Demographic dynamics and molecular evolution of the rare and endangered subsect. Gerardianae of Pinus: insights from chloroplast genomes and mitochondrial DNA markers.

MAIN CONCLUSION: The divergence of subsect. Gerardianae was likely triggered by the uplift of the Qinghai-Tibetan Plateau and adjacent mountains. Pinus bungeana might have probably experienced expansion since Last Interglacial period. Historical geological and climatic oscillations have profoundly affected patterns of nucleotide variability, evolutionary history, and species divergence in numerous plants of the Northern Hemisphere. However, how long-lived conifers responded to geological and climatic fluctuations in East Asia remain poorly understood. Here, based on paternally inherited chloroplast genomes and maternally inherited mitochondrial DNA markers, we investigated the population demographic history and molecular evolution of subsect. Gerardianae (only including three species, Pinus bungeana, P. gerardiana, and P. squamata) of Pinus. A low level of nucleotide diversity was found in P. bungeana (π was 0.00016 in chloroplast DNA sequences, and 0.00304 in mitochondrial DNAs). The haplotype-based phylogenetic topology and unimodal distributions of demographic analysis suggested that P. bungeana probably originated in the southern Qinling Mountains and experienced rapid population expansion since Last Interglacial period. Phylogenetic analysis revealed that P. gerardiana and P. squamata had closer genetic relationship. The species divergence of subsect. Gerardianae occurred about 27.18 million years ago (Mya) during the middle to late Oligocene, which was significantly associated with the uplift of the Qinghai-Tibetan Plateau and adjacent mountains from the Eocene to the mid-Pliocene. The molecular evolutionary analysis showed that two chloroplast genes (psaI and ycf1) were under positive selection, the genetic lineages of P. bungeana exhibited higher transition and nonsynonymous mutations, which were involved with the strongly environmental adaptation. These findings shed light on the population evolutionary history of white pine species and provide striking insights for comprehension of their species divergence and molecular evolution.

Accumulation of livestock manure-derived heavy metals in the Hexi Corridor oasis agricultural alkaline soil and bioavailability to Chinese cabbage (Brassica pekinensis L.) after 4-year continuous application.

Hexi Corridor is one of the most important base of vegetable producing areas in China. Livestock manure (LM) applied to agricultural field could lead to soil heavy metal (HM) pollution. Previous studies have focused on HM pollution following LM application in acidic polluted soils; however, fewer studies have been conducted in alkaline unpolluted soils. A 4-year field vegetable production experiment was conducted using pig manure (PM) and chicken manure (CM) at five application rates (0, 15, 30, 45, and 60 t ha-1) to elucidate potential risks of HMs in an alkaline unpolluted soil in the Hexi Corridor oasis agricultural area and HM uptake by Chinese cabbage. The results showed that LM application caused a significant build-up of Cu, Zn, Pb, Cd, and Ni content in topsoil by 30.6-99.7%, 11.4-51.7%, 1.4-31.3%, 5.6-44.9%, 14%-40.8%, respectively. The Cd, Cu, Zn could potentially exceed the soil threshold in next 8-65 years after 15-60 t ha-1 LM application. Under LM treatment, the soil DTPA-extractable Cu, Zn, Fe, the acid-extractable fraction of Cu, Zn, Fe, Cd, Ni, and the Oxidable fraction of Cu, Zn, Fe, Mn, Cd, Ni significantly increased, but the DTPA-extractable Pb, Cd, the acid-extractable fraction of Pb, and the reducible fraction of Cd significantly decreased. Cu and Zn could migrate to the deeper soil and relatively increase in DTPA-extracted Cu, Zn were found in 20-40 cm soil depth after LM application. The pH and SOM could influence the bioavailability of HMs in soil. The bioaccumulation factor and transfer factor (TF) values were <1 except Mn (TF > 1). HMs in leaf did not approach the threshold for HM toxicity due to the "dilution effect". Recommend the type of manure was the PM and the annual PM application rate was 30 t ha-1 to ensure a 20-year period of clean production in alkaline unpolluted Fluvo-aqiuc vegetable soils.

Impacts of Climate Changes on Geographic Distribution of Primula filchnerae, an Endangered Herb in China.

