Plant Omics最新文献

{"title":"De novo transcriptome sequencing, assembly and characterization of Heliopsis longipes roots vs. leaves to discover putative genes involved in specialized metabolites biosynthesis","authors":"G. V. Buitimea-Cantúa, J. Molina-Torres","doi":"10.21475/poj.14.01.21.p3067","DOIUrl":"https://doi.org/10.21475/poj.14.01.21.p3067","url":null,"abstract":"Heliopsis longipes is a valuable source of specialized metabolites (or secondary metabolites) with medicinal properties mainly in roots. However, little is known about genes involved in the biosynthesis of these metabolites, primarily due to the lack of genome or transcriptome resources. In this work, the genes of the biosynthetic pathway of the specialized metabolism from H. longipes roots and leaves through de novo RNA sequencing (RNA-Seq) using the platform of Illumina paired-end sequencing were studied. After de novo transcriptome assembly using the software Newbler, a total of 172,342 non-redundant transcripts with an N50 value of 816 bp was obtained. Further functional classification and annotation with Gene Ontology (GO), BLAST2GO, Kyoto Encyclopedia of Genes and Genome (KEGG), and KEGG automatic annotation server (KAAS), revealed that active genes in tissues are predominately involved in the metabolic process and biosynthesis of specialized metabolite pathways. Differential expression analysis of roots vs. leaves using Cuffdiff software (p-value ≤0.05 and log-fold change ratio (log2) ≥1) revealed that differentially expressed genes (DEGs) were in an organ-specific manner, such as in leaf, DEGs were significantly enriched in photosynthesis, while in roots, were a higher enriched function of plant hormone signal transduction. A total of 63 transcripts DEGs were related to 9 specialized metabolites pathways, in roots the most abundant was the phenylpropanoid biosynthesis, and in leaves was the carotenoids biosynthesis. Several regulatory genes including the basic-helix-loop-helix and basic leucine zipper domain, transcriptions factor families involved in the regulation of phenylpropanoids and carotenoid biosynthesis, respectively, were discovered. This study established a global transcriptome dataset for H. longipes. Data shall be useful to study the functional genomics or genetic engineering of this specie. These results will promote the understanding of the genetic mechanism involved in the biosynthesis of specialized metabolites in H. longipes","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46467379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pre-emergence herbicidal activity and persistence of 2,4-di-tertbutylphenol in relation to soil types","authors":"N. Zain, Mazira Che Mat, C. Seng","doi":"10.21475/poj.14.01.21.p3265","DOIUrl":"https://doi.org/10.21475/poj.14.01.21.p3265","url":null,"abstract":"Although 2,4-di-tert-butylphenol (2,4-DTBP) has demonstrated strong phytotoxic effect on various weedy plants in previous findings, research on its pre-emergence herbicidal activity in the soil is still scanty. The aim of this study was to investigate the effects of two soil types on pre-emergence herbicidal activity and persistence of 2,4-DTBP. The bioassay was carried out in a growth chamber where goosegrass [Eleusine indica (L.) Gaertn.] seeds were sown in different rates of 2,4-DTBP in two soil series under sterilized and non-sterilized soil conditions. Bioassays of each treatment were conducted in four replicates and arranged in completely randomized design. 2,4-DTBP exhibited potent pre-emergence activity as a root inhibitor where it completely inhibited (100% inhibition) of the root growth of E. indica in sandy loam soil at an application rate of 6.14 kg ai/ha. 2,4-DTBP was rapidly detoxified in silt loam soil as a result of high microbial activity where it completely lost its phytotoxicity by giving 100% emergence within 10 weeks even it was applied at an application as high as 20.4 kg ai/ha. However, 2,4-DTBP remained highly phytotoxic in sandy loam soil where it reduced the root and shoot growth by 47 and 36%, respectively, throughout 10 weeks duration of the investigation. The presence of microbes in non-sterilized soil further suggest that soil microbes may modify the chemical structure of the 2,4-DTBP, which in turn decreased its toxicity. The high level of pre-emergence herbicidal activity in conjunction with its biodegradation in silt loam soil imply that 2,4-DTBP may have potential for development as a natural-soil applied herbicide","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Root proteome alterations in sugarcane promoted by the regrowth cycle in commercial production","authors":"R. C. Maranho, M. M. Benez, G. B. Maranho, E. Pilau, C. A. Mangolin, M. F. Machado","doi":"10.21475/poj.14.01.21.p3286","DOIUrl":"https://doi.org/10.21475/poj.14.01.21.p3286","url":null,"abstract":"The decrease in agricultural productivity in successive cutting of sugarcane plants is associated with several extrinsic and intrinsic factors. However, no studies have focused on the physiological potential of sett roots in successive cuts in sugarcane