Transcriptome Analysis of ‘Haegeum’ Gold Kiwifruit Following Ethylene Treatment to Improve Postharvest Ripening Quality

Fruit ripening involves changes in physical, physiological and metabolic activities through the actions of enzymes and regulatory genes. This study was initiated to identify the genes related to the ripening of kiwifruit. Gold ‘Haegeum’ kiwifruit is a yellow-fleshed kiwifruit cultivar usually used for fresh marketing. The fruit is harvested at a physiologically mature but unripe stage for proper storage, marketing distribution and longer shelf life. To identify the differentially expressed genes (DEGs) during ripening, fruit treated with ethylene were compared with control fruit that ripened naturally without ethylene treatment. Firmness, respiration rate, ethylene production rate, total soluble solids (TSS), titratable acidity (TA), brix acid ratio (BAR) and overall acceptability were taken during the study as fruit ripening indicators. Total mRNAs were sequenced by Illumina high-throughput sequencing platform and the transcriptome gene set was constructed by de novo assembly. We identified 99,601 unigenes with an average length of 511.77 bp in transcriptome contigs. A total of 28,582 differentially expressed unigenes were identified in the ethylene treatment vs. control. Of these 28,582 unigenes, 13,361 and 15,221 genes were up- and downregulated, respectively, in the treated fruit. The results also showed that 1682 and 855 genes were up- and downregulated, respectively, more than 2-fold at p < 0.05 in fruit treated with ethylene as compared with the control fruit. Moreover, we identified 75 genes showing significantly different expression; 42 were upregulated, and 33 were downregulated. A possible category of the identified ripening-related genes was also made. The findings of this study will add to the available information on the effect of ethylene treatment on ripening and the related changes of kiwifruit at the genomic level, and it could assist the further study of genes related to ripening for kiwifruit breeding and improvement.

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1-Methylcyclopropene delays tomato fruit ripening

Horticultura Brasileira ◽

10.1590/s0102-05362002000400030 ◽

2002 ◽

Vol 20 (4) ◽

pp. 659-663 ◽

Cited By ~ 12

Author(s):

Celso Luiz Moretti ◽

Alessandra L. Araújo ◽

Waldir Aparecido Marouelli ◽

Washington Luiz C. Silva

Keyword(s):

Fruit Ripening ◽

Skin Color ◽

Tomato Fruit ◽

Storage Period ◽

Titratable Acidity ◽

Soluble Solids ◽

Ambient Conditions ◽

Total Carotenoids ◽

Cold Room ◽

Tomato Fruit Ripening

Tomato (Lycopersicon esculentum Mill.) fruits, cv. Santa Clara, were harvested at the breaker stage from commercial fields in Brazlândia, Brazil, to investigate the ability of 1-methylcyclopropene (1-MCP) to retard tomato fruit ripening. Fruit without external blemishes were graded for size (diameter = 80±5 mm) and mass (m = 130±10 g), placed inside hermetically sealed boxes, and 1-MCP was applied for 12 hours (T = 22±1°C; RH = 80-85%) at four different concentrations: 0 (control), 250, 500 and 1000 mL.L-1. Fruits were held at ambient conditions (T = 23±2°C; RH 80-85%) for 2 days and then stored inside a cold room (T = 20±1°C; RH = 85-95%). Every 3 days, during a 15-day period, fruits were analyzed for firmness, total soluble solids, titratable acidity, external color, and total carotenoids. Firmness of fruit treated with 1000 mL.L-1 was about 88% higher than control fruits after 17 days. The a*/b* ratio, an indicator of skin color, for fruit treated with 1000 mL.L-1 of 1-MCP was 38% lower than control fruits at the end of the storage period. Treatments with higher concentrations of 1-MCP delayed total carotenoids synthesis and color development. Control fruits stored for 17 days had about 190% more total carotenoids than fruits treated with 1000 mL.L-1 of 1-MCP. Postharvest application of 1-MCP was an efficient method to delay tomato fruit ripening. As 1-MCP concentration increased, ripening was further delayed. Tomatoes treated with 250, 500, and 1000 mL.L-1 of 1-MCP were delayed by 8 to 11, 11 to 13 and 15 to 17 days, respectively.

