Chloroplast genome data of five Amygdalus species: Clarifying genome structure and phylogenetic relationships.

Amygdalus species have considerable ecological and economic value, however, the phylogenetic relationships among Amygdalus remain controversy. In this study, we sequenced and assembled the chloroplast (cp) genomes of five Amygdalus species: Prunus communis, P. mongolica, P. pedunculata, P. triloba, and P. mira. We then conducted comparative genomic analyses and constructed their phylogenetic relationships. The genome length ranged from 157,870 to 158,451 bp, and 131 genes were annotated (86 protein-coding genes, 37 tRNAs, and 8 rRNAs). Additionally, 49-57 simple sequence repeats were detected, with most in the large single-copy region and with AT base preferences. Comparative genomic analyses revealed high similarities in structure, order, and gene content. However, we identified four highly divergent sequences: trnR-UCU-atpA, nbdhC-trnV-UAC, ycf4-cemA, and rpl32-trnL-UAG. The phylogenomic relationship analysis suggested that the Amygdalus species were grouped together, in which P. pedunculata, P. triloba, and Prunus tangutica were categorized into a branch, P. mongolica and Prunus davidiana were clustered a branch. This study provides an improved understanding of the genetic relationships among the Amygdalus and provides a basis for the development and utilization of Amygdalus resources.

Sequencing and Phylogenetic Analysis of the Chloroplast Genome of Three Apricot Species.

The production and quality of apricots in China is currently limited by the availability of germplasm resource characterizations, including identification at the species and cultivar level. To help address this issue, the complete chloroplast genomes of Prunus armeniaca L., P. sibirica L. and kernel consumption apricot were sequenced, characterized, and phylogenetically analyzed. The three chloroplast (cp) genomes ranged from 157,951 to 158,224 bp, and 131 genes were identified, including 86 protein-coding genes, 37 rRNAs, and 8 tRNAs. The GC content ranged from 36.70% to 36.75%. Of the 170 repetitive sequences detected, 42 were shared by all three species, and 53-57 simple sequence repeats were detected with AT base preferences. Comparative genomic analysis revealed high similarity in overall structure and gene content as well as seven variation hotspot regions, including psbA-trnK-UUU, rpoC1-rpoB, rpl32-trnL-UAG, trnK-rps16, ndhG-ndhI, ccsA-ndhD, and ndhF-trnL. Phylogenetic analysis showed that the three apricot species clustered into one group, and the genetic relationship between P. armeniaca and kernel consumption apricot was the closest. The results of this study provide a theoretical basis for further research on the genetic diversity of apricots and the development and utilization of molecular markers for the genetic engineering and breeding of apricots.

Dynamic transcriptome analysis identifies genes related to fatty acid biosynthesis in the seeds of Prunus pedunculata Pall.

BACKGROUND: Prunus pedunculata Pall, the deciduous shrub of Amygdalus subgenus in Rosaceae, is a new kind of desert oil-bearing tree. It has a long story of being planted in the West and North of China for sand fixation and desert control. In addition, the seeds of P. pedunculata are rich of oil, especially the monounsaturated fatty acid and polyunsaturated fatty acid. However, little is known about the molecular mechanisms of oil accumulation during the seed development of P. pedunculata. RESULTS: The seeds of P. pedunculata from three independent plants at 10, 18, 24, 31, 39, 45, 59 and 73 days after flowering (DAF) were obtained and the oil compositions were evaluated. It showed that oleic acid was the dominant type of oil content in the mature seeds (from 32.724% at 10DAF to 72.06% at 73DAF). Next, transcriptome sequencing for the developing seeds produced 988.795 million high quality reads and TRINITY assembled 326,271 genes for the first transcriptome for P. pedunculata. After the assembled transcriptome was evaluated by BUSCO with 85.9% completeness, we identified 195,342, 109,850 and 121,897 P. pedunculata genes aligned to NR, GO and KEGG pathway databases, respectively. Then, we predicted 23,229 likely proteins from the assembled transcriptome and identified 1917 signal peptides and 5512 transmembrane related proteins. In the developing seeds we detected 91,362 genes (average FPKM > 5) and correlation analysis indicated three possible development stages - early (10 ~ 24DAF), middle (31 ~ 45DAF) and late (59 ~ 73DAF). We next analyzed the differentially expressed genes (DEGs) in the developing seeds. Interestingly, compared to 10DAF the number of DEGs was increased from 4406 in 18DAF to 27,623 in 73DAF. Based on the gene annotation, we identified 753, 33, 8 and 645 DEGs related to the fatty acid biosynthesis, lipid biosynthesis, oil body and transcription factors. Notably, GPAT, DGD1, LACS2, UBC and RINO were highly expressed at the early development stage, ω6-FAD, SAD, ACP, ACCA and AHG1 were highly expressed at the middle development stage, and LACS6, DGD1, ACAT1, AGPAT, WSD1, EGY2 and oleosin genes were highly expressed at the late development stage. CONCLUSIONS: This is the first time to study the developing seed transcriptome of P. pedunculata and our findings will provide a valuable resource for future studies. More importantly, it will improve our understanding of molecular mechanisms of oil accumulation in P. pedunculata.