culture. There have been no proteomic studies on sugarcane sett roots at different stages of cutting. In this study, the UPLC-ESI-TOF-MS system and bioinformatics tools were used to identify proteins of sett roots in the first and fifth cuts of sugarcane cultivar RB966928 in the sprouting stage. Differences in the proteome of sett roots of RB966928 in the first and fifth cuts detected in this study supports the hypothesis that the proteome of sett roots may change after successive cuts in sugarcane culture. A reduction in the number of proteins was observed in the roots of the fifth cut, whereas 34% of proteins, identified exclusively in the first cut, were absent in the fifth cut. Proteome analysis of sett roots in the first and fifth cuts showed that the changes after successive cuts were quantitative (number of proteins) and mainly qualitative. In this study, the detailed list of proteins identified in the first cut but absent in the fifth cut is relevant. The findings of this study may aid further research that employ biotic or abiotic elicitors to induce gene expression of essential proteins absent in sett roots of the fifth cut, and thus increasing the agricultural productivity and longevity of cane fields","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48103080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quality of soybean seeds submitted to different treatments and storage conditions","authors":"F. L. Silva, Letícia Barão Medeiros, Fabiano Carlos Ferreira, G. Meneghello, F. A. Villela, T. Z. Aumonde, T. Pedó","doi":"10.21475/poj.14.01.21.p3247","DOIUrl":"https://doi.org/10.21475/poj.14.01.21.p3247","url":null,"abstract":"Chemical seed treatment is a recommended technique to protect seeds from pathogens that can affect their quality. The objective of this work was to analyse the quality of soybean seeds with different treatments under different storage temperatures. Seeds of cultivar ‘M 8378 IPRO’ produced in Mato Grosso, Brazil were used. A completely randomised design was used in a 4 × 3 two-factorial scheme. The seeds were treated with three different combinations of chemicals (fungicides, insecticides, polymer and drying powder) in addition to the control (untreated seeds) combined with three different storage temperatures (13 °C, 19 °C and uncontrolled temperature), with three repetitions. Quality was assessed by the germination test (TG), accelerated aging (AA), field emergence (FE), tetrazolium test (TZ) and isoenzyme analysis. The uncontrolled storage temperature negatively influenced the variables germination, accelerated aging and field emergence. The vigour and viability of the tetrazolium test showed that untreated seeds had better physiological quality than seeds with chemical treatment. The expression of isoenzymes showed a difference between treatments. Even with the stress caused by the seed treatment, this tool is very important for the initial protection of the seedlings.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44092761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MtNOOT gene enhanced high productivity and economical characteristics of tomato (Lycopersicon esculentum)","authors":"G. A. A. El-Heba","doi":"10.21475/poj.14.01.21.p3141","DOIUrl":"https://doi.org/10.21475/poj.14.01.21.p3141","url":null,"abstract":"Tomato (Lycopersicon esculentum) is the main vegetal crop that has tremendous popularity around the world. Medicago truncatula NOOT gene (Mt-NOOT) encodes a BTB/POZ-ankyrin repeat protein of the NONEXPRESSOR OF PR GENES1 (NPR1 family). It was introduced into Lycopersicon esculentum (Tomato) genome. The tomato plants that ectopically expressed Mt-NOOT obtained several favorable traits and fruit quality. Heteroblasty between the transgenic and the non-transgenic tomato leaves and flower architecture were used to distinguish transgenic and wild lines. Transgenic tomato plants accumulated a significant amount of phenolic compounds and plant pigmentations compared to the wild type. On the other hand, transgenic plants acquired a considerable amount of antioxidant such as CuZnSO superoxide dismutase (SOD), tomato Catalase (CAT), and tomato Cell wall-associated peroxidase (TPX1) than the wild type. Antioxidant high content together with the high content of phenolic compounds enabled the transgenic tomato fruits to gain not only edible benefits, but also a significant higher shelf-time, extended to six months more than the wild type stored at 25°C in dark and dry condition. Surprisingly, transgenic tomato fruits did not show any rotten process during long time storage as they did not acquire any contagious microorganism. Total fruit productivity in transgenic tomato was greater than the control with an estimated ratio of 84%.