Phylogenomic analysis, cryptic species discovery, and DNA barcoding of the genus Cibotium in China based on plastome data.

Germplasm resources are the source of herbal medicine production. The cultivation of superior germplasm resources helps to resolve the conflict between long-term population persistence and growing market demand by consistently producing materials with high quality. The fern species Cibotium barometz is the original plant of cibotii rhizoma ("Gouji"), a traditional Chinese medicine used in the therapy of pain, weakness, and numbness in the lower extremities. Long-history medicinal use has caused serious wild population decline in China. Without sufficient understanding of the species and lineage diversity of Cibotium, it is difficult to propose a targeted conservation scheme at present, let alone select high-quality germplasm resources. In order to fill such a knowledge gap, this study sampled C. barometz and relative species throughout their distribution in China, performed genome skimming to obtain plastome data, and conducted phylogenomic analyses. We constructed a well-supported plastome phylogeny of Chinese Cibotium, which showed that three species with significant genetic differences are distributed in China, namely C. barometz, C. cumingii, and C. sino-burmaense sp. nov., a cryptic species endemic to NW Yunnan and adjacent regions of NE Myanmar. Moreover, our results revealed two differentiated lineages of C. barometz distributed on the east and west sides of a classic phylogeographic boundary that was probably shaped by monsoons and landforms. We also evaluated the resolution of nine traditional barcode loci and designed five new DNA barcodes based on the plastome sequence that can distinguish all these species and lineages of Chinese Cibotium accurately. These novel findings on a genetic basis will guide conservation planners and medicinal plant breeders to build systematic conservation plans and exploit the germplasm resources of Cibotium in China.

[Response of Soil Respiration Rates to Soil Temperature and Moisture at Different Soil Depths of Caragana korshinskii Plantation in the Loess-Hilly Region].

It is of great significance to clarify the influence of soil temperature and moisture on soil respiration rate and its characteristics in ecologically fragile regions under the background of climate change for the accurate assessment and prediction of carbon budgets in this region. The average CO2 concentration and soil temperature and moisture at different soil depths (10, 50, and 100 cm) were measured using a CO2 analyzer and temperature and moisture sensors. The soil respiration rate was calculated using Fick's first diffusion coefficient method. The dynamic characteristics of soil temperature, soil moisture, and soil respiration rate in different soil depths were explored, and the response of soil respiration rate to soil temperature and moisture were further analyzed. The results showed that the diurnal variation in soil respiration rate decreased significantly with the increase in soil depth (P<0.05), and the peak time lagged behind. Soil respiration rate in adjacent soil depths (10, 50, and 100 cm) lagged 1 h from top to bottom. The monthly variation in soil respiration rate was a multi-peak curve, in which the maximum soil respiration rates of 10, 50, and 100 cm soil depths were on July 25th, August 6th, and August 10th, reaching 13.96, 2.96, and 1.47 µmol·(m2·s)-1, respectively. The effect of soil temperature on soil respiration rate decreased with the increase in soil depth. Soil temperature at 50 cm and below had no significant effect on soil respiration rate (P>0.05). The fitting index of 10 cm soil depth was the best (R2=0.96), but the fitting indexes of 50 cm and 100 cm soil depths were poor (R2=0.00 and R2=0.01, respectively). The temperature sensitivity coefficient Q10 decreased with the increase in soil depth. Soil moisture in different soil depths had significant effects on soil respiration rate (P<0.05), and the quadratic fitting indicated that 50 cm (R2=0.35)>10 cm (R2=0.22)>100 cm (R2=0.31). The combined effects of soil temperature and moisture in different soil depths could explain 96%, 6%-50%, and 22%-24% of soil respiration rate, respectively. In summary, the effects of soil temperature and moisture at different soil depths of the Caragana korshinskii plantation in the loess-hilly region on soil respiration rate differed. The soil respiration rate of the 10 cm soil depth was affected by the comprehensive effect of soil temperature and moisture; however, the relative contribution of soil temperature was higher, and soil moisture at and below a soil depth of 50 cm was the key factor. These results could help improve predictions on the impact of future climate change on the carbon cycle of terrestrial ecosystems in the region and provide a theoretical basis for greenhouse gas regulation in the future.

Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity.

The formation of spatial genetic structure with the presence of extensive gene flow, an evolutionary force which is generally expected to eliminate population-specific variation and maintain genetic homogeneity, remains poorly understood. Homosporous ferns, which spread by spores through wind and possess long distance dispersal capacity, provide an ideal system to investigate such a process. Here, using a homoploid fern lineage, the Athyrium sinense complex, we used reduced-representation genomic data to examine spatial genetic structure and explored potential driving forces including geographical distance, environment, climatic history and external dispersal constraints. Our findings showed a clear north-south divergence at the genetic, morphological and ecological levels between both sides of 35°N in East Asia. Fluctuant and heterogeneous climatic condition was demonstrated to play a crucial role during the formation of the divergence. Our results suggested that this lineage was able to migrate southward and colonize new habitat as a result of the Quaternary climatic fluctuation. Furthermore, the present genetic structure is attributed to adaptation to heterogeneous environments, especially temperature difference. In addition to ecological adaptation, we found clues showing that canopy density, wind direction as well as habitat continuity were all likely to constrain the effect of gene flow. These results demonstrated a diversification process without ploidy changes in ferns providing new insights for our present knowledge on ferns' spatio-temporal evolutionary pattern. In particular, our study highlights the influence of environmental heterogeneity in driving genetic divergence against strong dispersal capacity.