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Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

Journal of Insect Science ◽

10.1093/jisesa/iew053 ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 7

Author(s):

Juan Ma ◽

Rongyan Wang ◽

Xiuhua Li ◽

Bo Gao ◽

Shulong Chen

Keyword(s):

Sweet Potato ◽

Molecular Mechanisms ◽

Developmental Stages ◽

De Novo ◽

Average Length ◽

Expression Profiles ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Cylas Formicarius ◽

Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

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De novo assembly of expressed transcripts and analysis of pistil to identify genes involved in early stage of pollination in Liriodendron chinense

10.7287/peerj.preprints.2803 ◽

2017 ◽

Author(s):

Ming Li ◽

Kun Wang ◽

Rebecca Njeri Damaris ◽

Pingfang Yang

Keyword(s):

Pollen Tube ◽

Sexual Reproduction ◽

Differentially Expressed Genes ◽

De Novo ◽

Early Stage ◽

Average Length ◽

Differentially Expressed ◽

Seed Setting ◽

Sequencing Data ◽

Liriodendron Chinense

Plant sexual reproduction is a complicated and a key biological process with profuse interactions between pollen and pistil. This process determines whether fertilization will be successful or not and thus affect the seed setting. To explore the reason why L. chinense has a low seed setting ratio, transcriptome analysis on pistils of L. chinense during pollination were conducted. After analyzing the sequencing data, 206,858 unigenes with an average length of 646 bp were generated using the assembled transcripts. Among total unigenes, 3844 genes which expression fold change during early stage of pollination was higher or lower than 10 were selected as significant differentially expressed genes. 54 differentially expressed genes involved in sexual reproduction processes including the regulation of pollen tube growth process and double fertilization process might be partially causing the low seed setting in L. chinense. These results indicated that the barrier between pollen tube and pistil might be the reason why L. chinense have low seed setting. This study might be helpful to understand why L. chinense has such a low seed setting ratio.

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Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes

Marine Drugs ◽

10.3390/md17080466 ◽

2019 ◽

Vol 17 (8) ◽

pp. 466 ◽

Cited By ~ 2

Author(s):

Ronghua Li ◽

Michaël Bekaert ◽

Luning Wu ◽

Changkao Mu ◽

Weiwei Song ◽

...

Keyword(s):

High Throughput Sequencing ◽

De Novo ◽

Average Length ◽

Bioactive Molecules ◽

Asian Countries ◽

Marine Gastropod ◽

Sequencing Technologies ◽

First Time ◽

Aquaculture Development ◽

Simple Sequence

The marine gastropod Hemifusus tuba is served as a luxury food in Asian countries and used in traditional Chinese medicine to treat lumbago and deafness. The lack of genomic data on H. tuba is a barrier to aquaculture development and functional characteristics of potential bioactive molecules are poorly understood. In the present study, we used high-throughput sequencing technologies to generate the first transcriptomic database of H. tuba. A total of 41 unique conopeptides were retrieved from 44 unigenes, containing 6-cysteine frameworks belonging to four superfamilies. Duplication of mature regions and alternative splicing were also found in some of the conopeptides, and the de novo assembly identified a total of 76,306 transcripts with an average length of 824.6 nt, of which including 75,620 (99.1%) were annotated. In addition, simple sequence repeats (SSRs) detection identified 14,000 unigenes containing 20,735 SSRs, among which, 23 polymorphic SSRs were screened. Thirteen of these markers could be amplified in Hemifusus ternatanus and seven in Rapana venosa. This study provides reports of conopeptide genes in Buccinidae for the first time as well as genomic resources for further drug development, gene discovery and population resource studies of this species.

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Transcriptomic Analysis Identifies New Non-Target Site Glyphosate-Resistance Genes in Conyza bonariensis

Plants ◽

10.3390/plants8060157 ◽

2019 ◽

Vol 8 (6) ◽

pp. 157 ◽

Cited By ~ 7

Author(s):

Cristiano Piasecki ◽

Yongil Yang ◽

Daiane P. Benemann ◽

Frederico S. Kremer ◽

Vanessa Galli ◽

...

