68.86±6.83). Russula, Geopora, Inocybe, Tomentella, Hebeloma, Sebacina, Amanita, Rhizopogon, Amphinema, and Lactarius were the dominant genera in the three parks. EM fungal community composition was significantly different among the three parks. Results of linear discriminant analysis effect size (LEfSe) indicated that all parks had biomarker EM fungi that exhibiting significantly different abundance. The normalized stochasticity ratio (NST) and the inferring community assembly mechanisms by phylogenetic-bin-based null model analysis (iCAMP) showed that both stochastic and deterministic processes determined soil EM fungal communities in the three urban parks, with a dominant role of the stochastic process. Drift and dispersal limitation in the stochastic process and homogeneous selection in the deterministic process were the dominant ecological processes of soil EM fungal community assembly in the three urban parks.

Characterization of the complete chloroplast genome of Hedysarum polybotrys var. alaschanicum (Fabaceae) and its phylogeny.

Hedysarum polybotrys var. alaschanicum is an important medicinal plant and is widely used in traditional Chinese medicine. The complete chloroplast genome of H. polybotrys var. alaschanicum was assembled from Illumina pair-end sequence reads. The whole chloroplast genome is 122,933 bp in length and encodes a total of 110 genes, including 76 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The overall GC content of the cp genome is 35.3%. A maximum likelihood (ML) phylogenetic analysis revealed that H. polybotrys var. alaschanicum was close to Hedysarum semenovii.

Characteristic and phylogenetic analyses of chloroplast genome for Ephedra monosperma (Ephedraceae), an important medicinal species.

Ephedra monosperma is an important medicinal plant of Ephedra (Ephedraceae). The complete chloroplast genome of E. monosperma was assembled from Illumina pair-end sequence reads. The whole chloroplast (cp) genome is 109,548 bp in length and presents a quadripartite structure consisting of two copies of inverted repeat (IR) regions (20,398) separated by a large single copy (LSC) region (60,674 bp) and a small single copy (SSC) region (8078 bp). The cp genome of E. monosperma encodes a total of 118 genes, including 73 protein-coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of E. monosperma cp genome is 36.6%. A maximum likelihood (ML) phylogenetic analysis revealed that E. monosperma was close to Ephedra equisetina. The ML tree also showed Ephedraceae appeared more closely related to Gnetaceae than to the other families in Gymnospermae.

Evaluating Population Genetic Structure and Demographic History of Quercus spinosa (Fagaceae) Based on Specific Length Amplified Fragment Sequencing.

Effectively identifying the genetic structure and related factors of a species can facilitate understanding the evolutionary history of the species. Phylogeographic patterns and genetic data are essential in investigating the species historical processes and diversification that response to environmental, climatic and geological influences. In this study, Specific Length Amplified Fragment Sequencing (SLAF-seq) data and ecological niche models (ENMs) are combined to identify the genetic structure and demographic modeling of Quercus spinosa, and evaluate the impacts of historical range shifts, climatic variation, and landscape factors on this species. The population topology and genetic divergence of the Cenozoic were inferred by a site frequency spectrum based composite-likelihood approach which is a novel strategy for maximizing the utility of linked SLAF markers. The overall genetic structure using model-based and model-free clustering methods was consistently identified as two geographically distinct genetic clusters. A deep divergence between two natural lineages (i.e., a western Himalaya-Hengduan Mountains lineage and an eastern Qin-ling Mountains lineage) was observed. The demographic modeling and Niche reconstruction indicated that the two groups were diverged in the late Miocene and then presented as two distinct genetic lineages. With the Quaternary glacial climate fluctuation, two groups had continuous asymmetrical secondary contact and gene exchange in the Sichuan Basin during the last glacial maximum. Besides, a significant relationship between genetic distance and geography in all individuals was identified by the Mantel test. Overall, this study 1) contributes to a better understanding of the role played by Quaternary climatic fluctuation in the present-day distributions of Q. spinosa; 2) provides a comprehensive view of the genome-wide variation of sclerophyllous forests in ecological adaptive evolution; 3) indicates that dispersal limitation and ecological divergence contribute to the genome-wide differentiation of Q. spinosa, which supports a hypothesis that complex geography and climatic changes strongly influence the evolutionary origin and history of the species.

The complete chloroplast genome of Dipteronia sinensis (Aceraceae), an endangered endemic species to China.

The complete chloroplast sequence of D. sinensis was reported in this study. The total length was 157 080 bp containing a pair of 26 766 bp inverted repeat regions (IRa and IRb), which were separated by a small single copy regions and a large single copy regions (SSC and LSC) of 18 093 and 85 455 bp, respectively. A total of 138 functional genes were annotated, which included 90 protein-coding genes, 40 tRNAs, and eight rRNA genes. The overall GC content of the complete chloroplast genome is 37.8% and in LSC, SSC and IR regions were 35.9%, 32.1%, and 42.7%, respectively. The maximum likelihood (ML) phylogenetic analysis revealed that D. sinensis was closely related to A. buergerianum subsp. Ningpoense in Sapindales order.

The complete chloroplast genome of Quercus baronii (Quercus L.).

Quercus baronii is an endemic species to China. The total length of the Q. baronii chloroplast genome is 161 072 bp. It exhibits typical quadripartite structure, composed of two copies of inverted repeat (IR) regions (25 843 bp), large single copy (LSC) region (90 341 bp), and small single copy (SSC) region (19 045 bp). The genome contains 134 genes, including 86 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed its relationship with reported Quercus L. species.