Generation of ESTs for Flowering Gene Discovery and SSR Marker Development in Upland Cotton

BACKGROUND: Upland cotton, Gossypium hirsutum L., is one of the world's most important economic crops. In the absence of the entire genomic sequence, a large number of expressed sequence tag (EST) resources of upland cotton have been generated and used in several studies. However, information about the flower development of this species is rare. METHODOLOGY/PRINCIPAL FINDINGS: To clarify the molecular mechanism of flower development in upland cotton, 22,915 high-quality ESTs were generated and assembled into 14,373 unique sequences consisting of 4,563 contigs and 9,810 singletons from a normalized and full-length cDNA library constructed from pooled RNA isolated from shoot apexes, squares, and flowers. Comparative analysis indicated that 5,352 unique sequences had no high-degree matches to the cotton public database. Functional annotation showed that several upland cotton homologs with flowering-related genes were identified in our library. The majority of these genes were specifically expressed in flowering-related tissues. Three GhSEP (G. hirsutum L. SEPALLATA) genes determining floral organ development were cloned, and quantitative real-time PCR (qRT-PCR) revealed that these genes were expressed preferentially in squares or flowers. Furthermore, 670 new putative microsatellites with flanking sequences sufficient for primer design were identified from the 645 unigenes. Twenty-five EST-simple sequence repeats were randomly selected for validation and transferability testing in 17 Gossypium species. Of these, 23 were identified as true-to-type simple sequence repeat loci and were highly transferable among Gossypium species. CONCLUSIONS/SIGNIFICANCE: A high-quality, normalized, full-length cDNA library with a total of 14,373 unique ESTs was generated to provide sequence information for gene discovery and marker development related to upland cotton flower development. These EST resources form a valuable foundation for gene expression profiling analysis, functional analysis of newly discovered genes, genetic linkage, and quantitative trait loci analysis

Chloroplast genome of a pair of Triticum aestivum L. recombinant inbred lines with significant difference in seed size

Wheat (Triticum aestivum L.), one of the most important crops belong to the Triticum genus of family Poaceae. Some of important cytoplasmic genes come from chloroplast genome. In this study, the chloroplast genome of a pair of T. aestivum recombinant inbred lines were sequenced, assembled, and annotated. Our results show this chloroplast genome consists of 137 unique genes, including 87 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. A maximum-likelihood phylogenetic tree based on 15 chloroplast genomes revealed that the two T. aestivum are closely related to Triticum genus. The chloroplast genome could be used for wheat species identification, cytoplasmic inheritance gene functional study and breeding

Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut (Juglans Regia L.)

Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regia PAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans

The complete chloroplast genome of Cirsium shansiense and its phylogenetic analysis

Cirsium shansiense is a common species in China, which can be used for traditional Chinese medicine. The chloroplast (cp) genome of C. shansiense exhibited a typical quadripartite cycle with 152,396 bp, including a pair of inverted repeat regions (IRa and IRb, 25,072 bp each), a large single-copy region (LSC, 83,517 bp), and a small single-copy region (SSC, 18,735 bp). One-hundred-thirty-three unique genes were assembled in the cp genome, including 88 protein genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 17 cp genomes of related species of Asteraceae showed that C. shansiense was closely related to Cirsium vulgare. This study provides important information for identification and conservation of species of Cirsium spp

The complete chloroplast genome of Euonymus szechuanensis

The complete chloroplast genome from Euonymus szechuanensis, a rare deciduous shrub of the Celastraceae endemic to China, which is classified as vulnerable on the list of Threatened species in China because species diversity decreased sharply, is determined in this study. The whole chloroplast genome sequence of Euonymus szechuanensis has been characterized by Illumina pair-end sequencing. The circular genome is 157,465 bp long, containing a large single-copy region (LSC) of 86,401 bp and a small single-copy region (SSC) of 18,472 bp, which are separated by a pair of 26,296 bp inverted repeat regions (IRs). It encodes a total of 136 genes, including 84 protein-coding genes (76 PCG species), 44 tRNA genes (30 tRNA species), and 8 ribosomal RNA genes (4 rRNA species). Most of the gene species occur as a single copy, while 19 gene species occur in double copies. The overall A + T content of the circular genome is 62.8%, while the corresponding values of the LSC, SSC and IR regions are 65.0, 68.4 and 57.3%, respectively. Phylogenetic analysis suggested that E. szechuanensis was relatively close to Euonymus schensianus among the species analyzed. This complete chloroplast genome will provide valuable insight into conservation and restoration efforts for this rare and Threatened species

The complete plastome sequence of Platanthera japonica (Orchidaceae): an endangered medicinal and ornamental plant

Platanthera japonica (Thunb. ex A. Marray) Lindl belongs to the genus Platanthera within family Orchidaceae, is an endangered herbal species in the East Asia area. In this study, the complete plastome sequence (cpDNA) of P. japonica was determined by next-generation Illumina sequencing. The cpDNA of this herbal plant is 155,409 bp in size, with a pair of inverted repeat (IR) regions of 26,933 bp that separate a large single-copy (LSC) region of 84,049 bp and a small single-copy (SSC) region of 17,494 bp. The GC content in plastome is 36.9%, and the IR region (43.2%) is higher than that of the LSC and SSC region (34.4% and 29.7%, respectively), which is similar with other Orchidaceae plastomes. The assembled plastome encoded 133 genes, which included 38 tRNA genes, 8 rRNA genes, and 87 protein-coding genes. A total of 24 species were used to construct the phylogenetic relationships among P. japonica and other related species within Orchidaceae. The results showed that P. japonica is closely related to Platanthera chlorantha