Primula filchnerae, an endangered plant endemic to China, has drawn people's attention in recent years due to its ornamental value in flower. It was rarely recorded since being described in 1902, but it was rediscovered in 2009 and is now known from a limited number of sites located in Hubei and Shaanxi Provinces. Since the species is still poorly known, a number of unanswered questions arise related to it: How has P. filchnerae responded to past climate change and how might it respond in the future? Why was P. filchmerae so rarely collected during the past century? We assembled geographic coordinates for P. filchnerae through the field surveys and website searches, and then used a maximum entropy model (MaxEnt) to simulate its potential suitable distribution in six periods with varied carbon emission levels by combining bioclimatic and environmental factors. MaxEnt showed that Min Temperature of the Coldest Month (bio6) and Precipitation of the Coldest Quarter (bio19) affected P. filchnerae's distribution most, with an aggregate contribution >60% and suitable ranges above -5 °C and below 40 mm, respectively. We also analyzed potential habitat distribution in various periods with differing impacts of climate change compared to today's suitable habitats, and in most cases, Shaanxi and Sichuan remained the most stable areas and with possible expansion to the north under various carbon emission scenarios, but the 2050s SSP5-8.5 scenario may be an exception. Moreover, we used MaxEnt to evaluate population shifts, with various scenarios indicating that geometric center would be concentrated in Sichuan Province in China. Finally, conservation strategies are suggested, including the creation of protected areas, long-term monitoring, raising public awareness of plant conservation, situ conservation measures, assisted migration, and species introduction. This study demonstrates how P. filchnerae may have adapted to changes in different periods and provides a scientific basis for germplasm conservation and management.

FAM3 family genes are associated with prognostic value of human cancer: a pan-cancer analysis.

Family with sequence similarity three member (FAM3) plays a crucial role in the malignant development of various cancers of human. However, there remains doubtful what specific role of FAM3 family genes in pan-cancer. Our study aimed to investigate the role of FAM3 family genes in prognosis, immune subtype, tumor immune microenvironment, stemness score, and anticancer drug sensitivity of pan-cancer. We obtained data from UCSC Xena GDC and CellMiner databases, and used them to study the correlation of the expression, survival, immune subtype, tumor microenvironment, stemness score, and anticancer drug sensitivity between FAM3 family genes with pan-cancer. Furthermore, we investigated the tumor cellular functions and clinical prognostic value FAMC3 in pancreatic cancer (PAAD) using cellular experiments and tissue microarray. Cell Counting Kit-8 (CCK-8), transwell invasion, wound-healing and apoptosis assays were performed to study the effect of FAM3C on SW1990 cells' proliferation, migration, invasion and apoptosis. Immunohistochemical staining was used to study the relationship between FAM3C expression and clinical characteristics of pancreatic cancer patients. The results revealed that FAM3 family genes are significantly differential expression in tumor and adjacent normal tissues in 7 cancers (CHOL, HNSC, KICH, LUAD, LUSC, READ, and STAD). The expression of FAM3 family genes were negatively related with the RNAss, and robust correlated with immune type, tumor immune microenvironment and drug sensitivity. The expression of FAM3 family genes in pan-cancers were significantly different in immune type C1 (wound healing), C2 (IFN-gamma dominant), C3 (inflammatory), C4 (lymphocyte depleted), C5 (immunologically quiet), and C6 (TGF-beta dominant). Meanwhile, overexpression FAM3C promoted SW1990 cells proliferation, migration, invasion and suppressed SW1990 cells apoptosis. While knockdown of FAM3C triggered opposite results. High FAM3C expression was associated with duodenal invasion, differentiation and liver metastasis. In summary, this study provided a new perspective on the potential therapeutic role of FAM3 family genes in pan-cancer. In particular, FAM3C may play an important role in the occurrence and progression of PAAD.

Clinicopathological Characteristics, Prognosis, and Correlated Tumor Cell Function of Tropomodulin-3 in Pancreatic Adenocarcinoma.

