12.1–21.7 actor raw reads per library from gynodioecious papaya var. “Zhongbai” and 13.1–18.3 actor raw reads per library from dioecious papaya var. “Zhonghuang” were generated. Afterwards removing low affection reads, the apple-pie reads were mapped to papaya abstract genome by STAR aligner. The reads abnormally mapped to genome accounted for 81.3–87.2% of apple-pie reads (Supplementary Tab. 1).
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To anticipate abeyant differences of gene announcement arrangement from altered abiogenetic background, we normalized and affected gene announcement ethics in FPKM (fragments per kilobase of exon per actor bits mapped) back compared the gynoecium samples from papaya array “Zhongbai”. The anatomic gynoecium of hermaphroditic ascendant flowers and changeable flowers were advised as advertence (baseline) back comparing adjoin the abecedarian ones. Appliance changeable anatomic gynoecium as reference, 2837 genes bidding abnormally amid F-FG and H_dom-RG, while comparing F-FG with H_aux-RG, 2222 genes were differentially expressed. Appliance anatomic gynoecium of hermaphroditic ascendant flowers as reference, 2402 and 2841 DEGs were articular while comparing H_dom-FG adjoin H_dom-RG and H_aux-RG, respectively. In total, 1050 accepted DEGs were begin amid these four types of comparisons (Fig. 1a).
a DEGs from changeable and hermaphrodite flowers of “Zhongbai” (b) DEGs from macho and changeable flowers of dioecious array “Zhonghuang” (c) Key accepted DEGs from both “Zhongbai” and “Zhonghuang” abecedarian gynoecium
The aforementioned access was acclimated to assay samples from macho and changeable flowers of dioecious array “Zhonghuang”. We begin 3620 DEGs from the allegory of anatomic gynoecium of changeable with abecedarian gynoecium of macho annual (Fig. 1b).
Interestingly, we begin 896 key accepted DEGs back compared 1050 accepted DEGs from “Zhongbai” and 3620 DEGs from “Zhonghuang”. Out of 896, 448 DEGs were upregulated while 438 were downregulated in both “Zhongbai” and “Zhonghuang” abecedarian gynoecium samples. While, 10 DEGs showed inconsistent announcement arrangement amid these two varieties and were alone (Fig. 1c).
To added analyze the differences in metabolism and development which associated with phenotypic character, we advised the biological roles of 896 key DEGs appliance GO comment and accessory analysis. The after-effects showed that the best abounding 20 GO agreement of 896 key DEGs were mainly classified into three biological pathways categories (Fig. 2), i.e., acknowledgment to bang (indicated by square), the advance and development (by rhombuses), and acknowledgment to phytohormone (by triangle).
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GO accessory assay of 896 key accepted DEGs
Based on the agnate akin protein of Arabidopsis by protein arrangement affinity Blast searches, we conducted the KEGG accessory assay for 896 key DEGs. The after-effects appropriate that the bulb phytohormone arresting transduction was the alleyway of best cogent accessory (corrected P-value 3.15e-07) in the comparisons amid anatomic and abecedarian gynoecium samples, while the added pathways such as phenylpropanoid biosynthesis and accessory metabolites biosynthesis had P-value > 0.001. So the phytohormone signaling ability comedy a analytical role in transitioning from accustomed gynoecium to abecedarian gynoecium.
To get a bigger identification on the above phytohormone arresting transduction acclimation the phenotypic development of altered gynoecium, DEGs were represented in agnate signaling pathways (Fig. 3). There was a acutely authentic accessory in auxin arresting transduction. In TIR1/AFB-Aux/IAA-ARF auxin signaling pathway, TIR1/AFB (TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX PROTEIN) is a amount subunit of SCF multi-protein E3 ubiquitin ligase complex, and acts as an intracellular receptor. AUX1 encodes a specific membrane-bound auxin arrival transporter. In all of abecedarian samples, added TIR1/AFB archetype announcement was begin to be accessory with the accumulating AUX1 archetype expression, in acknowledgment to extracellular auxin stimulus. Aux/IAA(AUXIN/INDOLE ACETIC ACID, auxin acknowledgment factors transcriptional repressors) genes showed decreased announcement arrangement in these abecedarian samples, which maintained Aux/IAA protein agreeable at a almost low akin in the beef and added advance the archetype of ARF(AUXIN RESPONSIVE FACTORS) and ARF-mediated aboriginal auxin acknowledgment genes (SAURs and GH3.9) as able-bodied as access the auxin effect. And the abatement in archetype announcement of some GH3s involving in auxin conjugation, such as GH 3.1 and GH3.6, appropriate there would be added accession of alive auxin appointment a connected auxin bang in abecedarian gynoecium. Besides that, PIN archetype was downregulated (Supplementary Tab. 2), which ability account added auxin accession and affect arresting transduction.
KEGG assay emphasized the cogwheel gene announcement of phytohormone signaling transduction in abecedarian gynoecium compared to anatomic gynoecium, red boxes announce upregulated gene, cyan boxes announce downregulated gene, Ub in chicken circles appearance the abasement of signaling atom by the ubiquitin-proteasome, ①TIR1/AFB circuitous answer ubiquitination and abasement of Aux/IAA, ②degradation of Aux/IAA appear the archetype repression of ARF
Further assay on the changes of DEGs in phytohormone arresting transduction was fabricated by presenting heatmaps (Fig. 4, gene symbol, gene id, and FPKM ethics were provided in Supplementary Tab. 2). For bristles signaling transduction, the acute and apocalyptic phytohormones acknowledging factors showed agnate arrangement of gene expression, which could be interpreted as agnate phytohormone adjustment or acknowledgment back comparing abecedarian and anatomic gynoecium in papaya.
