Genome-wide identification, evolution analysis of cytochrome P450 monooxygenase multigene family and their expression patterns during the early somatic embryogenesis in Dimocarpus longan Lour

Comparative genomic survey and functional analysis of DKKL1 during spermatogenesis in the Chinese soft-shelled turtle (Pelodiscus sinensis)

A feature of the Chinese soft-shelled turtle (Pelodiscus sinensis) is seasonal spermatogenesis; however, the underlying molecular mechanism is not well clarified. Here, we firstly cloned and characterized P. sinensis DKKL1, and then performed comparative genomic studies, expression analysis, and functional validation. P. sinensis DKKL1 had 2 putative N-glycosylation sites and 16 phosphorylation sites. DKKL1 also had classic transmembrane structures that were extracellularly localized. DKKL1's genetic distance was close to turtles, followed by amphibians and mammals, but its genetic distance was far from fishes. DKKL1 genes from different species shared distinct genomic characteristics. Meanwhile, they were also relatively conserved among themselves, at least from the perspective of classes. Notably, the transcription factors associated with spermatogenesis were also identified, containing CTCF, EWSR1, and FOXL2. DKKL1 exhibited sexually dimorphic expression only in adult gonads, which was significantly higher than that in other somatic tissues (P < 0.001), and was barely expressed in embryonic gonads. DKKL1 transcripts showed a strong signal in sperm, while faint signals were detected in other male germ cells. DKKL1 in adult testes progressively increased per month (P < 0.05), displaying a seasonal expression trait. DKKL1 was significantly downregulated in testes cells after the sex hormones (17β-estradiol and 17α-methyltestosterone) and Wnt/β-catenin inhibitor treatment (P < 0.05). Likewise, the Wnt/β-catenin inhibitor treatment dramatically repressed CTCF, EWSR1, and FOXL2 expression. Conversely, they were markedly upregulated after the 17β-estradiol and 17α-methyltestosterone treatment, suggesting that the three transcription factors might bind to different promoter regions, thereby negatively regulating DKKL1 transcription in response to the changes in the estrogen and androgen pathways, and positively controlling DKKL1 transcription in answer to the alterations in the Wnt/β-catenin pathway. Knockdown of DKKL1 significantly reduced the relative expression of HMGB2 and SPATS1 (P < 0.01), suggesting that it may be involved in seasonal spermatogenesis of P. sinensis through a positive regulatory interaction with these two genes. Overall, our findings provide novel insights into the genome evolution and potential functions of seasonal spermatogenesis of P. sinensis DKKL1.

Molecular mechanism of somatic embryogenesis in paeonia ostii 'Fengdan' based on transcriptome analysis combined histomorphological observation and metabolite determination

BACKGROUND

Tree peony (Paeonia sect. Moutan DC.) is a famous flower native to China with high ornamental, medicinal, and oil value. However, the low regeneration rate of callus is one of the main constraints for the establishment of a genetic transformation system in tree peony. By histomorphological observation, transcriptomic analysis and metabolite determination, we investigated the molecular mechanism of somatic embryogenesis after the establishment of a culture system and the induction of somatic embryo(SE) formation.

RESULTS

We found that SE formation was successfully induced when cotyledons were used as explants. A total of 3185 differentially expressed genes were screened by comparative transcriptomic analysis of embryogenic callus (EC), SE, and non-embryogenic callus (NEC). Compared to NEC, the auxin synthesis-related genes GH3.6 and PCO2 were up-regulated, whereas cytokinin dehydrogenase (CKX6) and CYP450 family genes were down-regulated in somatic embryogenesis. In SE, the auxin content was significantly higher than the cytokinin content. The methyltransferase-related gene S-adenosylmethionine synthase (SAMS) and the flavonoid biosynthesis-related gene (ANS and F3'5'H) were down-regulated in somatic embryogenesis. The determination of flavonoids showed that rhoifolin and hyperoside had the highest content in SE. The results of transcriptome analysis were consistent with the relative expression of 8 candidate genes by quantitative polymerase chain reaction analysis.

CONCLUSION

The results revealed that auxin and cytokinin may play a key role in 'Fengdan' somatic embryogenesis. The genes related to somatic embryogenesis were revealed, which has partly elucidated the molecular mechanism of somatic embryogenesis in 'Fengdan'.