Plastid phylogenomics provides novel insights into the infrafamilial relationship of Polypodiaceae.

The polygrammoids (Polypodiaceae) are the most species-rich and diversified epiphytic fern lineages, and hold an important role to understand the deep diverging events and rapid adaptation to changing environments in the plant tree of life. Despite progress in the phylogeny of this group of ferns in previous multilocus phylogenetic studies, uncertainty remains especially in backbone relationships among closely related clades, and the phylogenetic placement of recalcitrant species or lineages. Here, we investigated the deep phylogenetic relationships within Polypodiaceae by sampling all major lineages and using 81 plastid genomes (plastomes), of which 70 plastomes were newly sequenced with high-throughput sequencing technology. Based on parsimony, maximum-likelihood, Bayesian and multispecies coalescent analyses of genome skimming data, we achieved a better resolution of the backbone phylogeny of Polypodiaceae. Using simulated data matrices, we detected that potential phylogenetic artefacts, such as long-branch attraction and insufficient taxonomic sampling, may have a confounding impact on the incongruence of phylogenetic inferences. Furthermore, our phylogenetic analyses offer greater resolution than previous multilocus studies, providing a robust framework for future phylogenetic implications on the subfamilial taxonomy of Polypodiaceae. Our phylogenomic study not only demonstrates the advantage of a character-rich plastome dataset for resolving the recalcitrant lineages that have undergone rapid radiation, but also sheds new light on integrative explorations understanding the evolutionary history of large fern groups in the genomic era.

Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae.

Plastids and mitochondria are endosymbiotic organelles that store genetic information. The genomes of these organelles generally exhibit contrasting patterns regarding genome architecture and genetic content. However, they have similar genetic features in Selaginellaceae, and little is known about what causes parallel evolution. Here, we document the multipartite plastid genomes (plastomes) and the highly divergent mitochondrial genomes (mitogenomes) from spikemoss obtained by combining short- and long-reads. The 188-kb multipartite plastome has three ribosomal operon copies in the master genomic conformation, creating the alternative subgenomic conformation composed of 110- and 78-kb subgenomes. The long-read data indicated that the two different genomic conformations were present in almost equal proportions in the plastomes of Selaginella nipponica. The mitogenome of S. nipponica was assembled into 27 contigs with a total size of 110 kb. All contigs contained directly arranged repeats at both ends, which introduced multiple conformations. Our results showed that plastomes and mitogenomes share high tRNA losses, GC-biased nucleotides, elevated substitution rates and complicated organization. The exploration of nuclear-encoded organelle DNA replication, recombination and repair proteins indicated that, several single-targeted proteins, particularly plastid-targeted recombinase A1, have been lost in Selaginellaceae; conversely, the dual-targeted proteins remain intact. According to the reported function of recombinase A1, we propose that the plastomes of spikemoss often fail to pair homologous sequences during recombination, and the dual-targeted proteins play a key role in the convergent genetic features of plastomes and mitogenomes. Our results provide a distinctive evolutionary pattern of the organelle genomes in Selaginellaceae and evidence of their convergent evolution.

[Responses of productivity of typical natural secondary forests and plantations to climate change in Shaanxi Province, China]. / é™•è¥¿çœå ¸åž‹å¤©ç„¶æ¬¡ç”Ÿæž—å’Œäººå·¥æž—ç”Ÿäº§åŠ›å¯¹æ°”å€™å˜åŒ–çš„å“åº”.

We analyzed the changes of net primary productivity (NPP) and net ecosystem productivity (NEP) of Quercus spp. forest and Robinia pseudoacacia plantation under different future climate scenarios in Shaanxi Province during 2015-2100, using the process-based dynamic vegetation model-LPJ-GUESS. The results showed that compared with the benchmark period (1961-1990), NPP of Quercus spp. forest and R. pseudoacacia plantation in northern Shaanxi would decrease by 4.9%-29.5% and 22.5%-56.2% respectively, while that in Guanzhong and southern Shaanxi would increase by 13.0%-49.0% and 21.3%-62.9% respectively in the future. The NPP of Quercus spp. forest and R. pseudoacacia plantation under the RCP8.5 scenario was the highest, followed by that under the RCP4.5 and RCP2.6 scenarios. Those two types of forest would be carbon sink in three subregions in the future. Quercus spp. forest would have stronger carbon sink function in nor-thern Shaanxi and Guanzhong, while R. pseudoacacia plantation would have stronger carbon sink function in Southern Shaanxi. Under different RCP scenarios, the NEP variation range of R. pseu-doacacia plantation was greater than that of Quercus spp. forest in three subregions.