Keyword(s):

Molecular Mechanisms ◽

Target Genes ◽

De Novo ◽

Average Length ◽

Transcriptome Assembly ◽

Glyphosate Resistance ◽

Target Site ◽

Differentially Expressed ◽

Irreversible Damage ◽

Conyza Bonariensis

Conyza bonariensis (hairy fleabane) is one of the most problematic and widespread glyphosate-resistant weeds in the world. This highly competitive weed species significantly interferes with crop growth and substantially decreases crop yield. Despite its agricultural importance, the molecular mechanisms of glyphosate resistance are still unknown. The present RNA-Seq study was performed with the goal of identifying differentially expressed candidate transcripts (genes) related to metabolism-based non-target site glyphosate resistance in C. bonariensis. The whole-transcriptome was de novo assembled from glyphosate-resistant and -sensitive biotypes of C. bonariensis from Southern Brazil. The RNA was extracted from untreated and glyphosate-treated plants at several timepoints up to 288 h after treatment in both biotypes. The transcriptome assembly produced 90,124 contigs with an average length of 777 bp and N50 of 1118 bp. In response to glyphosate treatment, differential gene expression analysis was performed on glyphosate-resistant and -sensitive biotypes. A total of 9622 genes were differentially expressed as a response to glyphosate treatment in both biotypes, 4297 (44.6%) being up- and 5325 (55.4%) down-regulated. The resistant biotype presented 1770 up- and 2333 down-regulated genes while the sensitive biotype had 2335 and 2800 up- and down-regulated genes, respectively. Among them, 974 up- and 1290 down-regulated genes were co-expressed in both biotypes. In the present work, we identified 41 new candidate target genes from five families related to herbicide transport and metabolism: 19 ABC transporters, 10 CYP450s, one glutathione S-transferase (GST), five glycosyltransferases (GT), and six genes related to antioxidant enzyme catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). The candidate genes may participate in metabolic-based glyphosate resistance via oxidation, conjugation, transport, and degradation, plus antioxidation. One or more of these genes might ‘rescue’ resistant plants from irreversible damage after glyphosate treatment. The 41 target genes we report in the present study may inform further functional genomics studies, including gene editing approaches to elucidate glyphosate-resistance mechanisms in C. bonariensis.

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CHARACTERIZATION OF RIPENING STAGES OF MYRTLE FRUIT

Revista Brasileira de Fruticultura ◽

10.1590/0100-29452016712 ◽

2016 ◽

Vol 38 (2) ◽

Cited By ~ 1

Author(s):

DYALLA RIBEIRO DE ARAUJO ◽

ELISEU MARLÔNIO PEREIRA DE LUCENA ◽

JOSIVANDA PALMEIRA GOMES ◽

ROSSANA MARIA FEITOSA DE FIGUEIRÊDO ◽

CLARISSE PONTES DA SILVA

Keyword(s):

Fruit Ripening ◽

Developmental Stages ◽

Titratable Acidity ◽

Fruit Production ◽

Soluble Solids ◽

Human Consumption ◽

Ripening Stage ◽

Production Chain ◽

Fruit Species ◽

Ripening Stages

ABSTRACT The myrtle (Eugenia gracillima Kiaersk.) is a native fruit species in the Chapada of Araripe, state of Pernambuco, Brazil. The fruits are collected from the wild and are consumed fresh or processed as pulp, juice, jelly, liquor or desserts. Myrtle fruit production is of significant socioeconomic value for the region and, therefore, the description of myrtle fruit ripening stages may contribute to the development of its production chain. As a result, the objective of the present study was to evaluate the physical, quality and ripening changes of myrtle fruits at different developmental stages. The fruits were picked at five distinctive stages and evaluated for longitudinal and transverse diameters; fresh, dry and water mass; water contents; soluble solids (SS); titratable acidity (TA); pH; SS/TA ratio; carbohydrates (starch, total, reducing and nonreducing sugars); ascorbic acid; total pectin, soluble pectins and percentage of pectin solubilization; polymeric, oligomeric and dimeric phenolics; total anthocyanins, carotenoids and chlorophyll; and yellow flavonoids. Along fruit ripening processes increases in SS, anthocyanins and carotenoids, in the SS/TA ratio and of percentages of pectin solubilization were determined. On the other hand, decreases in TA and total chlorophyll were observed. The ripening stage at which peel color is completely dark red (ripening stage 4) is most appropriate to harvest myrtle fruits for human consumption.