Comprehensive and evolutionary analysis of Spodoptera litura-inducible Cytochrome P450 monooxygenase gene family in Glycine max elucidate their role in defense

Plants being sessile organisms and lacking both circulating phagocytic cells and somatic adaptive immune response, have thrived on various defense mechanisms to fend off insect pests and invasion of pathogens. CYP450s are the versatile enzymes, which thwart plants against insect pests by ubiquitous biosynthesis of phytohormones, antioxidants, and secondary metabolites, utilizing them as feeding deterrents and direct toxins. Therefore, a comprehensive analysis of biotic stress-responsive CYPs from Glycine max was performed to ascertain their function against S. litura-infestation. Phylogenetic analysis and evolutionary studies on conserved domains and motifs disclosed the evolutionary correspondence of these GmCYPs with already characterized members of the CYP450 superfamily and close relatedness to Medicago truncatula. These GmCYPs were mapped on 13 chromosomes; they possess 1-8 exons; they have evolved due to duplication and are localized in endoplasmic reticulumn. Further, identification of methyl-jasmonate, salicylic acid, defense responsive and flavonoid biosynthesis regulating cis-acting elements, their interaction with biotic stress regulating proteins and their differential expression in diverse types of tissues, and during herbivory, depicted their responsiveness to biotic stress. Three-dimensional homology modelling of GmCYPs, docking with heme cofactor required for their catalytic activity and enzyme-substrate interactions were performed to understand the functional mechanism of their action. Moreover, to gain insight into their involvement in plant defense, gene expression analysis was evaluated, which revealed differential expression of 11 GmCYPs upon S. litura-infestation, 12 GmCYPs on wounding while foliar spray of ethylene, methyl-jasmonate and salicylic acid differentially regulated 11 GmCYPs, 6 GmCYPs, and 10 GmCYPs respectively. Our study comprehensively analysed the underlying mechanism of GmCYPs function during S. litura-infestation, which can be further utilized for functional characterization to develop new strategies for enhancing soybean resistance to insect pests.

In Silico Analysis: Genome-Wide Identification, Characterization and Evolutionary Adaptations of Bone Morphogenetic Protein (BMP) Gene Family in Homo sapiens

We systematically analyzed BMP gene family in H. sapiens to elucidate genetic structure, phylogenetic relationships, adaptive evolution and tissue-specific expression pattern. Total of 13 BMPs genes were identified in the H. sapiens genome. Bone morphogenetic proteins (BMPs) are composed of a variable number of exons ranging from 2 to 21. They exhibit a molecular weight ranging from 31,081.81 to 82,899.61 Da. These proteins possess hydrophilic characteristics, display thermostability, and exhibit a pH range from acidic to basic. We identified four segmental and two tandem duplication events in BMP gene family of H. sapiens. All of the vertebrate species that were studied show the presence of BMPs 1, 2, 3, 4, 5, 6, 7, 8A, and 15, however only Homo sapiens demonstrated the presence of BMP9 and BMP11. The pathway and process enrichment analysis of BMPs genes showed that these were considerably enriched in positive regulation of pathway-restricted SMAD protein phosphorylation (92%) and cartilage development (77%) biological processes. These genes exhibited positive selection signals that were shown to be conserved across vertebrate lineages. The results showed that BMP2/3/5/6/8a/15 proteins underwent adaptive selection at many amino acid locations and increased positive selection was detected in TGF-β propeptide and TGF-β super family domains which were involved in dorso-ventral patterning, limb bud development. More over the expression pattern of BMP genes revealed that BMP1 and BMP5; BMP4 and BMP6 exhibited substantially identical expression patterns in all tissues while BMP10, BMP15, and BMP3 showed tissue-specific expression.

Transcriptomic Profiling of Embryogenic and Non-Embryogenic Callus Provides New Insight into the Nature of Recalcitrance in Cannabis