Effect of Coal Blending on Ash Fusibility and Slurryability of Xinjiang Low-Rank Coal

This work investigated the effect of coal blending on ash fusibility and slurryability of Xinjiang low-rank coal. The results showed that Xinjiang low-rank coals were characterized by high internal water content, high volatile content, high ash fusing point, and poor slurryability, which can not be directly used in coal water slurry gasification. The blending method not only reduced the ash fusibility but also improved the slurryability of these low-rank coals. When the coals with low calcium and high silicon contents (KG and YK) were blended with coal with high calcium content (SH), the ash fusion temperatures of the blended coal were significantly reduced. Moreover, the SH coal showed the worst slurryability performance with a concentration of 48.56%. The slurryability of HS coal can be dramatically improved by blending with KG. When the mass fraction of KG coal reached 70%, the concentration of coal water slurry increased by 11%. For the blended coal of KG and YK, the concentration and stability of coal water slurry gradually increase with the increasing mass ratio of KG. The coal blending method can effectively improve the concentration of coal water slurry for the low-rank coals, which were difficult-to-prepare slurry

Synergistic Catalysis of Reservoir Minerals and Exogenous Catalysts on Aquathermolysis of Heavy Oil

In this study, based on existing heavy oil extraction technology, combined with the mineral composition in a reservoir, the synergistic catalytic effect of reservoir minerals and exogenous catalysts under the reaction system of a hydrogen-rich environment not only reduces the viscosity of thick oil but also reduces the extraction cost and further improves the recovery rate of heavy oil. In this study, the impacts of different reservoir minerals and exogenous catalysts on the aquathermolysis of heavy oil were investigated. The research results showed that the sodium montmorillonite within the reservoir minerals exhibited an optimal catalytic effect, and the synergistic catalytic effect of sodium montmorillonite and catalyst C-Fe (catechol iron) resulted in a viscosity reduction rate of 60.47%. Furthermore, the efficiency of different alcohols as hydrogen donors was screened, among which ethanol had the best catalytic effect. Under the optimal reaction conditions, the viscosity reduction rate after the addition of ethanol was 75.25%. Infrared spectroscopy, elemental analysis, thermogravimetry, and differential scanning calorimetry were used to study the changes in heavy oil before and after hydrothermal cracking. Element analysis showed that the synergistic catalytic effect of sodium-based montmorillonite and catalyst C-Fe increased the hydrocarbon ratio from 0.116 to 0.117, and the content of S and N elements decreased. This fully confirms the catalytic effect of sodium-based montmorillonite and C-Fe catalyst for he hydrogenation reaction of the unsaturated carbon in heavy oil

Phylogenetic relationship and comparative analysis of the main Bupleuri Radix species in China

Background Bupleuri Radix (Chaihu) is a famous traditional Chinese medicine derived from Bupleurum, Apiaceae. The origin of cultivated Chaihu germplasm in China is unclear, which has led to unstable Chaihu quality. In this study, we reconstructed the phylogeny of the main Chaihu germplasm species in China and identified potential molecular markers to authenticate its origin. Methods Three Bupleurum species (eight individuals), B. bicaule, B. chinense, and B. scorzonerifolium, were selected for genome skimming. Published genomes from B. falcatum and B. marginatum var. stenophyllum were used for comparative analysis. Results Sequences of the complete plastid genomes were conserved with 113 identical genes ranging from 155,540 to 155,866 bp in length. Phylogenetic reconstruction based on complete plastid genomes resolved intrageneric relationships of the five Bupleurum species with high support. Conflicts between the plastid and nuclear phylogenies were observed, which were mainly ascribed to introgressive hybridization. Comparative analysis showed that noncoding regions of the plastomes had most of the variable sequences. Eight regions (atpF-atpH, petN-psbM, rps16-psbK, petA-psbJ, ndhC-trnV/UAC and ycf1) had high divergence values in Bupleurum species and could be promising DNA barcodes for Chaihu authentication. A total of seven polymorphic cpSSRs and 438 polymorphic nSSRs were detected across the five Chaihu germplasms. Three photosynthesis-related genes were under positive selection, of which accD reflected the adaptation fingerprint of B. chinense to different ecological habitats. Our study provides valuable genetic information for phylogenetic investigation, germplasm authentication, and molecular breeding of Chaihu species

The complete chloroplast genome sequence of Mentha canadensis (Labiatae), a traditional Chinese herbal medicine

Mentha canadensis is a well-known resource of traditional Chinese herbal medicine, belonging to the Mentha of the Labiatae family. In this study, the whole chloroplast genome of the M. canadensis chloroplast genome was sequenced, assembled and annotated, which contains 134 unique genes, including 89 protein-coding genes, 37 tRNA genes and 8 rRNA genes. A maximum likelihood phylogenetic tree based on 11 complete chloroplast genomes revealed that M. canadensis is closely related to M. longifolia and M. spicata. The chloroplast genome could be used for variety identification, genetic engineering and effective protection of germplasm resources