BACKGROUND: Pancreatic adenocarcinoma (PAAD) is a frequent malignant tumor with a high mortality rate. Searching for novel biomarkers that can influence its prognosis may help patients. It has been shown that tropomodulin-3 (TMOD3) may influence tumor progression, but its role in pancreatic cancer is not clear. We aimed to explore the expression and prognostic value of TMOD3 in PAAD. METHODS: We used bioinformatics analysis to analyze the relationship between TMOD3 expression and clinicopathological features and prognosis and verified it with clinical data from tissue microarray. We also conducted in vitro cell experiments to explore the effects of TMOD3 on the function of PAAD cells. RESULTS: TMOD3 expression was found to be significantly higher in PAAD tissues than in matched paracancerous tissues (P < 0.05). Meanwhile, high TMOD3 expression was associated with significantly poorer overall survival (P < 0.05). Analysis of relevant clinicopathological characteristics data obtained from TCGA showed that high TMOD3 expression correlated with age, TNM stage, N stage, and M stage (P < 0.05). Analysis of correlation data obtained from tissue microarrays showed that high TMOD3 expression was associated with lymph node invasion, nerve invasion, macrovascular invasion, and TNM stage (P < 0.05). In addition, siRNA knockdown of TMOD3 significantly reduced the migration and invasion of PAAD cells. CONCLUSION: Our study shows that TMOD3 may be associated with the progression of PAAD cells, and that it is an independent risk factor for poor pathological features and prognosis of PAAD. It may be helpful as a prognostic indicator of clinical outcomes in PAAD patients.

Characterization of the complete chloroplast genome of Gypsophila huashanensis Y. W. Tsui & D. Q. Lu, an endemic herb species in China.

Gypsophila huashanensis Y. W. Tsui & D. Q. Lu (Caryophyllaceae) is an endemic herb species to the Qinling Mountains in China. In this study, we characterized its whole plastid genome using the Illumina sequencing platform. The complete plastid genome of G. huashanensis is 152,457 bp in length, including a large single-copy DNA region of 83,476 bp, a small single-copy DNA region of 17,345 bp, and a pair of inverted repeat DNA sequences of 25,818 bp. The genome contains 130 genes comprising 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Evolutionary analysis showed that the non-coding regions of Caryophyllaceae exhibit a higher level of divergence than the exon regions. Gene site selection analysis suggested that 11 coding protein genes (accD, atpF, ndhA, ndhB, petB, petD, rpoCl, rpoC2, rps16, ycfl, and ycf2) have some sites under protein sequence evolution. Phylogenetic analysis showed that G. huashanensis is most closely related to the congeneric species G. oldhamiana. These results are very useful for studying phylogenetic evolution and species divergence in the family Caryophyllaceae.

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.

Change of geographic distributions of the genus Morchella species responding to climate oscillations in East Asia.

Morchella is a rare macrofungi taxon with high medicinal and edible values. Influenced by recent climate oscillations and human activities, habitat fragmentation of this genus has been critical, leading to a rapid decline of the resource of Morchella. It is thus urgent to preserve Morchella species. Based on maximum entropy model (MaxEnt), and 102 geographic distribution records of Morchella species with 10 environmental factors, we simulated the changes of potential geographic distributions under the climatic conditions of the last glacial maximum (LGM), last interglacial (LIG), in contemporary period and future (2050, 2070). We further analyzed the potential changes of geographic distributions of Morchella species in East Asia under climate change and formulated the effective conservation strategies for Morchella. The results showed that the dominant environmental factors affecting the geographic distributions of Morchella species were mean temperature of coldest quarter, annual precipitation, elevation and temperature annual range, with the mean temperature of coldest quarter having the greatest contribution. Results of the species distribution models showed that the highly suitable regions for Morchella species were mainly distributed in parts of western China under contemporary period. From the LIG to LGM and then the current to the future period, the total suitable regions of Morchella species showed a trend of firstly decrease and then increase, while the highly suitable regions showed similar change with the total suitable regions. At present, there is an urgent need to conduct in situ conservation for the resources of Morchella species in highly suitable regions in western China, and to carry out ex situ conservation in the marginal ranges of highly suitable regions and moderately suitable regions of Shaanxi, Hebei, Shandong, and other regions in China.

The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis.

Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.

Distributional Response of the Rare and Endangered Tree Species Abies chensiensis to Climate Change in East Asia.