Differential gene expression profiles of various cannabis calli including non-embryogenic and embryogenic (i.e., rooty and embryonic callus) were examined in this study to enhance our understanding of callus development in cannabis and facilitate the development of improved strategies for plant regeneration and biotechnological applications in this economically valuable crop. A total of 6118 genes displayed significant differential expression, with 1850 genes downregulated and 1873 genes upregulated in embryogenic callus compared to non-embryogenic callus. Notably, 196 phytohormone-related genes exhibited distinctly different expression patterns in the calli types, highlighting the crucial role of plant growth regulator (PGRs) signaling in callus development. Furthermore, 42 classes of transcription factors demonstrated differential expressions among the callus types, suggesting their involvement in the regulation of callus development. The evaluation of epigenetic-related genes revealed the differential expression of 247 genes in all callus types. Notably, histone deacetylases, chromatin remodeling factors, and EMBRYONIC FLOWER 2 emerged as key epigenetic-related genes, displaying upregulation in embryogenic calli compared to non-embryogenic calli. Their upregulation correlated with the repression of embryogenesis-related genes, including LEC2, AGL15, and BBM, presumably inhibiting the transition from embryogenic callus to somatic embryogenesis. These findings underscore the significance of epigenetic regulation in determining the developmental fate of cannabis callus. Generally, our results provide comprehensive insights into gene expression dynamics and molecular mechanisms underlying the development of diverse cannabis calli. The observed repression of auxin-dependent pathway-related genes may contribute to the recalcitrant nature of cannabis, shedding light on the challenges associated with efficient cannabis tissue culture and regeneration protocols.

Transcriptome Analysis of Embryogenic and Non-Embryogenic Callus of Picea Mongolica

Picea mongolica is a rare tree species in China, which is of great significance in combating desertification and improving the harsh ecological environment. Due to the low rate of natural regeneration, high mortality, and susceptibility to pests and cold springs, Picea mongolica has gradually become extinct. At present, somatic embryogenesis (SE) is the most effective method of micro-proliferation in conifers, but the induction rate of embryogenic callus (EC) is low, and EC is difficult to differentiate from non-embryonic callus (NEC). Therefore, the EC and NEC of Picea mongolica were compared from the morphology, histological, physiological, and transcriptional levels, respectively. Morphological observation showed that the EC was white and transparent filamentous, while the NEC was compact and brownish-brown lumpy. Histological analyses showed that the NEC cells were large and loosely arranged; the nuclei attached to the edge of the cells were small; the cytoplasm was low; and the cell gap was large and irregular. In the EC, small cells, closely arranged cells, and a large nucleus and nucleolus were observed. Physiological studies showed significant differences in ROS-scavenging enzymes between the EC and NEC. Transcriptome profiling revealed that 13,267 differentially expressed genes (DEGs) were identified, 3682 were up-regulated, and 9585 were down-regulated. In total, 63 GO terms had significant enrichment, 32 DEGs in plant hormone signal transduction pathway were identified, and 502 different transcription factors (TFs) were characterized into 38 TF families. Meanwhile, we identified significant gene expression trends associated with somatic embryo development in plant hormones (AUX/IAA, YUCCA, LEA, etc.), stress (GST, HSP, GLP, etc.), phenylpropanoid metabolism (4CL, HCT, PAL, etc.), and transcription factors (AP2/ERF, MYB, WOX, etc.). In addition, nine genes were chosen for RT-qPCR, and the results were consistent with RNA-Seq data. This study revealed the changes in morphology, histology, physiology, and gene expression in the differentiation of NEC into EC and laid the foundation for finding the key genes to promote EC formation.

Genome-wide identification, evolution and expression analysis of bone morphogenetic protein (BMP) gene family in chinese soft-shell turtle (Pelodiscus sinensis)

Introduction: Bone morphogenetic proteins (BMPs) play a crucial role in bone formation and differentiation. Recent RNA-Seq results suggest that BMPs may be involved in the sex differentiation of P. sinensis, yet more relevant studies about BMPs in P. sinensis are lacking. Methods: Herein, we identified BMP gene family members, analyzed the phylogeny, collinear relationship, scaffold localization, gene structures, protein structures, transcription factors and dimorphic expression by using bioinformatic methods based on genomic and transcriptomic data of P. sinensis. Meanwhile, qRT-PCR was used to verify the RNA-Seq results and initially explore the function of the BMPs in the sex differentiation of P. sinensis. Results: A total of 11 BMP genes were identified, 10 of which were localized to their respective genomic scaffolds. Phylogenetic analysis revealed that BMP genes were divided into eight subfamilies and shared similar motifs ("WII", "FPL", "TNHA", "CCVP", and "CGC") and domain (TGF-β superfamily). The results of the sexually dimorphic expression profile and qRT-PCR showed that Bmp2, Bmp3, Bmp15l, Bmp5, Bmp6 and Bmp8a were significantly upregulated in ovaries, while Bmp2lb, Bmp7, Bmp2bl and Bmp10 were remarkable upregulated in testes, suggesting that these genes may play a role in sex differentiation of P. sinensis. Discussion: Collectively, our comprehensive results enrich the basic date for studying the evolution and functions of BMP genes in P. sinensis.