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47784898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Karyotype and genome size determination of Jarilla chocola, an additional sister clade of Carica papaya","authors":"Dessireé Zerpa‑Catanho, T. Jatt, R. Ming","doi":"10.21475/poj.14.01.21.p2944","DOIUrl":"https://doi.org/10.21475/poj.14.01.21.p2944","url":null,"abstract":"Jarilla chocola is an herbaceous plant species that belongs to the Jarilla genus and the Caricaceae family. No information on chromosome number or genome size has been reported for J. chocola that confirms the occurrence of dysploidy events and explore the existence of heteromorphic sex chromosomes. Therefore, the total number of chromosomes of this species was determined by karyotyping and counting the number of chromosomes observed, and the genome size of female and male plants was estimated separately by flow cytometry. Results showed that J. chocola has eight pairs of chromosomes (2n = 2x = 16), and its chromosomes are classified as metacentric for five pairs, submetacentric for two pairs and telocentric for one pair. The nuclear DNA content (1C-value) in picograms and diploid genome size was estimated separately from female and male plants using two species as the standards, Phaseolus vulgaris (1C = 0.60 pg) and Carica papaya (1C = 0.325 pg), to look for the possible existence of heteromorphic sex chromosomes. C. papaya proved to be a better standard for the determination of J. chocola DNA content and diploid genome size. No significant difference on the DNA content was observed between female (1C = 1.02 ± 0.003 pg) and male (1C = 1.02 ± 0.008 pg) plants. The estimated genome size of J. chocola per haploid genome in base pairs was calculated from the obtained C-values. Results showed an estimated genome size per haploid genome of 1018.44 ± 3.07 Mb and 1022.08 ± 7.76 Mb for female and male plants, respectively. Due to the observed chromosome number and genome size, only the occurrence of one of two previously reported dysploidy events in Jarilla could be confirmed for J. chocola and no evidence of heteromorphic sex chromosomes was found. These results provide fundamental information of the J. chocola genome and will expedite investigation of sex chromosomes and genome evolution in this species, the Jarilla genus and the Caricaceae family","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658623","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimates of heterosis and combining ability of soybean diallel crossings","authors":"José Ricardo Bagateli, Carlos André Bahry, R. N. D. Silva, I. Carvalho, G. G. Conte, F. A. Villela, G. I. Gadotti, G. Meneghello","doi":"10.21475/poj.13.01.20.p2038","DOIUrl":"https://doi.org/10.21475/poj.13.01.20.p2038","url":null,"abstract":"This study aimed to estimate the general and specific combining ability of partial soybean diallel crossings. The parents were divided in two groups contrasting for the characteristics of mass of thousand seeds, maturity group, flowers’ color, lodging and growth aspect. The scheme of partial diallel followed the Griffing model, where it were included the parents and the F1 generation. There was predominance of additive genic effects for the characteristics number of seeds per pods, number of seeds per plant and plants height. For number of pods per plant, seeds per plant and mass of hundred seeds the dominance effects were expressed by the superiority of specific combining ability in the determination of these characters. The parents G3 and G7 were the ones that contributed the most to the increase in yield in function of general combining ability for the characters number of pods per plant, seeds per plant, plant yield and mass of hundred seeds. The hybrids from the crossings between G3 x G5 and G3 x G4 are more promising for the characteristics related to yield, since they present elevated heterosis effect and high specific combining ability associated to increase general combining ability presented by the parent G3.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"1 1","pages":"7-14"},"PeriodicalIF":0.0,"publicationDate":"2020-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44385080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Micropropagtion and DNA-barcoding of the endangered endemic Phlomis aurea plant of Saint Katherine","authors":"H. Ghareb, S. Ibrahim, G. Hegazi","doi":"10.21475/poj.13.01.20.p2398","DOIUrl":"https://doi.org/10.21475/poj.13.01.20.p2398","url":null,"abstract":"Saint Katherine is considered a “biodiversity hotspot” because of the high level of endemism of reported plant species. In this study, conservation of the endangered endemic plant; Phlomis aurea of Saint Katherine, Southern Sinai, Egypt, was carried out through micropropagation and DNA barcoding. The first efficient micropropagation protocol for Phlomis aurea was established as a mean of ex situ conservation of the plant. Shoot tips and nodal segments of in vitro germinated seedlings were established on Murashige and Skoog medium supplemented with 0.54 μM β-naphthalene acetic acid (NAA) and 2.46 μM N6-(2-isopentenyl) adenine (2iP) in combination with 6-benzylaminopurine (BA) or kinetin (Kin). The medium supplemented with 3.48 μM Kin considered optimum for both explants. For multiplication, BA was the most efficient cytokinin. The percentage of rooted explants reached 100% at the concentration of 14.7 μM indolebutyric acid (IBA), whereas the highest number of roots