The Chromosome-Level Genome of Miracle Fruit (Synsepalum dulcificum) Provides New Insights Into the Evolution and Function of Miraculin

Miracle fruit (Synsepalum dulcificum) is a rare valuable tropical plant famous for a miraculous sweetening glycoprotein, miraculin, which can modify sour flavors to sweet flavors tasted by humans. Here, we present a chromosome-level high-quality genome of S. dulcificum with an assembly genome size of ∼550 Mb, contig N50 of ∼14.14 Mb, and 37,911 annotated protein-coding genes. Phylogenetic analysis revealed that S. dulcificum was most closely related to Camellia sinensis and Diospyros oleifera, and that S. dulcificum diverged from the Diospyros genus ∼75.8 million years ago (MYA), and that C. sinensis diverged from Synsepalum ∼63.5 MYA. Ks assessment and collinearity analysis with S. dulcificum and other species suggested that a whole-genome duplication (WGD) event occurred in S. dulcificum and that there was good collinearity between S. dulcificum and Vitis vinifera. On the other hand, transcriptome and metabolism analysis with six tissues containing three developmental stages of fleshes and seeds of miracle fruit revealed that Gene Ontology (GO) terms and metabolic pathways of “cellular response to chitin,” “plant–pathogen interaction,” and “plant hormone signal transduction” were significantly enriched during fruit development. Interestingly, the expression of miraculin (Chr10G0299340) progressively increased from vegetative organs to reproductive organs and reached an incredible level in mature fruit flesh, with an fragments per kilobase of transcript per million (FPKM) value of ∼113,515, which was the most highly expressed gene among all detected genes. Combining the unique signal peptide and the presence of the histidine-30 residue together composed the main potential factors impacting miraculin’s unique properties in S. dulcificum. Furthermore, integrated analysis of weighted gene coexpression network analysis (WGCNA), enrichment and metabolite correlation suggested that miraculin plays potential roles in regulating plant growth, seed germination and maturation, resisting pathogen infection, and environmental pressure. In summary, valuable genomic, transcriptomic, and metabolic resources provided in this study will promote the utilization of S. dulcificum and in-depth research on species in the Sapotaceae family.

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Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2101767118 ◽

2021 ◽

Vol 118 (20) ◽

pp. e2101767118

Author(s):

Wenbing Su ◽

Yi Jing ◽

Shoukai Lin ◽

Zhen Yue ◽

Xianghui Yang ◽

...

Keyword(s):

Metabolic Pathways ◽

Genome Duplication ◽

Developmental Stages ◽

Plant Evolution ◽

Metabolic Diversity ◽

Medicinal Properties ◽

And Function ◽

Genomic Basis ◽

Triterpene Biosynthesis ◽

Chromosome Level

Whole-genome duplication (WGD) plays important roles in plant evolution and function, yet little is known about how WGD underlies metabolic diversification of natural products that bear significant medicinal properties, especially in nonmodel trees. Here, we reveal how WGD laid the foundation for co-option and differentiation of medicinally important ursane triterpene pathway duplicates, generating distinct chemotypes between species and between developmental stages in the apple tribe. After generating chromosome-level assemblies of a widely cultivated loquat variety and Gillenia trifoliata, we define differentially evolved, duplicated gene pathways and date the WGD in the apple tribe at 13.5 to 27.1 Mya, much more recent than previously thought. We then functionally characterize contrasting metabolic pathways responsible for major triterpene biosynthesis in G. trifoliata and loquat, which pre- and postdate the Maleae WGD, respectively. Our work mechanistically details the metabolic diversity that arose post-WGD and provides insights into the genomic basis of medicinal properties of loquat, which has been used in both traditional and modern medicines.

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A transcription factor DAF-5 functions in Haemonchus contortus development

Parasites & Vectors ◽

10.1186/s13071-021-05036-2 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Wenda Di ◽

Fangfang Li ◽

Li He ◽

Chunqun Wang ◽

Caixian Zhou ◽

...