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Ripening Behavior and Quality of `Brazilian' Bananas following Hot Water Immersion to Disinfest Surface Insects

HortScience ◽

10.21273/hortsci.39.6.1349 ◽

2004 ◽

Vol 39 (6) ◽

pp. 1349-1353 ◽

Cited By ~ 6

Author(s):

Marisa M. Wall

Keyword(s):

Exposure Time ◽

Water Immersion ◽

Titratable Acidity ◽

Hot Water ◽

Soluble Solids ◽

Banana Fruit ◽

Control Fruit ◽

Solids Content ◽

Water Treatments ◽

Hot Water Immersion

The fruit quality and ripening response of `Brazilian' bananas (Musa sp., group AAB) were determined following hot water immersion treatments for surface disinfestation. Summer-harvested fruit were exposed to 47, 49, or 51 °C water for 10, 15 and 20 minutes and ripened at 20 °C. The summer experiment established the exposure time and temperature limits for fruit injury. Winter-harvested fruit were immersed in 48, 49, or 50 °C water for 5, 10 and 15 minutes, stored for 12 d at 14 °C, and ripened at 22 °C. The hot water exposure time had a greater effect than the water temperature on banana fruit ripening. Nontreated bananas ripened after 13 to 15 d, and ripening was delayed by 2 to 7 d when fruit were exposed for 15 or 20 minutes to hot water. Hot water treatments did not inhibit pulp softening, but peels tended to be firmer for bananas immersed in 49 to 51 °C water than control fruit. Heat-treated bananas were not different from control fruit in soluble solids content or titratable acidity, however the conversion of starch to sugars was reduced at higher temperatures and exposure times. Bananas exposed for 20 minutes to hot water had delayed respiratory peaks and ethylene production, especially at 51 °C. Mild peel injury was observed on fruit exposed to higher temperatures (49 to 51 °C) for longer durations (15 or 20 minutes).

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Peach Latent Mosaic Viroid Reduces Tree Growth and Affects Fruit Quality in Peach

HortScience ◽

10.21273/hortsci.39.4.850c ◽

2004 ◽

Vol 39 (4) ◽

pp. 850C-850

Author(s):

Gregory Reighard* ◽

David Ouellette ◽

Kathy Brock ◽

Duy Nguyen

Keyword(s):

Skin Color ◽

Blot Hybridization ◽

Fruit Size ◽

Titratable Acidity ◽

Fruit Weight ◽

Soluble Solids ◽

Dot Blot ◽

Cross Sectional ◽

Control Fruit ◽

Fruit Maturity

`Coronet' peach on Lovell rootstock was planted near Clemson, S.C., in Dec. 1995 in 4 rows (= reps) 6.1 meters apart with trees 2.2 meters apart in-row. Trees were trained to a Kearney-V. In the 2nd leaf (Aug. 1997), `Ta Tao 5' buds were grafted to half (= 6-tree plot) the trees in each row. These trees received 2 `Ta Tao 5' chip buds infected with Peach Latent Mosaic Viroid (PLMVd) per scaffold at ≈0.75 to 1.15 m above ground. Dot blot hybridization confirmed that the chip buds successfully (100%) inoculated the treated trees, whereas the controls tested negative. Data collected in 2003 included bloom date, tree size, dormant and summer pruning times, fruit maturity date, fruit yield, mean fruit weight, skin color, soluble solids, flesh firmness, titratable acidity, and pH. Flowering and fruit maturity were delayed by ≈4 days in PLMVd-inoculated (PI) trees. PI trees produced larger fruit, but yield was 23% less than that of non-inoculated trees. Both fruit size and yield had been larger in PI trees in previous years. There were no differences in yield efficiency in 2003, but PI trees were 26% smaller in trunk cross-sectional area and 9% shorter. PI trees took 34% and 23% less time to dormant and summer prune, respectively and had 34% and 28% less wood removed by dormant and summer pruning, respectively than control trees. PLMVd increased fruit firmness, and PLMVd fruit lost firmness at a much slower rate. PLMVd did not significantly affect skin color, but PLMVD fruit were slightly less red. Soluble solid levels were higher in PLMVd fruit than control fruit during the first harvest, but were lower by the last harvest. Acidity was significantly higher and the soluble solids to acidity ratio significantly lower in PLMVd fruit. Control fruit had a slightly higher pH.