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Similar arrangement of gene announcement of accompanying phytohormone acknowledging signaling transduction factors in allegory amid anatomic and abecedarian gynoecium samples
RNA-seq assay after-effects accent the abeyant accession of alive auxin in abecedarian gynoecium. To beam the aftereffect of auxin in analyze gynoecium tissue, auxin carriage inhibitor (NPA) and constructed auxin analogs (NAA and 2,4-D) were sprayed appear the block acme of macho and changeable plants of diecious array Zhonghuang.
10 mg/L arctic auxin carriage inhibitors (NPA) appliance on papaya shoot acme resulted in arresting changes in morphological affection of macho papaya. Some long-rod macho flowers appeared in macho copse aboriginal (Fig. 5c), which afterwards approved that it was a aftereffect of the abatement in androecium numbers (<10) (Fig. 5d). We calm growing inflorescences alone from four macho copse to investigate the development of androecium in 100 macho flowers, of which 8%, 12%, 18%, 22% were articular as macho flowers with no traces of filaments and anthers but abecedarian gynoecium (Fig. 5e).
a Macho inflorescences on the macho plants. b Changeable flowers on the changeable plants. c Macho inflorescences advised by NPA. Arrow adumbrated a long-rod phenotype flowers due to a abatement in androecium number. d A long-rod phenotype macho annual with alone one androecium. Arrow adumbrated the abecedarian gynoecium. Bar = 2 mm. e A long-rod phenotype macho annual with no trace of filaments and anthers. Arrow adumbrated the abecedarian gynoecium. Bar = 2 mm (f) Accustomed macho flower. Arrow adumbrated the abecedarian gynoecium. Bar = 2 mm. g Phenotypically agnate absolute hermaphrodite flowers with abundant gynoecium in macho plant. Gynoecium-like structures (gyn-like) bore collapsed and bland stigmas(left), bore bristling stigmas (mid), and absolutely anchored in alloyed alien whorls of floral system(right). All anew induced hermaphrodite flowers referred to accept arresting androecium(an). h,i The adapted primary macho flowers amidst with adjoining clusters of macho flowers. Arrow adumbrated the adapted primary macho flowers. j The inflorescences of Vasconcellea monica. k,l The NPA-treated changeable annual bore a stalk-like gynoecium with stigma. Arrow adumbrated the stalk-like gynoecium, Bar = 1 mm (m) Accustomed changeable flower. Arrow adumbrated the anatomic gynoecium, Bar = 1 mm
Some phenotypically agnate absolute hermaphrodite flowers with abundant gynoecium appeared, surrounding with adjoining clusters of accustomed macho annual with 10 anthers. In these animal adapted flowers, some gynoecium-like structures bore collapsed and bland stigmas, some bore bristling one, and some were absolutely anchored in alloyed alien whorls of floral system, but all anew induced hermaphrodite flowers referred to accept arresting androecium (Fig. 5g). For best cases, accretion admeasurement of stout abject of adolescent annual buds on NPA-treated macho bulb beggarly gynoecium-like structures had accompanying protruded out of the bowl (Fig. 5h, i).
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The arragement of anew appeared ually adapted flowers in NPA-treated macho papaya was agnate to that of Vasconcellea monica (the alone monoecious bread in Caricaceae) inflorescent with changeable flowers amidst with adjoining macho flowers (Fig. 5j).
The axis breadth of the NPA-treated plants was abundant beneath than that of ascendancy macho plants. All these present observations acutely appropriate that the baby cardinal of hermaphrodite-like flowers alpha actualization in macho plants afterwards NPA treatment.
However, changeable plants did not appearance cogent changes in 10 mg/L NPA treatment. Alone few flowers on changeable copse bore a stalk-like gynoecium (Fig. 5k). It ability appear because of alarmingly low akin of auxin absorption due to blockage of auxin agent proteins, aforementioned phenotype was empiric in Arabidopsis pin/pid mutants17. The phenotypic appearance of stalk-like gynoecium agency (Fig. 5l) acquired by NPA spraying in changeable was begin to be altered from abecedarian gynoecium in macho annual or hermaphroditic abetting flowers.
The adequate changeable abundance in NPA-induced papaya plants was concentration-dependent. The acceptable NPA absorption (10 mg/L) acquired the accumulation of hermaphrodite-like annual in macho copse while college NPA absorption of 30 and 50 mg/L resulted in added askew flowers in both macho and changeable plants, which showed aberrant adverse of gynoecium organs. It appropriate that astringent auxin carriage disruption would abate gynoecium morphogenesis. Therefore, a able auxin absorption is all-important for gynoecium morphogenesis.
After the abeyance of NPA treatment, the accustomed inflorescences gradually adequate in the aciculate shoot as expected. The induced foliage admixture was the adverse aftereffect of abiding NPA analysis (Supplementary Fig. 1).
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On the added hand, NAA and 2,4-D (synthetic auxin analogs) anon sprayed to macho and changeable individuals could not affect the bloom morphologies, although baby and acutely pinnate lobed leaves arose.
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