Keyword(s):

Haemonchus Contortus ◽

Developmental Stages ◽

Reproductive Organs ◽

Bimolecular Fluorescence Complementation ◽

Parasitic Nematodes ◽

Small Interfering Rnas ◽

C Elegans ◽

Dauer Formation ◽

And Function

Abstract Background Abnormal dauer formation gene (daf-5), located downstream of the DAF-7 signalling pathway, mainly functions in dauer formation and reproductive processes in the free-living nematode Caenorhabditis elegans. Although the structure and function of daf-5 have been clarified in C. elegans, they still remain totally unknown in Haemonchus contortus, a socio-economically important parasitic nematode of gastric ruminants. Methods A homologue of daf-5, Hc-daf-5, and its inferred product (Hc-DAF-5) in H. contortus were identified and characterized in this study. Then the transcriptional profiles of Hc-daf-5 and the anatomical expression of Hc-DAF-5 in H. contortus were studied using an integrated molecular approach. RNA interference (RNAi) was performed to explore its function in transition from the exsheathed third-stage larvae (xL3s) to the fourth-stage larvae (L4s) in vitro. Finally, the interaction between Hc-DAF-5 and Hc-DAF-3 (a co-Smad) was detected by bimolecular fluorescence complementation (BiFc) in vitro. Results It was shown that Hc-DAF-5 was a member of the Sno/Ski superfamily. Hc-daf-5 was transcribed in all developmental stages of H. contortus, with significant upregulation in L3s. Native Hc-DAF-5 was localized in the reproductive organs, cuticle, and intestine via immunohistochemistry. RNAi revealed that specific small interfering RNAs (siRNAs) could retard xL3 development. In addition, the interaction between Hc-DAF-5 and Hc-DAF-3 indicated that the SDS box of Hc-DAF-5 was dispensable for the binding of Hc-DAF-5 to Hc-DAF-3, and the MH2 domain was the binding region between Hc-DAF-3 and Hc-DAF-5. Conclusions In summary, these findings show that Hc-daf-5 functions in the developmental processes of H. contortus, and this study is the first attempt to characterize the daf-5 gene in parasitic nematodes. Graphical abstract

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A Transcription Factor DAF5 Functions in Haemonchus Contortus Development

10.21203/rs.3.rs-768609/v1 ◽

2021 ◽

Author(s):

Wenda Di ◽

Fangfang Li ◽

Li He ◽

Chunqun Wang ◽

Caixian Zhou ◽

...

Keyword(s):

Haemonchus Contortus ◽

Developmental Stages ◽

Reproductive Organs ◽

Bimolecular Fluorescence Complementation ◽

Parasitic Nematodes ◽

C Elegans ◽

Free Living Nematode ◽

And Function ◽

Reproductive Processes

Abstract Background: Daf5 (Dauer abnormal formation gene), located in the downstream of DAF-7 signalling pathway, mainly functions in dauer formation and reproductive processes in the free-living nematode Caenorhabditis elegans. Although its structure and function have been studied clearly in C. elegans, it was totally unknown in Haemonchus contortus, a socio-economically important parasitic nematode of gastric ruminants.Methods: Here, we identified and characterized a homologue of Daf5, Hcdaf5 and its inferred product (HcDAF5) in H. contortus. Using an integrated molecular approach, we studied the transcriptional profiles of Hcdaf5 and the anatomical expression of HcDAF5 in H. contortus. RNA interference (RNAi) was performed to explore its function in transition from the exsheathed third-stage larvae (xL3) to the fourth-stage larvae (L4) in vitro. Interaction of HcDAF5 and HcDAF3 (a co-SMAD) was also detected by bimolecular fluorescence complementation system (BiFc) in vitro.Results: Here, we showed that HcDAF5 is a member of the Sno/Ski superfamily. Hcdaf5 was transcribed in all developmental stages of H. contortus, with a significant up-regulation in L3. Immunohistochemistry localized native HcDAF5 to the reproductive organs, cuticle and intestine. RNAi revealed specific siRNAs (small interfering RNA) could retard the xL3 development. In addition, the interaction between HcDAF5 and HcDAF3 indicated the SDS box region of HcDAF5 is dispensable for the binding of HcDAF5 to HcDAF3 and the region in HcDAF3 that binds to HcDAF5 is MH2 domain.Conclusion: In summary, these findings show that Hcdaf5 functions in developmental processes of H. contortus, and this is the first characterization of daf-5 gene in parasitic nematodes.

