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Digital Transcriptome Analysis of Putative Sex-Determination Genes in Papaya (Carica papaya)  [PDF]
Naoya Urasaki, Kazuhiko Tarora, Ayano Shudo, Hiroki Ueno, Moritoshi Tamaki, Norimichi Miyagi, Shinichi Adaniya, Hideo Matsumura
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0040904
Abstract: Papaya (Carica papaya) is a trioecious plant species that has male, female and hermaphrodite flowers on different plants. The primitive sex chromosomes genetically determine the sex of the papaya. Although draft sequences of the papaya genome are already available, the genes for sex determination have not been identified, likely due to the complicated structure of its sex-chromosome sequences. To identify the candidate genes for sex determination, we conducted a transcriptome analysis of flower samples from male, female and hermaphrodite plants using high-throughput SuperSAGE for digital gene expression analysis. Among the short sequence tags obtained from the transcripts, 312 unique tags were specifically mapped to the primitive sex chromosome (X or Yh) sequences. An annotation analysis revealed that retroelements are the most abundant sequences observed in the genes corresponding to these tags. The majority of tags on the sex chromosomes were located on the X chromosome, and only 30 tags were commonly mapped to both the X and Yh chromosome, implying a loss of many genes on the Yh chromosome. Nevertheless, candidate Yh chromosome-specific female determination genes, including a MADS-box gene, were identified. Information on these sex chromosome-specific expressed genes will help elucidating sex determination in the papaya.
Analysis of simple sequence repeats markers derived from Phytophthora sojae expressed sequence tags
Zhendong Zhu,Yunlong Huo,Xiaoming Wang,Junbin Huang,Xiaofei Wu
Chinese Science Bulletin , 2004, DOI: 10.1360/04wc0248
Abstract: Five thousand and eight hundred publicly available expressed sequence tags (ESTs) of Phytophthora sojae were electronically searched and 415 simple sequence repeats (SSRs) were identified in 369 ESTs. The average density of SSRs was one SSR per 8.9 kb of EST sequence screened. The most frequent repeats were trinucleotide repeats (50.1%) and the least frequent were tetranucleotide repeats (8.2%). Forty primer pairs were designed and tested on 5 strains of P. sojae. Thirty-three primer pairs had successful PCR amplifications. Of the 33 functional primer pairs, 28 primer pairs produced characteristic SSR bands of the expected size, and 15 primer pairs (45.5%) detected polymorphism among 5 tested strains of P. sojae. Based on the polymorphisms detected with 20 EST-SSR markers, the 5 tested strains of P. sojae were clustered into 3 groups. In this study, the SSR markers of P. sojae were developed for the first time. These markers could be useful for identification, genetic variation study, and molecular mapping of P. sojae and its relative species.
Characterization of simple sequence repeats (SSRs) from Phlebotomus papatasi (Diptera: Psychodidae) expressed sequence tags (ESTs)
Omar Hamarsheh, Ahmad Amro
Parasites & Vectors , 2011, DOI: 10.1186/1756-3305-4-189
Abstract: Simple sequence repeats (SSRs) were characterized in P. papatasi expressed sequence tags (ESTs) derived from a public database, National Center for Biotechnology Information (NCBI). A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AX)n repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation.The first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.The sand fly Phlebotomus (Phlebotomus) papatasi (Scopoli) is a natural vector of Leishmania major (Yakimov & Schokov), which is the causative agent of zoonotic cutaneous leishmaniasis in the Middle East and other countries [1,2]. Simple sequence repeats (SSRs) or microsatellites, are common components of eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions [3,4]. SSRs often harbour high levels of polymorphism, in terms of repeat number, and have been developed into one of the most common classes of genetic markers due to their high degree of ubiquity, co-dominance and variability in number among individuals. In recent years, microsatellites were extensively used to investigate genetic variability and the population structures of a wide range of organisms, including parasites and vectors of infectious diseases [5-13]. In the absence of genome sequences for sand flies,
Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines
Jon Slate, Matthew C Hale, Timothy R Birkhead