Relationship between Methylation of FHIT and CDH13 Gene Promoter Region and Liver Cancer.

In order to demonstrate the relationship between methylation of fragile histidine triad (FHIT) and T-cadherin/H-cadherin (CDH13) genes and liver cancer, the methylation status of FHIT and CDH13 was detected in healthy individuals and in Mongolian and Han patients with liver cancer. The phenol-chloroform method was used to extract genomic DNA. The methylation specific polymerase chain reaction method was applied to detect the methylation status of FHIT and CDH13. The relationship between smoking and alcohol consumption and gene (FHIT and CDH13) methylation was analyzed. There was significant difference in methylation rate of FHIT (72.67%, 34.67%) and CDH13 (72.0%, 28.0%) between liver cancer patients and healthy individuals of Mongolian descent (P<0.05), as well as that of FHIT (68%, 30.67%) and CDH13 (64%, 26%) between liver cancer patients and healthy individuals of Han individuals (P<0.05). There was also a relationship between smoking and drinking and the methylation of FHIT and CDH13 (P<0.05). Thus, the methylation of FHIT and CDH13 had a relationship with liver cancer incidence. Smoking and alcohol ingestion may promote the methylation of FHIT and CDH13.

The molecular mechanism of the effect of benzoαpyrene on autophagy of molecular chaperones under simulated hypoxia / 药学学报

In this study, the effect of benzo[α]pyrene (BaP) on chaperone-mediated autophagy (CMA) in a simulated hypoxia environment was observed and the relationship to heat shock protein 90 (HSP90) was clarified. With HSP90 inhibitor geldanamycin (GA) and HSP90α silenced, the mRNA and protein expression of hypoxia-inducible factor-1α (HIF-1α), HSP90, heat shock cognate protein 70 (HSC70), and lysosomal associated protein 2A (LAMP-2A) of A549 cells on hypoxic environment by BaP were tested. Alkaline comet experiment, immunofluorescence γ-H2AX focus experiment, quantitative real-time PCR (qPCR), and Western blot analyses were used to clarify the relationship between the DNA damage of different concentrations of BaP in A549 cells and the mRNA and protein expression of CMA-related factors. The results show that hypoxia can promote the expression of mRNA and protein of CMA-related factors in A549 cells. This study found that BaP has an inhibitory effect on CMA under the hypoxic environment. The inhibition or silencing of HSP90 will enhance the inhibitory effect of BaP on CMA. In a normoxic environment, BaP causes DNA damage and promotes CMA.

The complete chloroplast genome of Prunus mira koehne (Prunoideae, Rosaceae), a wild and indigenous peach on Tibet, China.

Prunus mira Koehne belonging to family Rosaceae, is an indigenous species distributed in Tibet, China. De novo assembly with low coverage whole genome sequencing data facilitated to generate the complete chloroplast (cp) genome of P. mira in this study. The genome was a circular DNA molecule with 158,153 bp in length. It exhibited a typical quadripartite structure comprising a large single-copy region (LSC, 86,319 bp), a small single-copy region (SSC, 19,022 bp) and a pair of inverted repeat regions (IRs, 26,406 bp each). A total of 112 genes were predicted, which included 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated that P. mira was the most ancestral and basal lineage within the subgenus Amygdalus (Prunoideae subfamily), which is conform to the traditional classification.

[Study on the effect of electric field on the secondary structure of HRP by circular dichroism].

After the HRP was treated with different strength of electric field, the effect of electric field on the secondary structure of HRP was studied by circular dichroism. The results show that different electric field strength ranging from 1.0 to 6.0 kV x cm(-1) has a different effect on the relative contents of alpha-helix, beta-sheet, beta-turn and random coil of the HRP. As compared with the contrast, the relative contents of alpha-helix, beta-turn and random coil decreased by 0.3%-11.4%, 1.7%-15.3% and 0.9%-20.4% respectively, while beta-sheet content increased by 0.9%-82.7%. The electric treatment tends to transform the alpha-helix, beta-turn and random coil into beta-sheet for the HRP. The result of this study has important meaning to explain the biological effect of electric treatment seeds.

[Study on the effect of electric field on the secondary structure of lipase by circular dichroism].

After the lipase was treated with electric field for five minutes, the effect of electric field on the secondary structure of lipase was studied by circular dichroism (CD). The results showed that different electric field strength in the range from 0. 5 to 6. 0 kV x cm(-1) has a different effect on the relative contents of alpha-helix, beta-sheet, beta-turn and random coil of the lipase, and whose changes were non-monotonous with the raising of electric field. In general, the electric treatment tends to transform the alpha-helix and beta-sheet into beta-turn and random coil. The decrease in alpha-helix and beta-sheet ranged respectively from 4. 6% to 48. 0% and from 13. 2% to 35. 1%, and the increase in beta-turn and random coil ranged respectively from 2. 8% to 33. 3% and from 0. 9% to 48. 1%. The result of this study has important meaning to explain the biological effect of electric treatment seeds.