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Oligochaete taxonomy – The rise of earthworm DNA barcode in India

Science Vision ◽

10.33493/scivis.18.01.01 ◽

2018 ◽

Vol 18 (1) ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

H. Lalthanzara ◽

Ruth Lalfelpuii ◽

C. Zothansanga ◽

M. Vabeiryureilai ◽

N. Senthil Kumar ◽

...

Keyword(s):

Dna Barcoding ◽

Developmental Stages ◽

Dna Barcode ◽

Soil Classification ◽

Reproductive Organs ◽

Diagnostic Features ◽

Protein Coding ◽

Anatomical Characters ◽

Ecological Importance

Oligochaeta is a class of segmented worms under the phylum Annelida that are characterised by the presence of tiny setae in each body segment. Earthworms are the main members, consisting of approximately 6200 species. Their ecological importance is well known as they are the major soil macro-fauna; Aristotle had named them as “the intestines of soil”. Classification of earthworms is a controversial issue since the introduction of modern taxonomical system on earthworm by Michaelsen in 1921. This is mainly because conventional identification using morphological and anatomical characters are complicated and confusing. The key diagnostic features such as the position and structure of the reproductive organs, clitellum and the associated tubercular pubertatis are not always reliable, particularly in different developmental stages, especially when the available specimens are the juveniles. DNA barcoding has offered a potential solution, even at the levels of identifying the juveniles or cocoons. Several genes including mitochondrial cytochrome-c oxidase I, 16S, 18S and 28S ribosomal RNAs, and protein-coding histone H3 genes have been introduced in the taxonomy and phylogeny of earthworm. It is anticipated that DNA barcoding will help conflicting taxonomy and further exploration of species diversity in India.

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Chromosome-level Genome Assembly of the Blue Crab, Callinectes sapidus

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab212 ◽

2021 ◽

Author(s):

Tsvetan R Bachvaroff ◽

Ryan C McDonald ◽

Louis V Plough ◽

J Sook Chung

Keyword(s):

Blue Crab ◽

Developmental Stages ◽

Callinectes Sapidus ◽

Atlantic Coast ◽

Portunus Trituberculatus ◽

Protein Coding ◽

Important Species ◽

Protein Coding Genes ◽

Repeat Content ◽

Chromosome Level

Abstract The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200x coverage Illumina paired-end reads, a 60x 8 kb mate-paired library, and 50x PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The fifty largest scaffolds span 810 Mb are 1.5 to 37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10kb with a repeat content of 68%. The final assembly N50 is 18.9 Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, ∼88% (888/1,013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but nine scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, of which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species.

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Spring Freeze Damage of Pecan Bloom: A Review

Horticulturae ◽

10.3390/horticulturae6040082 ◽

2020 ◽

Vol 6 (4) ◽

pp. 82

Author(s):

Amandeep Kaur ◽

Louise Ferguson ◽

Niels Maness ◽

Becky Carroll ◽

William Reid ◽

...