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-52
Abstract: A total of 48,862 ESTs were downloaded from GenBank and assembled into contigs, representing an estimated 17,404 unique sequences. The unique sequence set contained 638 simple sequence repeats (SSRs) or microsatellites of length ≥20 bp and purity ≥90% and 144 simple sequence repeats of length ≥30 bp. A chromosomal location for the majority of SSRs was predicted by BLASTing against assembly 2.1 of the chicken genome sequence. The relative exonic location (5' untranslated region, coding region or 3' untranslated region) was predicted for 218 of the SSRs, by BLAST search against the ENSEMBL chicken peptide database. Ten loci were examined for polymorphism in two zebra finch populations and two populations of a distantly related passerine, the house sparrow Passer domesticus. Linkage was confirmed for four loci that were predicted to reside on the passerine homologue of chicken chromosome 7.We show that SSRs are abundant within zebra finch ESTs, and that their genomic location can be predicted from sequence similarity with the assembled chicken genome sequence. We demonstrate that a useful proportion of zebra finch EST-SSRs are likely to be polymorphic, and that they can be used to build a linkage map. Finally, we show that many zebra finch EST-SSRs are likely to be useful in evolutionary genetic studies of other passerines.Passerines (perching birds) are one of the most-widely studied taxonomic groups in evolutionary and ecological research [1,2]. They are frequently studied in the wild because they are easy to observe, often breed in nest-boxes or natural cavities, and have short-generation times and large broods. Quantitative genetic studies of passerines have advanced our understanding of natural selection [3,4], sexual selection [5], the effects of inbreeding [6,7], speciation [8,9], the causes of evolutionary stasis [10,11], and the heritability of fitness traits [12,13]. For the latter two areas enormous progress has been made in recent years by quantitative gene
Induction of somatic embryogenesis in Papaya (Carica papaya)
Ravindra B. Malabadi,,S. Vijaya Kumar,Gangadhar S. Mulgund,K. Nataraja
Research in Biotechnology , 2011,
Abstract: This study highlights the induction of somatic embryogenesis using immaturezygotic embryos of Carica papaya commercial varieties viz. Coorg Honey dew, Washington,Honey dew, Pusa delicious, Pusa nanha, Taiwan 786, Taiwan 785, Sunrise, Solo, Co-1, C0-7,and Co-3 respectively. Somatic embryos formed in the presence of thidiazuron (TDZ) incombination with 2, 4-dichlorophenoxy acetic acid (2, 4-D), but never on explants culturedon control medium lacking plant growth regulators. Embryogenic callus could be inducedfrom immature zygotic embryos after 4-6 weeks of culture on full-strength Murashige andSkoog inorganic salts, which served as the basal medium supplemented with 4.52 μM 2, 4-Dand 2.27 μM TDZ (induction and maintenance medium). The ability to induce embryogenictissue varied for different papaya tested varieties, and there was a mixed genotypic responseon the induction of embryogenic cultures. The highest percentage of somatic embryogenesiswas noticed in a papaya variety Taiwan-786 (87.0±4.2a), followed by Taiwan- 785 (85.0±3.0a),and Coorg Honey dew (81.0±3.2a) respectively. This protocol is simple and reproducible,and could be useful for regenerating large number of plants as well as provide a targettissue for genetic transformation experiments.
Chemical Profile of Unripe Pulp of Carica papaya  [PDF]
O.I. Oloyede
Pakistan Journal of Nutrition , 2005,
Abstract: Unripe pulp of Carica papaya was screened to test for the presence of certain phytochemicals. Chemical composition of the pulp were determined. Phytochemical screening of mature unripe pulp of Carica papaya (dry weight) showed the presence of saponins and cardenolides while chemical analysis revealed the presence of potassium (223.0mg/100g) as well as sodium, calcium, iron, phosphorus, zinc, copper, magnesium and manganese in considerable quantities. Proximate analysis of the pulp showed that it contained starch (43.28%), sugars (15.15%), crude protein (13.63%), crude fat (1.29%), moisture (10.65%) and fibre (1.88%). All these results indicate that the pulp of mature unripe Carica papaya contains nutrients and mineral elements that may be useful in nutrition. The presence of some phytochemicals like saponins and cardenolides explained the astringent action of the plant encountered in the numerous therapeutic uses.