was recorded for 4.90 μM, which considered the optimum concentration with a percentage of 80% of rooting. Rooted plantlets were transplanted in the greenhouse with 75% survival rate. The present study also aimed to carry out DNA barcoding of Phlomis aurea for accurate identification to provide a database for establishing an efficient conservation program for the plant. Three chloroplast DNA markers were used [ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL), maturase K (matK) and RNA polymerase C1 (rpoC1)] and all were successful in amplifying target regions, however the performance of both rbcL and matK markers seemed to be species‐specific. The similarity percentage was maximum for rbcL (99.81%) and matK (100%) compared to the database of the same species.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"1 1","pages":"65-77"},"PeriodicalIF":0.0,"publicationDate":"2020-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41333242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of the LUminometric Methylatoion Assay for plant ecological researches: the study of global DNA methylation in leaves of Elodea canadensis under laboratory conditions and in leaves of fen orchid from wild populations","authors":"N. Škute, Marina Savicka, A. Petjukevics, N. Harlamova","doi":"10.21475/poj.13.01.20.p2111","DOIUrl":"https://doi.org/10.21475/poj.13.01.20.p2111","url":null,"abstract":"The epigenetic changes in the genome of plants are one of the important regulatory mechanisms in response to the environmental factors. The LUminometric Methylation Assay (LUMA) requires a relatively small DNA amount, a short processing time and is easily adapted for species with a non-resolved genome. The LUMA has not been previously used for ecological research of plants. In this research, LUMA was used for the first time to investigate the changes of global DNA methylation under different environmental factors in the leaves of different plants. The influence of salinity on global DNA methylation was studied on aquatic macrophyte Elodea canadensis Michx, which grew in aquatic tanks under different NaCl concentrations. After the third week of growth, the HpaII/MspI ratio was measured by LUMA and global DNA methylation percentages were calculated. The results showed salt stressinduced changes in the global DNA methylation level in E.canadensis leaves, compared to control. The response was salt dosedependent. The changes of global DNA methylation in wildlife plant populations were analogically assessed on fen orchid Liparis loeselii (L.) Rich. It was shown that global DNA methylation level was higher in leaves of these plants in Engure Lake, where there are temporary changes in water regime, compared to leaves of plants from other places. It was assumed that global GC-DNA methylation plays an essential role in the survival of this plant. Therefore, we show the possibilities of using the LUMA method for epigenetic study of different plants ecological researches.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"1 1","pages":"30-36"},"PeriodicalIF":0.0,"publicationDate":"2020-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43489293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome analysis of oil palm (Elaeis guineensis Jacq.) roots under waterlogging stress","authors":"S. Nuanlaong, S. Wuthisuthimethavee, M. Mekanawakul, P. Suraninpong","doi":"10.21475/poj.13.01.20.p2327","DOIUrl":"https://doi.org/10.21475/poj.13.01.20.p2327","url":null,"abstract":"Waterlogging seriously constrains growth and yields in oil palm. To date, the responsive molecular changes caused by waterlogging in oil palm remain elusive. To elucidate the molecular genetic mechanisms of waterlogging stress, two varieties of oil palm Deli x Lamé and Deli x Ghana were used. The transcriptome profiles of the roots under waterlogging stress and normal conditions were compared via Ion Torrent Sequencing. Four libraries (GNR, GSR, SNR, and SSR) of oil palm roots after 45 days of normal watering and waterlogging stress were constructed. Approximately 6.2 million sequenced reads per library were obtained, with 5.5 million mapped reads (88.64%) similar to the oil palm genome in the GenBank database. A comparison of GNR/GSR showed a high of 3,289 DEGs with most genes up-regulated (1,863 DEGs). The GO analysis revealed the distribution of the DEGs among various pathways, suggesting a wide spectrum of physiological processes impacted by waterlogging stress. Moreover, qRT-PCR showed strong expression of all selected RNA-seq genes in waterlogged Deli x Ghana (GSR), especially GST, SAPK10 and NAC29 that are reported for the time to respond to waterlogging stress. Thus, this study not only reveals the comprehensive mechanisms of waterlogging responsive transcription in oil palm, but also establishes Deli x Ghana as a highly-adaptable variety to waterlogging conditions.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"1 1","pages":"46-56"},"PeriodicalIF":0.0,"publicationDate":"2020-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46792724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}