Proteome profiles during early stage of somatic embryogenesis of two Eucalyptus species

BACKGROUND

Somatic embryogenesis (SE) was recognized as an important tool for plants to propagate. However, our knowledge about the proteins involved in early SE including the callus dedifferentiation is still limited, especially in the economic woody tree - Eucalyptus.

RESULTS

We used the data-independent acquisition mass-spectrometry to study the different proteome profiles of early SE of two Eucalyptus species-E. camaldulensis (high regeneratively potential) and E. grandis x urophylla (low regenerative potential). Initially, 35,207 peptides and 7,077 proteins were identified in the stem and tissue-culture induced callus of the two Eucalyptus species. MSstat identified 2,078 and 2,807 differentially expressed proteins (DEPs) in early SE of E. camaldulensis and E. grandis x urophylla, respectively. They shared 760 upregulated and 420 downregulated proteins, including 4 transcription factors, 31 ribosomal proteins, 1 histone, 3 zinc finger proteins (ZFPs), 16 glutathione transferases, 10 glucosyltransferases, ARF19, WOX8 and PIN1. These proteins might be involved in the early SE of Eucalyptus. By combining the miRNA and RNA-Seq results, some miRNA ~ gene/protein regulatory networks were identified in early SE of Eucalyptus, such as miR160 ~ TPP2, miR164 ~ UXS2, miR169 ~ COX11 and miR535 ~ Eucgr.E01067. Further, we found SERK, WRKY, ZFP and ABC transporter might be related with high SE potential.

CONCLUSIONS

Overall, our study identified proteins involved in the early SE and related to the high regeneration potential of Eucalyptus. It greatly enhanced our understanding of the early SE and the SE capacity of Eucalyptus.

Genome-wide identification of Oryza sativa: A new insight for advanced analysis of ABC transporter genes associated with the degradation of four pesticides

ATP-binding cassette (ABC) transporter is a large genes superfamily. It involves transportation of diverse substrates (e.g., heavy metal, amino acids, pesticides, metabolites). The ABC transporters can be strongly induced by environmental stress and responsible for the phase III metabolic process of toxic compounds in plants. To investigate the potential molecular and biochemical function of ABC transporters in response to pesticides, we used bioinformatics and high-throughput sequencing to identify 107 loci from rice (Oryza sativa) exposed to different pesticides (ametryn, AME; bentazone, BNTZ; fomesafen, FSA; mesotrione, MTR) and annotated as ABC transporter genes. ABC transporter genes were categorized to eight subfamilies including ABCA-G and ABCI. ABCG subfamily was the largest group in rice genome followed by ABCC subfamily and ABCB subfamily. The distribution of each ABC transporter on twelve chromosomes was identified. The result showed that a large number of genes were scattered around chromosome. Differentially expressed genes (DEGs) were selected for cis-acting analysis under pesticide stress. Multiple cis-elements for biological functions such as hormone-sensitive elements and defense-related elements were found to involve the initiation and regulation of transcription. Comprehensive phylogenetic analysis and domain prediction of all ABC DEGs from rice and Arabidopsis were carried out. The docking analysis of ABC transporters and pesticides provided insights into the key amino acid residues involved in the binding of the pesticides. Consequently, the results provided applicable information and reference for a more functional analysis of ABC transporter genes on regulation of pesticide metabolism and transport in plants.

The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View

Lignans, as secondary metabolites synthesized within a phenylpropanoid pathway, play various roles in plants, including their involvement in growth and plant defense processes. The health and nutritional benefits of lignans are unquestionable, and many studies have been devoted to these attributes. Although the regulatory role of miRNAs in the biosynthesis of secondary metabolites has been widely reported, there is no systematic review available on the miRNA-based regulatory mechanism of lignans biosynthesis. However, the genetic background of lignan biosynthesis in plants is well characterized. We attempted to put together a regulatory mosaic based on current knowledge describing miRNA-mediated regulation of genes, enzymes, or transcription factors involved in this biosynthesis process. At the same time, we would like to underline the fact that further research is necessary to improve our understanding of the miRNAs regulating plant lignan biosynthesis by exploitation of current approaches for functional identification of miRNAs.