Keyword(s):

Tree Height ◽

The United States ◽

Reproductive Organs ◽

Tree Age ◽

The Us ◽

Nut Production ◽

Freeze Damage ◽

Terminal Buds ◽

And Function ◽

The Impact

Pecan is native to the United States. The US is the world’s largest pecan producer with an average yearly production of 250 to 300 million pounds; 80 percent of the world’s supply. Georgia, New Mexico, Texas, Arizona, Oklahoma, California, Louisiana, and Florida are the major US pecan producing states. Pecan trees frequently suffer from spring freeze at bud break and bloom as the buds are quite sensitive to freeze damage. This leads to poor flower and nut production. This review focuses on the impact of spring freeze during bud differentiation and flower development. Spring freeze kills the primary terminal buds, the pecan tree has a second chance for growth and flowering through secondary buds. Unfortunately, secondary buds have less bloom potential than primary buds and nut yield is reduced. Spring freeze damage depends on severity of the freeze, bud growth stage, cultivar type and tree age, tree height and tree vigor. This review discusses the impact of temperature on structure and function of male and female reproductive organs. It also summarizes carbohydrate relations as another factor that may play an important role in spring growth and transition of primary and secondary buds to flowers.

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Comparative effects of Orchis anatolica vs. the red Korean Panax ginseng treatments on testicular structure and function of adult male mice

Journal of Complementary and Integrative Medicine ◽

10.1515/jcim-2012-0035 ◽

2015 ◽

Vol 12 (1) ◽

Author(s):

Nabil A. Khouri ◽

Haytham M. Daradka ◽

Mohammed Z. Allouh ◽

Ahmad S. Alkofahi

Keyword(s):

Panax Ginseng ◽

Male Fertility ◽

Virgin Female ◽

Reproductive Organs ◽

Serum Markers ◽

Structure And Function ◽

Control Group ◽

Male Mice ◽

Fertility Potential ◽

And Function

Abstract: The effects of: Both plants were administered orally to two separate mice groups at a dose of 800 mg/kg/day for 35 days and compared with control group. After treatment, 5 mice of each group were sacrificed and total mice weights, reproductive organs’ weights, spermatogenesis, and androgenic serum markers were investigated. The remaining mice from all groups were allowed to mate with virgin female mice to explore male fertility potential.: Results indicated that body and organs’ weights were increased significantly in mice treated with: We can conclude that

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Common and rare genetic variants that could contribute to severe otitis media in an Australian Aboriginal population

Clinical Infectious Diseases ◽

10.1093/cid/ciab216 ◽

2021 ◽

Author(s):

Sarra E Jamieson ◽

Michaela Fakiola ◽

Dave Tang ◽

Elizabeth Scaman ◽

Genevieve Syn ◽

...

Keyword(s):

Hair Cell ◽

Otitis Media ◽

Genetic Risk ◽

Transforming Growth Factor ◽

Rare Variants ◽

Protein Coding ◽

Gene Sets ◽

Growth Factor Signalling ◽

Rare Genetic Variants ◽

And Function

Abstract Background Our goal was to identify genetic risk factors for severe otitis media (OM) in Aboriginal Australians. Methods Illumina ® Omni2.5 BeadChip and imputed data were compared between 21 children with severe OM (multiple episodes chronic suppurative OM and/or perforations or tympanic sclerosis) and 370 individuals without this phenotype, followed by FUnctional Mapping and Annotation (FUMA). Exome data filtered for common (EXaC_all≥0.1) putative deleterious variants influencing protein coding (CADD-scaled scores ≥ 15) were used to compare 15 severe OM cases with 9 mild cases (single episode of acute OM recorded over ≥ 3 consecutive years). Rare (ExAC_all≤0.01) such variants were filtered for those present only in severe OM. Enrichr was used to determine enrichment of genes contributing to pathways/processes relevant to OM. Results FUMA analysis identified two plausible genetic risk loci for severe OM: NR3C1 (Pimputed_1000G=3.62x10 -6) encoding the glucocorticoid receptor, and NREP (Pimputed_1000G=3.67x10 -6) encoding neuronal regeneration related protein. Exome analysis showed: (i) association of severe OM with variants influencing protein coding (CADD-scaled ≥ 15) in a gene-set (GRXCR1, CDH23, LRP2, FAT4, ARSA, EYA4) enriched for Mammalian Phenotype Level 4 abnormal hair cell stereociliary bundle morphology and related phenotypes; (ii) rare variants influencing protein coding only seen in severe OM provided gene-sets enriched for “abnormal ear” (LMNA, CDH23, LRP2, MYO7A, FGFR1), integrin interactions, transforming growth factor signalling, and cell projection phenotypes including hair cell stereociliary bundles and cilium assembly. Conclusions This study highlights interacting genes and pathways related to cilium structure and function that may contribute to extreme susceptibility to OM in Aboriginal Australian children.

