Apollo: Democratizing genome annotation

PLoS Computational Biology, Год журнала: 2019, Номер 15(2), С. e1006790 - e1006790

Опубликована: Фев. 6, 2019

Genome annotation is the process of identifying location and function a genome's encoded features. Improving biological accuracy complex iterative requiring researchers to review incorporate multiple sources information such as transcriptome alignments, predictive models based on sequence profiles, comparisons features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number scientists sequencing routine laboratory technique, there widespread demand for tools that can assist deliberative analytical genomic information. To this end, we present Apollo, open source software package enables efficiently inspect refine precise structure role graphical browser-based platform. Some Apollo's newer user interface include support real-time collaboration, allowing distributed users simultaneously edit same while also instantly seeing updates made by other region manner similar Google Docs. Its technical architecture Apollo be integrated into existing analysis pipelines heterogeneous workflow platforms. Finally, consider implications applications may have how results genome research published accessible.

Язык: Английский

---

Two Y-chromosome-encoded genes determine sex in kiwifruit

Nature Plants, Год журнала: 2019, Номер 5(8), С. 801 - 809

Опубликована: Авг. 5, 2019

Язык: Английский

---

A MYB / bHLH complex regulates tissue‐specific anthocyanin biosynthesis in the inner pericarp of red‐centered kiwifruit Actinidia chinensis cv. Hongyang

The Plant Journal, Год журнала: 2019, Номер 99(2), С. 359 - 378

Опубликована: Март 26, 2019

Summary Many Actinidia cultivars are characterized by anthocyanin accumulation, specifically in the inner pericarp, but underlying regulatory mechanism remains elusive. Here we report two interacting transcription factors, Ac MYB 123 and Acb HLH 42, that regulate tissue‐specific biosynthesis pericarp of chinensis cv. Hongyang. Through transcriptome profiling analysis identified five three bHLH factors were upregulated pericarp. We show combinatorial action them, is required for activating promoters AcANS AcF3GT1 encode dedicated enzymes biosynthesis. The presence appears to be tightly associated with elevated expression AcMYB123 AcbHLH42 . RNA interference repression , ‘Hongyang’ fruits resulted significantly reduced Using both transient assays Nicotiana tabacum leaves or arguta stable transformation Arabidopsis, demonstrate co‐expression a prerequisite production homologous genes. Phylogenetic suggests 42 closely related TT 2 8, respectively, which determines proanthocyanidin regulators monocots rather than dicots. All these experimental results suggest components involved spatiotemporal regulation kiwifruit.

Язык: Английский

---

A high-quality Actinidia chinensis (kiwifruit) genome

Horticulture Research, Год журнала: 2019, Номер 6(1)

Опубликована: Окт. 14, 2019

Actinidia chinensis (kiwifruit) is a perennial horticultural crop species of the Actinidiaceae family with high nutritional and economic value. Two versions A. genomes have been previously assembled, based mainly on relatively short reads. Here, we report an improved chromosome-level reference genome (v3.0), PacBio long reads Hi-C data. The high-quality assembled 653 Mb long, 0.76% heterozygosity. At least 43% consists repetitive sequences, most abundant terminal repeats were further identified account for 23.38% our novel genome. It has clear improvements in contiguity, accuracy, gene annotation over two previous contains 40,464 annotated protein-coding genes, which 94.41% are functionally annotated. Moreover, analyses genetic collinearity revealed that kiwifruit undergone whole-genome duplications: one affecting all Ericales families near K-T extinction event recent genus-specific duplication. presented here will be highly useful molecular elucidation diverse traits breeding this crop, as well evolutionary studies related taxa.

Язык: Английский

---

Chromosome-level genome assembly of a parent species of widely cultivated azaleas

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Окт. 19, 2020

Abstract Azaleas (Ericaceae) comprise one of the most diverse ornamental plants, renowned for their cultural and economic importance. We present a chromosome-scale genome assembly Rhododendron simsii , primary ancestor azalea cultivars. Genome analyses unveil remnants an ancient whole-genome duplication preceding radiation Ericaceae, likely contributing to genomic architecture flowering time. Small-scale gene duplications contribute expansion families involved in pigment biosynthesis. reconstruct entire metabolic pathways anthocyanins carotenoids potential regulatory networks by detailed analysis time-ordered co-expression networks. MYB, bHLH, WD40 transcription factors may collectively regulate anthocyanin accumulation R. particularly at initial stages flower coloration, with WRKY controlling progressive coloring later stages. This work provides cornerstone understanding underlying genetics governing timing coloration could accelerate selective breeding azalea.

Язык: Английский

---

Kiwifruit MYBS1‐like and GBF3 transcription factors influence l‐ascorbic acid biosynthesis by activating transcription of GDP‐L‐galactose phosphorylase 3

New Phytologist, Год журнала: 2022, Номер 234(5), С. 1782 - 1800

Опубликована: Март 15, 2022

Plant-derived Vitamin C (l-ascorbic acid (AsA)) is crucial for human health and wellbeing thus increasing AsA content of interest to plant breeders. In plants GDP-l-galactose phosphorylase (GGP) a key biosynthetic control step here evidence presented two new transcriptional activators GGP. measurement, transcriptomics, transient expression, hormone application, gene editing, yeast 1/2-hybrid, electromobility shift assay (EMSA) methods were used identify positively regulating transcription factors. AceGGP3 was identified as the most highly expressed GGP in Actinidia eriantha fruit, which has high fruit AsA. A encoding 1R-subtype myeloblastosis (MYB) protein, AceMYBS1, found bind promoter activate its expression. Overexpression gene-editing show AceMYBS1 effectively increases accumulation. The bZIP factor AceGBF3 (a G-box binding factor), also shown increase content, confirmed interact with AceMYBS1. Co-expression experiments showed that additively promoted Furthermore, but not GBF3, repressed by abscisic acid, resulting reduced expression accumulation This study sheds light on roles MYBS1 homologues ABA modulating synthesis, adds understanding mechanisms underlying