Evaluation of platelet augmentation activity of Carica papaya leaf aqueous extract in rats  [PDF]
Swati Patil,Supritha Shetty,Rama Bhide,Shridhar Narayanan
Journal of Pharmacognosy and Phytochemistry , 2013,
Abstract: Carica papaya leaves have been used traditionally to treat indigestion, as a vermifuge. Carica papayaleaves have also been shown to possess anti-tumor and immunomodulatory effects. The current study aims at determining the effect of Carica papaya leaves aqueous extract in increasing the platelet count in thrombocytopenic rat model. Aqueous extract of Carica papaya leaves at concentration of 400mg/kg and 800mg/kg were given to cyclophosphamide induced thrombocytopenic rats for a period of fifteen days. Blood was withdrawn at various time intervals to determine the platelet count. Also, the clotting time was determined on the 15th day of the study by capillary method. Carica papaya leaf extract was found to increase the platelet count and also to decrease the clotting time in rats. The study aims at determining the possible effects of papaya leaves in thrombocytopenia occurring in dengue fever.
Substratum use fertilizer with potassium in the production of papaya (carica papaya) changes.  [PDF]
José Soares de Lacerda,Walter Esfrain Pereira,Thiago Jardelino Dias,Diógenes de Souza Costa
Engenharia Ambiental : Pesquisa e Tecnologia , 2009,
Abstract: The variation exists in the recommendations of employed materials in the composition of the substrata for production of papaya seedlings and usually, the organic fertilization is associated with the mineral fertilization. In this context, the objective of this work was to evaluate the effect of different substrata composed associated with the potassium fertilization on the growth of Carica papaya seedlings in. The Experiment was lead in the Center of Agrarians Science of the Federal University of Paraíba (UFPB), Areia-PB. The experimental delineation was block-type to perhaps, with three repetitions. The experimental unit was constituted of four bags with capacity for 1 dm3 contends a plant for bag. The collected data had been submitted analyze it of variance and regression, appropriate for experiment with mixtures. It was verified that the increase of the concentration of manure caused greater growth of the crop, while that the sand had the contrary effect. The maximum values of crop growth parameters of papaya had been gotten with 25% of land, 45% of sand, 30% of manure, without addition of KCl.
Protective effect of dried fruits of Carica papaya on hepatotoxicity in rat  [cached]
Md. Zafor Sadeque, Zinnat Ara Begum
Bangladesh Journal of Pharmacology , 2010,
Abstract: Aqueous and ethanol extracts of Carica papaya has been evaluated for its hepatoprotective activity in rat. The aqueous and ethanol extracts of Carica papaya showed significant hepatoprotection against carbon tetrachloride induced hepatotoxicity. The protective activity was evaluated by using biochemical parameters such as serum bilirubin, serum alanine amino transferase (ALT), aspartate amino transferase (AST) and alkaline phosphatase. The histopathological changes of liver were compared with control.
Effect of Biopreservatives on Storage Life of Papaya (Carica papaya L.)  [cached]
Fatema H. Brishti,Jawadul Misir,Ayesha Sarker
International Journal of Food Studies , 2013,
Abstract: In this experiment the effect on post-harvest preservation of papaya (Carica papaya L.) fruit coated with either Aloe gel (AG; 100%) or papaya leaf extract with Aloe gel (PLEAG; 1:1) was studied. To evaluate the role of coating on ripening behavior and quality of papaya the uncoated and coated fruits were stored and ripened at room temperature (25 °C-29 °C) and 82-84% relative humidity. Physico-chemical properties were analyzed at 4 day intervals during the storage period. The incidence of disease attack was also visually observed. The overall results showed the superiority of AG and PLEAG coating in lengthening the shelf-life of papaya fruit compared to controls which showed significant decay from 6th day onward and complete decay within 12 days of storage. The AG and PLEAG coated fruits maintained their shelf life for 12 days and decayed at 16th day. The coated fruits also maintained their color, flavor and firmness up to 12 days of storage. An increase in ascorbic acid content (120.2 mg/100 g) was also found in coated fruits in contrast to the control (59 mg/100 g). Only 27% disease incidence was observed in AG and 13% in PLEAG coated fruits as compared to control (100%) during the storage period. The results of this study show that both AG and PLEAG coatings have excellent potential to be used on fresh produce to maintain quality and extend shelf-life.
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