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Integrative Modelling of Gene Expression and Digital Phenotypes to Describe Senescence in Wheat

Genes ◽

10.3390/genes12060909 ◽

2021 ◽

Vol 12 (6) ◽

pp. 909

Author(s):

Anyela Valentina Camargo Rodriguez

Keyword(s):

Gene Expression ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Developmental Stages ◽

Computational Modelling ◽

Plant Morphology ◽

Reproductive Organs ◽

Biological Trait ◽

Cereal Grain ◽

Plant Level

Senescence is the final stage of leaf development and is critical for plants’ fitness as nutrient relocation from leaves to reproductive organs takes place. Although senescence is key in nutrient relocation and yield determination in cereal grain production, there is limited understanding of the genetic and molecular mechanisms that control it in major staple crops such as wheat. Senescence is a highly orchestrated continuum of interacting pathways throughout the lifecycle of a plant. Levels of gene expression, morphogenesis, and phenotypic development all play key roles. Yet, most studies focus on a short window immediately after anthesis. This approach clearly leaves out key components controlling the activation, development, and modulation of the senescence pathway before anthesis, as well as during the later developmental stages, during which grain development continues. Here, a computational multiscale modelling approach integrates multi-omics developmental data to attempt to simulate senescence at the molecular and plant level. To recreate the senescence process in wheat, core principles were borrowed from Arabidopsis Thaliana, a more widely researched plant model. The resulted model describes temporal gene regulatory networks and their effect on plant morphology leading to senescence. Digital phenotypes generated from images using a phenomics platform were used to capture the dynamics of plant development. This work provides the basis for the application of computational modelling to advance understanding of the complex biological trait senescence. This supports the development of a predictive framework enabling its prediction in changing or extreme environmental conditions, with a view to targeted selection for optimal lifecycle duration for improving resilience to climate change.

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Mitochondrial Processes during Early Development of Dictyostelium discoideum: From Bioenergetic to Proteomic Studies

Genes ◽

10.3390/genes12050638 ◽

2021 ◽

Vol 12 (5) ◽

pp. 638

Author(s):

Monika Mazur ◽

Daria Wojciechowska ◽

Ewa Sitkiewicz ◽

Agata Malinowska ◽

Bianka Świderska ◽

...

Keyword(s):

Life Cycle ◽

Developmental Stages ◽

Coupling Efficiency ◽

Slime Mold ◽

Intact Cells ◽

Life Cycle Stages ◽

Early Developmental Stages ◽

Proteomic Study ◽

And Function ◽

Early Developmental

The slime mold Dictyostelium discoideum’s life cycle includes different unicellular and multicellular stages that provide a convenient model for research concerning intracellular and intercellular mechanisms influencing mitochondria’s structure and function. We aim to determine the differences between the mitochondria isolated from the slime mold regarding its early developmental stages induced by starvation, namely the unicellular (U), aggregation (A) and streams (S) stages, at the bioenergetic and proteome levels. We measured the oxygen consumption of intact cells using the Clarke electrode and observed a distinct decrease in mitochondrial coupling capacity for stage S cells and a decrease in mitochondrial coupling efficiency for stage A and S cells. We also found changes in spare respiratory capacity. We performed a wide comparative proteomic study. During the transition from the unicellular stage to the multicellular stage, important proteomic differences occurred in stages A and S relating to the proteins of the main mitochondrial functional groups, showing characteristic tendencies that could be associated with their ongoing adaptation to starvation following cell reprogramming during the switch to gluconeogenesis. We suggest that the main mitochondrial processes are downregulated during the early developmental stages, although this needs to be verified by extending analogous studies to the next slime mold life cycle stages.

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