Язык: Английский

---

Super pan-genome reveals extensive genomic variations associated with phenotypic divergence in Actinidia

Molecular Horticulture, Год журнала: 2025, Номер 5(1)

Опубликована: Янв. 24, 2025

Abstract Kiwifruit is an economically and nutritionally important horticultural fruit crop worldwide. The genomic data of several kiwifruit species have been released, providing unprecedented opportunity for pan-genome analysis to comprehensively investigate the inter- intra-species genetic diversity facilitate utilization breeding. Here, we generated a super using 15 high-quality assemblies eight Actinidia species. For gene-based pan-genome, total 61,465 gene families were identified, softcore dispensable genes enriched in biological processes like response endogenous stimulus, hormone cell wall organization or biogenesis. Then, structural variations (SVs) against A. chinensis ‘Donghong’ identified then used construct graph-based genome. Further population-scale SVs based on resequencing from 112 individuals 20 revealed extensive which probably contributed phenotypic among SV hotspot regions found environmental adaptation. Furthermore, systematically resistance analogs (RGAs) pan-RGA dataset reveal potentially involved disease . pan-genomic obtained here useful evolutionary functional studies , facilitates breeding design.

Язык: Английский

---

Differential regulation of the anthocyanin profile in purple kiwifruit (Actinidia species)

Horticulture Research, Год журнала: 2018, Номер 6(1)

Опубликована: Дек. 31, 2018

Anthocyanins are a group of secondary metabolites that colour fruit and flowers orange, red, purple or blue depending on number factors, such as the basic structure, co-pigmentation, metal ion complexation vacuolar pH. The biosynthesis anthocyanin is regulated at transcriptional level by transcription MYB-bHLH-WD40 (MBW) complex. In this study, colouration in several kiwifruit (Actinidia) species was identified characterised red cyanidin-based delphinidin-based anthocyanins. differential pigmentation skin flesh can be attributed to ratio cyanidin delphinidin derivatives accumulated total profile. expression biosynthetic genes chalcone synthase (CHS), flavonoid 3-O-glucosyltransferase (F3GT), 3'-hydroxylase (F3'H) 3'5'-hydroxylase (F3'5'H) crucial for accumulation. However, balance F3'H F3'5'H appears responsible derivatives, while lack CHS, F3GT MYB110 regulation promoters R2R3 MYB factor markedly different tobacco transient assays. When MYB10 over-expressed Actinidia chinensis both anthocyanins elevated, but not strongly correlated with expression. These results suggest core pathway dependent other regulatory proteins more directly genes.

Язык: Английский

---

Mutagenesis of kiwifruit CENTRORADIALIS‐like genes transforms a climbing woody perennial with long juvenility and axillary flowering into a compact plant with rapid terminal flowering

Plant Biotechnology Journal, Год журнала: 2018, Номер 17(5), С. 869 - 880

Опубликована: Окт. 10, 2018

Annualization of woody perennials has the potential to revolutionize breeding and production fruit crops rapidly improve horticultural species. Kiwifruit (Actinidia chinensis) is a recently domesticated crop with short history tremendous for improvement. Previously, multiple kiwifruit CENTRORADIALIS (CEN)-like genes have been identified as repressors flowering. In this study, CRISPR/Cas9- mediated manipulation enabled functional analysis CEN-like AcCEN4 AcCEN. Mutation these transformed climbing perennial, which develops axillary inflorescences after many years juvenility, into compact plant rapid terminal flower development. The number affected alleles severity detected mutations correlated precocity change in stature, suggesting that bi-allelic mutation either or AcCEN may be sufficient early flowering, whereas affecting both further contributed enhanced growth habit. CRISPR/Cas9-mediated mutagenesis valuable means engineer Actinidia amenable accelerated breeding, indoor farming cultivation an annual crop.

Язык: Английский

---

Genome‐wide analysis of coding and non‐coding RNA reveals a conserved miR164‐NAC regulatory pathway for fruit ripening

New Phytologist, Год журнала: 2019, Номер 225(4), С. 1618 - 1634

Опубликована: Окт. 1, 2019

Kiwifruit (Actinidia spp.) is a climacteric fruit with high sensitivity to ethylene, influenced by multiple ethylene-responsive structural genes and transcription factors. However, the roles of other post-transcriptional regulators (e.g. miRNAs) necessary for ripening remain elusive. High-throughput sequencing sRNAome, degradome transcriptome methods were used identify further contributors control in kiwifruit (A. deliciosa cv 'Hayward'). Two NAM/ATAF/CUC domain factors (AdNAC6 AdNAC7), both predicted targets miR164, showed significant upregulation exogenous ethylene. Gene expression analysis luciferase reporter assays indicated that Ade-miR164 one its precursor miRNAs (Ade-MIR164b) repressed ethylene treatment negatively correlated AdNAC6/7 expression. Subsequent AdNAC6 AdNAC7 proteins are transcriptional activators physically bind promoters AdACS1 (1-aminocyclopropane-1-carboxylate synthase), AdACO1 (1-aminocyclopropane-1-carboxylic acid oxidase), AdMAN1 (endo-β-mannanase) AaTPS1 (terpene synthase). Moreover, subcellular location was Ade-miR164. Multiple omics-based approaches revealed novel regulatory link involved ethylene-miR164-NAC. The pathway miR164-NAC present various Rosaceae fruit, citrus, grape), implications regulation.

Язык: Английский

---