Genome-wide identification of the BmAKR gene family in the silkworm (Bombyx mori) and their expression analysis in diapause eggs and nondiapause eggs / 生物工程学报

The aldo-keto reductase super family (AKRs) has a wide range of substrate specificity. However, the systematic identification of insect AKR gene family members has not been reported. In this study, bioinformatics methods were used to predict the phylogenetic evolution, physical and chemical properties, chromosome location, conserved motifs, and gene structure of AKR family members in Bombyx mori (BmAKR). Transcriptome data or quantitative real time polymerase chain reaction (qRT-PCR) were used to analyze the expression level of BmAKR genes during different organizational periods and silkworm eggs in different developmental states. Moreover, Western blotting was used to detect the expression level of the BmAKR in silkworm eggs. The results showed that 11 BmAKR genes were identified. These genes were distributed on 4 chromosomes of the silkworm genome, all of which had the (α/β) 8-barrel motif, and their physical and chemical characteristics were relatively similar. Phylogenetic analysis showed that the BmAKR genes could be divided into 2 subgroups (AKR1 and AKR2). Transcriptome data analysis showed that the expression of BmAKR genes were quite different in different tissues and periods. Moreover, the expression analysis of BmAKR genes in silkworm eggs showed that some genes were expressed significantly higher in nondiapause eggs than in diapause eggs; but another gene, BmAKR1-1, was expressed significantly higher in diapause eggs than in nondiapause eggs. The detection of protein level found that the difference trend of BmAKR1-1 in diapause eggs and non-diapause eggs was consistent with the results of qRT-PCR. In conclusion, BmAKR1-1 was screened out as candidates through the identification and analysis of the BmAKR genes in silkworm, which may regulate silkworm egg development is worthy of further investigation.

Characterization and phylogenetic analysis of the complete chloroplast genome of Lycopus europaeus / 药学学报

We intend to study the structural characteristics of Lycopus europaeus Linn. chloroplast genome and compare the evolutionary relationship of species from Lamiaceae with similar medicinal effects. The total DNA of Lycopus europaeus was sequenced using the Illumina Hiseq 4000 Sequencing platform and was assembled using NOVOplasty software. And then we annotated and analyzed the genome using the CPGAVAS2 online tool. We constructed the phylogenetic tree using the Stellera chamaejasme and Potentilla chinensis as the outgroup. The whole length of Lycopus europaeus chloroplast genome was 152 085 bp. A total of 132 genes were annotated including 88 protein-coding genes, 8 rRNA genes and 36 tRNA genes. Among them, 8 protein-coding genes (ndhB, rps7, rps12, rps19, rpl2, rpl23, ycf2, ycf15), 7 tRNA coding genes (trnM-CAU, trnL CAA, trnN-GUU, trnE-UUC, trnV-GAC, trnA-UGC, trnR-ACG) and 4 rRNA coding genes (rrn16s, rrn23s, rrn4.5s, rrn5s) are located in the IR region. There are 13 protein coding genes [rps16, rps19 (×2), atpF, rpoC1, rpl2 (×2), petB, petD, rpl16, ndhB (×2), ndhA] each contains one intron, two protein-coding genes (ycf3, clpP) each contain two introns, and 8 tRNA coding genes each contain one intron. A total of 34 SSRs were detected in the chloroplast genome of Lycopus europaeus. Phylogenetic analysis revealed that two species in the Lycopus genus, four species in the Dracocephalum genus, Glechoma longituba, two species in the Mentha genus and Prunella vulgari, in total 10 species are most related. The complete genome sequence of Lycopus europaeus was obtained and analyzed, which clarified the evolutional relationship between the species of Lycopus europaeus and in the Lamiaceae family.

Identification and Expression Analysis of TIFY Transcription Factor in Eucommia ulmoides / 中国实验方剂学杂志

Objective:To identify the TIFY gene family in <italic>Eucommia ulmoides</italic> and analyze its expression from the whole genome level to lay the foundation for further study on <italic>EuTIFYs</italic> gene function. Method:Based on the <italic>E. ulmoides</italic> genome database，the TIFY gene family was identified through bioinformatics analysis tools such as National Center for Biotechnology Information（NCBI），MEME，PlantCare，Expert Protein Analysis System（ExPASy），and TBtools. Physicochemical properties，phylogenetic evolution，gene structure，<italic>cis</italic>-acting elements of the promoters and their expression patterns in leaf development and gum formation of the gene family were systematically analyzed. Result:In this study，fourteen <italic>EuTIFY</italic> genes （<italic>EuTIFY1</italic>-<italic>EuTIFY14</italic>） were identified in the <italic>E. ulmoides</italic> genome. The <italic>EuTIFYs</italic> were composed of 312-1 074 bp nucleotides encoding 102-357 amino acid residues，with isoelectric points of 4.99-10.06 and molecular weight in the range of 10.8-39.14 kDa. According to putative subcellular localization，proteins，which were mainly hydrophilic proteins，localized in the nucleus. The 14 <italic>EuTIFYs</italic> were unevenly distributed on 13 chromosomes. <italic>EuTIFY</italic> gene family was divided into four subfamilies： <italic>TIFY</italic>，<italic>JAZ</italic>，<italic>ZML</italic>，and <italic>PPD</italic>，which contained three，four，five，and two members respectively. The promoters of <italic>EuTIFYs</italic> contained multiple photoperiodic and abiotic stress-responsive cis-acting elements，which were involved in plant growth and abiotic stress regulation. Expression pattern analysis showed that <italic>EuTIFYs </italic>exhibited different expression levels in different development stages of <italic>E. ulmoides</italic> leaves and multiple interactions，and most of the genes were highly expressed in the early stage of leaf development and positively regulated the formation of <italic>E. ulmoides</italic> gum. Conclusion:Fourteen <italic>EuTIFYs</italic> were identified from the whole genome of <italic>E. ulmoides</italic>，and their structural characteristics and expression patterns were analyzed by bioinformatics. The findings of this study are expected to provide references for further research on the function of <italic>EuTIFYs</italic>.