Globally, increasing temperatures due to climate change have severely affected natural ecosystems in several regions of the world; however, the impact on the alpine plant may be particularly profound, further raising the risk of extinction for rare and endangered alpine plants. To identify how alpine species have responded to past climate change and to predict the potential geographic distribution of species under future climate change, we investigated the distribution records of A. chensiensis, an endangered alpine plant in the Qinling Mountains listed in the Red List. In this study, the optimized MaxEnt model was used to analyse the key environmental variables related to the distribution of A. chensiensis based on 93 wild distribution records and six environmental variables. The potential distribution areas of A. chensiensis in the last interglacial (LIG), the last glacial maximum (LGM), the current period, and the 2050s and 2070s were simulated. Our results showed that temperature is critical to the distribution of A. chensiensis, with the mean temperature of the coldest quarter being the most important climatic factor affecting the distribution of this species. In addition, ecological niche modeling analysis showed that the A. chensiensis distribution area in the last interglacial experiencing population expansion and, during the last glacial maximum occurring, a population contraction. Under the emission scenarios in the 2050s and 2070s, the suitable distribution area would contract significantly, and the migration routes of the centroids tended to migrate toward the southern high-altitude mountains, suggesting a strong response from the A. chensiensis distribution to climate change. Collectively, the results of this study provide a comprehensive and multidimensional perspective on the geographic distribution pattern and history of population dynamics for the endemic, rare, and endangered species, A. chensiensis, and it underscores the significant impact of geological and climatic changes on the geographic pattern of alpine species populations.

Niche divergence at the intraspecific level in an endemic rare peony (Paeonia rockii): A phylogenetic, climatic and environmental survey.

Ecological factors have received increasing attention as drivers of speciation but also in the maintenance of postspeciation divergence. However, the relative significance of the responses of species to climate oscillations for driving niche divergence or conservatism in the evolution of many species that pass through diverse environments and limited geographical boundaries remains poorly understood. Paeonia rockii (one of the ancient species of Paeonia) comprising two subspecies called Paeonia rockii subsp. rockii and Paeonia rockii subsp. taibaishanica is an endemic, rare, and endangered medicinal plant in China. In this study, we integrated whole chloroplast genomes, and ecological factors to obtain insights into ecological speciation and species divergence in this endemic rare peony. RAxML analysis indicated that the topological trees recovered from three different data sets were identical, where P. rockii subsp. rockii and P. rockii subsp. taibaishanica clustered together, and molecular dating analyses suggested that the two subspecies diverged 0.83 million years ago. In addition, ecological niche modeling showed that the predicted suitable distribution areas for P. rockii subsp. rockii and P. rockii subsp. taibaishanica differed considerably, although the predicted core distribution areas were similar, where the population contracted in the last interglacial and expanded in the last glacial maximum. Under the emissions scenarios for the 2050s and 2070s, the suitable distribution areas were predicted to contract significantly, where the migration routes of the two subspecies tended to migrate toward high latitudes and elevations, thereby suggesting strong responses of the distributions of the two subspecies to climate change. These findings combined with the phylogeographic relationships provide comprehensive insights into niche variation and differentiation in this endemic rare peony, and they highlight the importance of geological and climatic changes for species divergence and changes in the population geographic patterns of rare and endangered medicinal plants in East Asia.

Maximum Entropy Modeling the Distribution Area of Morchella Dill. ex Pers. Species in China under Changing Climate.

Morchella is a kind of precious edible, medicinal fungi with a series of important effects, including anti-tumor and anti-oxidation effects. Based on the data of 18 environmental variables and the distribution sites of wild Morchella species, this study used a maximum entropy (MaxEnt) model to predict the changes in the geographic distribution of Morchella species in different historical periods (the Last Glacial Maximum (LGM), Mid Holocene (MH), current, 2050s and 2070s). The results revealed that the area under the curve (AUC) values of the receiver operating characteristic curves of different periods were all relatively high (>0.83), indicating that the results of the maximum entropy model are good. Species distribution modeling showed that the major factors influencing the geographical distribution of Morchella species were the precipitation of the driest quarter (Bio17), elevation, the mean temperature of the coldest quarter (Bio11) and the annual mean temperature (Bio1). The simulation of geographic distribution suggested that the current suitable habitat of Morchella was mainly located in Yunnan, Sichuan, Gansu, Shaanxi, Xinjiang Uygur Autonomous Region (XUAR) and other provinces in China. Compared with current times, the suitable area in Northwest and Northeast China decreased in the LGM and MH periods. As for the future periods, the suitable habitats all increased under the different scenarios compared with those in contemporary times, showing a trend of expansion to Northeast and Northwest China. These results could provide a theoretical basis for the protection, rational exploitation and utilization of wild Morchella resources under scenarios of climate change.

Nucleotide Evolution, Domestication Selection, and Genetic Relationships of Chloroplast Genomes in the Economically Important Crop Genus Gossypium.