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De Novo Assembly and Transcriptome Profiling of Ethiopian Lowland Bamboo Oxytenanthera Abyssinica (A. rich) Munro Under Drought and Salt Stresses

The Open Biotechnology Journal ◽

10.2174/1874070701913010006 ◽

2019 ◽

Vol 13 (1) ◽

pp. 6-17

Author(s):

Muhamed Adem ◽

Dereje Beyene ◽

Tileye Feyissa ◽

Kai Zhao ◽

Tingbo Jiang

Keyword(s):

Differentially Expressed Genes ◽

De Novo ◽

Transcriptome Profiling ◽

Global Gene Expression ◽

Perennial Grasses ◽

Differentially Expressed ◽

Cdna Libraries ◽

Protein Families ◽

Sequencing Platform ◽

Genome Wide

Background: Bamboos are perennial grasses classified under family Poaceae and subfamily Bambusoideae and are among the fastest growing plants on earth. Despite ecological and economic significances, Ethiopian lowland bamboo (O. abyssinica) lacks global gene expression under abiotic stress. Methods: Plastic pot germinated seedlings of O. abyssinica were subjected to 200 µm NaCl and 25% PEG-6000 (Poly Ethylene glycol) to induce salt and drought stress, respectively. Using the Illumina sequencing platform, fifteen cDNA libraries were constructed and sequenced to generate the first drought and salt stress transcriptome profiling of the species so as to elucidate genome-wide transcriptome changes in response to such stresses. Results: Following quality control, 754,444,646 clean paired-ends reads were generated, and then de novo assembled into 406,181 unigenes. Functional annotation against the public databases presented annotation of 217,067 (53.4%) unigenes, where NCBI-Nr 203,777, Swissport 115,741, COG 81,632 and KEGG 80,587. Prediction of Transcripts Factors (TFs) have generated 4,332 TFs organized into 64 TF families. Analysis of Differentially Expressed Genes (DEGs) provided 65,471 genes where 569 genes belong to all stresses. Protein families with a higher number of differentially expressed genes include bZIP (49), WRKY (43), MYB (38), AP2/ERF (30), HD-ZIP (25) and MYB related (21). Conclusion: In addition to revealing the genome-wide level appraisal of transcriptome resources of the species, this study also uncovered the comprehensive understanding of key stress responsive protein-coding genes, protein families and pathways which could be used as the basis for further studies.

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Sepal Color Change Relates to Fruit Quality, Firmness, and Detachment Force in Erect and Semi-erect Thornless Blackberry Cultivars

HortScience ◽

10.21273/hortsci.33.3.538f ◽

1998 ◽

Vol 33 (3) ◽

pp. 538f-539

Author(s):

Herbert D. Stiles ◽

W. Malcolm Tilson

Keyword(s):

Fruit Quality ◽

Fruit Ripening ◽

Color Change ◽

Titratable Acidity ◽

Soluble Solids ◽

Quality Development ◽

Visual Cue ◽

Detachment Force ◽

Acid Ratio ◽

Thornless Blackberry

Black coloration occurs before the inception of horticultural maturity, so other cues (sheen, drupelet shapes, drupelet sizes, and fruit detachment force) have been employed as indicators of physiological and horticultural maturity among erect and semi-erect thornless blackberry cultivars. A more distinct visual cue might, however, allow reductions in the variability of quality, firmness, and shelflife among manually harvested berries. Such a maturity indicator would allow researchers to select more-uniform materials for genetic and physiologic studies of blackberry fruit ripening and quality development. Our 1996 and 1997 data confirm earlier observations of sepal color relationships to fruit quality attributes (soluble solids, pH, titratable acidity, and sugar/acid ratio) among semi-erect cultivars, and they show that such relationships exist among erect cultivars. These data also demonstrate relationships among sepal color, fruit detachment force, and berry firmness in both phenotypes.

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