Comparative analysis of three complete chloroplast genomes of Inula genus with phylogenetic analysis of 49 plants from Carduoideae / 药学学报

italic>Inula japonica, Inula hupehensis and Inula linaariifolia are all medicinal plants of Inula L. in the Compositae family, and Inula hupehensis is endemic to China. In order to compare their genomic sequence differences and provide scientific basis for their germplasm conservation and development, we obtained and analyzed the complete chloroplast genomes of these three species. Total DNAs were extracted from fresh leaves and subjected to next-generation DNA sequencing. NOVOPlasty was used to assemble the chloroplast genomes from the sequence reads. CPGAVAS2 was used to annotate the genes and repeats in each genome. Lastly, phylogenomics analysis was conducted using RAxML. The results showed that the total length of the chloroplast genome of Inula japonica, Inula hupehensis and Inula linaariifolia is 150 754, 150 909, and 150 812 bp respectively, each consisting of a large single copy region, a small single copy region and a pair of inverted repeat regions. In addition, the G/C content of all three chloroplast genomes was approximately 37.7% and each encoded 111 unique genes, including 79 protein-coding, 28 tRNA and 4 rRNA genes. Meanwhile, 32, 33, 34 simple repeat sequences, 18, 22, 18 tandem repeat sequences and 33, 37, 38 scattered repeat sequences were identified in three species. Phylogenomic analysis showed that all three species of Inula L. and Pluchea indica were clustered together, with the relationship between Inuleae and Senecioneae closer, suggesting that Inuleae may have originated from the Senecioneae, not the Cardueae. The data in this study not only enriches the chloroplast genome database of Inula L., but also lays the foundation for the future studies of species identification, phylogenetic relationships, evolution history and genetic diversity of Inula species.

Genome-wide analysis of LBD(lateral organ boundaries domain) gene family in Cannabis sativa of traditional Chinese medicine hemp seed / 中国中药杂志

LBD(lateral organ boundaries)transcription factors play an important role in the regulation of plant growth, development and secondary metabolism. In order to explore the function of LBD genes in cannabis, the Cannabis sativa genome and transcriptome were used to identify the C. sativa LBD gene family, and analyzed their expression patterns. Our results showed that the cannabis LBD contains 32 members, which were divided into two major categories, seven sub-families. Class Ⅰ was divided into 5 sub-families, named Class Ⅰ_a to Class Ⅰ_e, while Class Ⅱ was divided into 2 sub-families, including Class Ⅱ_a and Class Ⅱ_b. Analysis showed that the number of amino acids encoded LBDs was between 172 and 356, and the isoelectric point was between 4.92 and 9.43. The mole-cular weight of LBD was between 18 862.92 Da and 40 081.33 Da, and most members are located in the nucleus. Chromosome positioning of LBD showed that 32 members were unevenly distributed on 10 chromosomes of C. sativa LBD transcription factor domain, gene structure and motifs are relatively conservative, and the characteristics of different class members are similar. The upstream promoter region of the gene contains a variety of cis-acting elements related to plant hormones and environmental factors, C. sativa LBD genes have different expression patterns in the stems, leaves, and flowers of ZYS varieties(low tetrahydrocannabinol, high cannabidiol). The members of the LBD gene family are mainly expressed in the flowers and stems of ZYS varieties, while members expressed in the leaves very few; Class Ⅱ members CsLBD21 and CsLBD23 are expressed in flowers and stems, and CsLBD8 and CsLBD18 are expressed in flowers, stems and leaves. These genes may participate in the growth and development of cannabis and affect the biosynthesis of cannabinoids. This study laid the foundation for the subsequently functional research of the cannabis LBD gene family.

Sequence analysis on rDNA-ITS region of germplasm resources from Dioscoreae Rhizoma / 中草药

Objective: To provide the scientific evidence for molecular identification and phylogenetic evolution by analyzing internal transcribed spacer (ITS) sequences in 14 different germplasms from Dioscoreae Rhizoma. Methods: The ITS regions were cloned by PCR amplification and sequenced bi-directionally. The ITS sequences were aligned using Clustal X software (version 1.83), the genetic distances were calculated using Mega software (version 4.1), and the phylogenetic trees were constructed through the Neighbor-joining (NJ) and maximum parsimony (MP) methods. Results: The length of ITS sequences obtained ranged from 558 to 594 bp, of which ITS1 was from 141 to 165 bp and ITS2 was from 146 to 158 bp. There were a lot of transitions and transversions in ITS sequences, and the transition/transversion ratio among 14 different germplasms was 5.347. Both in ITS1 and ITS2, 102 variable sites were further observed. The kimura 2-parameter (K2-P) genetic distance among 14 different germplasms ranged form 0 to 0.5172. The phylogenetic trees suggested that there were close genetic relationship among Dioscorea opposita, D. persimilis, and D. japonica, they grouped closely into Clade I; Furthermore, D. alata and D. fordii also shared a closer genetic relationship comprised another clade (Clade II). Conclusion: The phylogenetic analyses based on ITS sequences can present a foundation for clearing the evolution of germplasm resources in Dioscoreae Rhizoma; The variable bases can also provide reliable molecular evidences for identifying different genotypic germplasms of Dioscoreae Rhizoma.