Gossypium hirsutum (upland cotton) is one of the most economically important crops worldwide, which has experienced the long terms of evolution and domestication process from wild species to cultivated accessions. However, nucleotide evolution, domestication selection, and the genetic relationship of cotton species remain largely to be studied. In this study, we used chloroplast genome sequences to determine the evolutionary rate, domestication selection, and genetic relationships of 72 cotton genotypes (36 cultivated cotton accessions, seven semi-wild races of G. hirsutum, and 29 wild species). Evolutionary analysis showed that the cultivated tetraploid cotton genotypes clustered into a single clade, which also formed a larger lineage with the semi-wild races. Substitution rate analysis demonstrated that the rates of nucleotide substitution and indel variation were higher for the wild species than the semi-wild and cultivated tetraploid lineages. Selection pressure analysis showed that the wild species might have experienced greater selection pressure, whereas the cultivated cotton genotypes underwent artificial and domestication selection. Population clustering analysis indicated that the cultivated cotton accessions and semi-wild races have existed the obviously genetic differentiation. The nucleotide diversity was higher in the semi-wild races compared with the cultivated genotypes. In addition, genetic introgression and gene flow occurred between the cultivated tetraploid cotton and semi-wild genotypes, but mainly via historical rather than contemporary gene flow. These results provide novel molecular mechanisms insights into the evolution and domestication of economically important crop cotton species.

Evolutionary characteristics and phylogeny of cotton chloroplast tRNAs.

MAIN CONCLUSION: The novel structural variations were identified in cotton chloroplast tRNAs and gene loss events were more obvious than duplications in chloroplast tRNAs. Transfer RNAs (tRNA) have long been believed an evolutionary-conserved molecular family, which play the key roles in the process of protein biosynthesis in plant life activities. In this study, we detected the evolutionary characteristics and phylogeny of chloroplast tRNAs in cotton plants, an economic and fibered important taxon in the world. We firstly annotated the chloroplast tRNAs of 27 Gossypium species to analyze their genetic composition, structural characteristics and evolution. Compared with the traditional view of evolutionary conservation of tRNA, some novel tRNA structural variations were identified in cotton plants. I.g., tRNAVal-UAC and tRNAIle-GAU only contained one intron in the anti-condon loop region of tRNA secondary structure, respectively. In the variable region, some tRNAs contained a circle structure with a few nucleotides. Interestingly, the calculation result of free energy indicated that the variation of novel tRNAs contributed to the stability of tRNA structure. Phylogenetic analysis suggested that chloroplast tRNAs have evolved from multiple common ancestors, and the tRNAMet seemed to be an ancestral tRNA, which can be duplicated and diversified to produce other tRNAs. The chloroplast tRNAs contained a group I intron in cotton plants, and the evolutionary analysis of introns indicated that group I intron of chloroplast tRNA originated from cyanobacteria. Analysis of gene duplication and loss events showed that gene loss events were more obvious than duplications in Gossypium chloroplast tRNAs. Additionally, we found that the rate of transition was higher than the ones of transversion in cotton chloroplast tRNAs. This study provided new insights into the structural characteristics and evolution of chloroplast tRNAs in cotton plants.

The complete chloroplast genome sequences of an endemic species of Urticaceae (Debregeasia hekouensis).

Debregeasia hekouensis, which belongs to the nettle family (Urticaceae), is a local endemic species in Hekou County, Yunnan Province, China. To provide a basis for the development of effective molecular markers for its conservation, we sequenced the chloroplast (cp) genome of D. hekouensis in the present study. The total length of the chloroplast(cp) genome was 155,941 bp, and exhibited a typical quadripartite structure, with a pair of IRs (inverted repeats; 25,664 bp in length) being separated by a small single copy (SSC) region of 19,085 bp and a large single copy (LSC) region of 85,528 bp. The cp genome contained a total of 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The GC content of the entire cp genome, LSC region, SSC region, and IR region was 36.3%, 34.0%, 29.4%, and 42.7%, respectively. Phylogenetic analysis indicated that D. hekouensis is evolutionarily closer to Debregeasia orientalis and Debregeasia squamata.

Evolution and structural variations in chloroplast tRNAs in gymnosperms.

