The complete chloroplast genome sequence of Picea schrenkiana (Pinaceae).
ABSTRACT: Picea is a phylogenetically complicate genus with great economic and ecological values. Here, we determined the whole complete chloroplast genome of Picea schrenkiana to provide genomic information for phylogenetic analysis of the genus. The plastome of P. schrenkiana is 124,060 bp in size and contains 114 genes, including 74 protein-coding genes, 36 tRNA genes, and four rRNA genes. The overall GC content is 38.7%. Unlike the typical plastome with a conserved quadripartite structure, loss of inverted repeat regions is found in the chloroplast genome. The phylogenetic tree shows that monophyly of P. schrenkiana is well supported.
Project description:Elucidating the evolutionary history of current species diversity, especially trees with large effective population sizes and long generation times, is a complicated exercise confounded by gene flow and incomplete lineage sorting. In the present study, we aim to determine the origin and speciation of <i>Picea schrenkiana</i> and <i>Picea smithiana</i> using population genetic data from chloroplast (cp), mitochondrial (mt), and nuclear (nr) genomes. These two species occur in the Central Asian Highlands and Himalayas, respectively, where they are isolated from other Asian congeneric species by the Qinghai-Tibet Plateau (QTP) or adjacent deserts. Previous studies based on both morphological and molecular evidence suggest that they have contrasting phylogenetic relationships with <i>Picea likiangensis</i> or <i>Picea wilsonii</i> which are closely related and both located in the QTP. We examined genetic variation among 16 loci of three genomes from 30 populations of these four species. At both cpDNA loci and mtDNA loci, <i>P. schrenkiana</i> appeared to be closely related to <i>P. likiangensis</i>, although statistical support for this was weak. However, phylogenetic analyses and speciation tests based on the nuclear data from 11 loci provided evidence that <i>P. schrenkiana</i> and <i>P. smithiana</i> are sister species. These two species diverged around five million years ago (Mya) while the divergence between them and the <i>P. likiangensis</i>-<i>P. wilsonii</i> clade occurred about 18.4 Mya. We also detected gene flow accompanying these speciation events. Our results highlight the complex speciation histories of these alpine conifers due to interspecific gene flow and/or incomplete lineage sorting, and the importance of the early QTP uplifts in promoting the origin of these important conifer species in the Asian highlands.
Project description:Picea Schrenkiana as one of the most important zonal vegetation was an endemic species in Middle Asia. Natural regeneration of P. Schrenkiana is a long existing problem troubling scientists. The autotoxicity of 3,4-dihydroxy-acetophenone (DHAP) was found to be a causative factor causing the failure of P. Schrenkiana natural regeneration. The effects of concentrations of DHAP treatment on the viability of root cell, activities of antioxidant enzymes and levels of P. Schrenkiana phytohormones were performed to disclose the physiological mechanism of DHAP autotoxicity. It was observed that high concentration of DHAP could inhibit the seed germination and seedling growth, but had a hormesis at low concentrations. Analyses showed that the root cells significantly lost their viability treated with high DHAP. The enzymes activities of seedlings were significantly stimulated by the treatment of 0.5 mM DHAP to give a transient increase and then decrease as DHAP concentration increased to 1.0 mM except for GR (glutathione reductase) in which DHAP treatment had little effect on its activity. Comparing with the control, an increase in the levels of phytohormones ZT (zeatin), GA3 (gibberellic acid) and IAA (indole acetic acid) was induced by the treatment of DHAP at low concentrations (0.1-0.25 mM), but the significant deficiency was found treated by high concentrations (0.5-1.0 mM). In addition, the ABA (abscisic acid) level increased in all experimental observations. These results suggested that DHAP significantly affected indices of growth and physiology, and provided some new information about different effect in P. Schrenkiana treated with DHAP.
Project description:Plastid sequences are a cornerstone in plant systematic studies and key aspects of their evolution, such as uniparental inheritance and absent recombination, are often treated as axioms. While exceptions to these assumptions can profoundly influence evolutionary inference, detecting them can require extensive sampling, abundant sequence data, and detailed testing. Using advancements in high-throughput sequencing, we analyzed the whole plastomes of 65 accessions of Picea, a genus of ?35 coniferous forest tree species, to test for deviations from canonical plastome evolution. Using complementary hypothesis and data-driven tests, we found evidence for chimeric plastomes generated by interspecific hybridization and recombination in the clade comprising Norway spruce (P. abies) and 10 other species. Support for interspecific recombination remained after controlling for sequence saturation, positive selection, and potential alignment artifacts. These results reconcile previous conflicting plastid-based phylogenies and strengthen the mounting evidence of reticulate evolution in Picea. Given the relatively high frequency of hybridization and biparental plastid inheritance in plants, we suggest interspecific plastome recombination may be more widespread than currently appreciated and could underlie reported cases of discordant plastid phylogenies.
Project description:Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3-0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4-8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.
Project description:Here, we present the complete chloroplast genome sequence of white spruce (Picea glauca, genotype WS77111), a coniferous tree widespread in the boreal forests of North America. This sequence contributes to genomic and phylogenetic analyses of the Picea genus that are part of ongoing research to understand their adaptation to environmental stress.
Project description:<i>Abies yuanbaoshanensis</i> is critically endangered and endemic to Guangxi province of China, with no more than 900 surviving individuals. In this study, we reported the complete chloroplast (cp) genome of <i>A. yuanbaoshanensis</i>. The complete chloroplast genome is 121897?bp in size. In total, 112 genes were identified, including 74 protein-coding genes, 34tRNA genes, and four rRNA genes. In phylogenetic analysis, the tree supported the monophyly of the genus <i>Abies</i>. The complete plastome of <i>A. yuanbaoshanensis</i> will provide potential genetic resources for further conservation and evolutionary studies of this highly endangered species.
Project description:As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies-Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix-Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix-Pseudotsuga-Piceae-Cathaya-Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, and Piceae-Cathaya-Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, Picea, and Cathaya-Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.
Project description:Knowledge about soil nitrogen (N) and phosphorus (P) concentrations, stocks, and stoichiometric ratios is crucial for understanding the biogeochemical cycles and ecosystem function in arid mountainous forests. However, the corresponding information is scarce, particularly in arid mountainous forests. To fill this gap, we investigated the depth and elevational patterns of the soil N and P concentrations and the N: P ratios in a Picea schrenkiana forest using data from soil profiles collected during 2012-2017. Our results showed that the soil N and P concentrations and the N: P ratios varied from 0.15 g kg-1 to 0.56 g kg-1 (average of 0.31 g kg-1), from 0.09 g kg-1 to 0.16 g kg-1 (average of 0.12 g kg-1), and from 2.42 g kg-1 to 4.36 g kg-1 (average of 3.42 g kg-1), respectively; additionally, values significantly and linearly decreased with soil depth. We did not observe a significant variation in the soil N and P concentrations and the N: P ratios with the elevational gradient. In contrast, our results revealed that the mean annual temperature and mean annual precipitation exhibited a more significant influence on the soil N and P concentrations and the N: P ratios than did elevation. This finding indicated that climatic variables might have a more direct impact on soil nutrient status than elevation. The observed relationship among the soil N and P concentrations and the N: P ratios demonstrated that the soil N was closely coupled with the soil P in the P. schrenkiana forest.