BACKGROUND: Chloroplast transfer RNAs (tRNAs) can participate in various vital processes. Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern Hemisphere. However, the evolution and structural changes in chloroplast tRNAs in gymnosperms remain largely unclear. RESULTS: In this study, we determined the nucleotide evolution, phylogenetic relationships, and structural variations in 1779 chloroplast tRNAs in gymnosperms. The numbers and types of tRNA genes present in the chloroplast genomes of different gymnosperms did not differ greatly, where the average number of tRNAs was 33 and the frequencies of occurrence for various types of tRNAs were generally consistent. Nearly half of the anticodons were absent. Molecular sequence variation analysis identified the conserved secondary structures of tRNAs. About a quarter of the tRNA genes were found to contain precoded 3' CCA tails. A few tRNAs have undergone novel structural changes that are closely related to their minimum free energy, and these structural changes affect the stability of the tRNAs. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors. The transition rate was higher than the transversion rate in gymnosperm chloroplast tRNAs. More loss events than duplication events have occurred in gymnosperm chloroplast tRNAs during their evolutionary process. CONCLUSIONS: These findings provide novel insights into the molecular evolution and biological characteristics of chloroplast tRNAs in gymnosperms.

Characterization of the DNA molecular sequence of complete plastid genome of Paeonia rockii subsp. taibaishanica, an endemic species in China.

Paeonia rockii subsp. taibaishanica (Paeoniaceae), one of the tree peony species, is endemic to the Qinling Mountains in central China. In this study, we characterized its whole plastid genome sequence using the Illumina sequencing platform. The complete plastid genome size of P. rockii subsp. taibaishanica is 153,368 bp in length, including a large single copy (LSC) region of 85,030 bp, a small single copy (SSC) region of 17,042 bp, and a pair of inverted repeats (IRs) of 25,648 bp. The genome contains 131 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC contents in chloroplast genome, LSC region, SSC region, and IR region were 38.3%, 36.6%, 32.6%, and 43.1%, respectively. A total of 16 species are used to construct the phylogenetic tree of Paeoniaceae, the results showed that P. rockii subsp. taibaishanica is more closely related with congeneric Paeonia suffruticosa and Paeonia ostii, these species were clustered into a clade with high bootstrap support.

Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants.

Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as "bridges" in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.

Phylogenetic relationships and molecular evolution of woody forest tree family Aceraceae based on plastid phylogenomics and nuclear gene variations.

The forest tree family Aceraceae is widespread in the northern hemisphere and it has ecological and economic importance. However, the phylogenetic relationships and classifications within the family are still controversial due to transitional intraspecific morphological characteristics and introgression hybridization among species. In this study, we determined the evolutionary relationships and molecular evolution of Aceraceae based on plastid phylogenomics and two nuclear gene variations. Phylogenetic analysis based on the plastid genomes suggested that Aceraceae species can be divided into two larger sub-clades corresponding to the two genera Acer and Dipteronia. Conjoint analysis of the plastid and nuclear gene sequences supported the classification with two genera in the family. Molecular dating showed that the two genera diverged 60.2 million years ago, which is generally consistently with previously reported results. Divergence hotspots and positively selected genes identified in the plastid genomes could be useful genetic resources in Aceraceae.

Phylogeny and evolution of chloroplast tRNAs in Adoxaceae.

Chloroplasts are semiautonomous organelles found in photosynthetic plants. The major functions of chloroplasts include photosynthesis and carbon fixation, which are mainly regulated by its circular genomes. In the highly conserved chloroplast genome, the chloroplast transfer RNA genes (cp tRNA) play important roles in protein translation within chloroplasts. However, the evolution of cp tRNAs remains unclear. Thus, in the present study, we investigated the evolutionary characteristics of chloroplast tRNAs in five Adoxaceae species using 185 tRNA gene sequences. In total, 37 tRNAs encoding 28 anticodons are found in the chloroplast genome in Adoxaceae species. Some consensus sequences are found within the Ψ-stem and anticodon loop of the tRNAs. Some putative novel structures were also identified, including a new stem located in the variable region of tRNATyr in a similar manner to the anticodon stem. Furthermore, phylogenetic and evolutionary analyses indicated that synonymous tRNAs may have evolved from multiple ancestors and frequent tRNA duplications during the evolutionary process may have been primarily caused by positive selection and adaptive evolution. The transition and transversion rates are uneven among different tRNA isotypes. For all tRNAs, the transition rate is greater with a transition/transversion bias of 3.13. Phylogenetic analysis of cp tRNA suggested that the type I introns in different taxa (including eukaryote organisms and cyanobacteria) share the conserved sequences "U-U-x2-C" and "U-x-G-x2-T," thereby indicating the diverse cyanobacterial origins of organelles. This detailed study of cp tRNAs in Adoxaceae may facilitate further investigations of the evolution, phylogeny, structure, and related functions of chloroplast tRNAs.