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Mahalle RM, Bosamia TC, Chakravarty S, Srivastava K, Meena RS, Kadam US, Srivastava CP. De Novo Mining and Validating Novel Microsatellite Markers to Assess Genetic Diversity in Maruca vitrata (F.), a Legume Pod Borer. Genes (Basel) 2023; 14:1433. [PMID: 37510337 PMCID: PMC10379186 DOI: 10.3390/genes14071433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/09/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Maruca vitrata (Fabricius) is an invasive insect pest capable of causing enormous economic losses to a broad spectrum of leguminous crops. Microsatellites are valuable molecular markers for population genetic studies; however, an inadequate number of M. vitrata microsatellite loci are available to carry out population association studies. Thus, we utilized this insect's public domain databases for mining expressed sequence tags (EST)-derived microsatellite markers. In total, 234 microsatellite markers were identified from 10053 unigenes. We discovered that trinucleotide repeats were the most predominant microsatellite motifs (61.53%), followed by dinucleotide repeats (23.50%) and tetranucleotide repeats (14.95%). Based on the analysis, twenty-five markers were selected for validation in M. vitrata populations collected from various regions of India. The number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) ranged from 2 to 5; 0.00 to 0.80; and 0.10 to 0.69, respectively. The polymorphic loci showed polymorphism information content (PIC), ranging from 0.09 to 0.72. Based on the genetic distance matrix, the unrooted neighbor-joining dendrogram differentiated the selected populations into two discrete groups. The SSR markers developed and validated in this study will be helpful in population-level investigations of M. vitrata to understand the gene flow, demography, dispersal patterns, biotype differentiation, and host dynamics.
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Affiliation(s)
- Rashmi Manohar Mahalle
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
- Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Tejas C Bosamia
- Plant Omics Division, Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Snehel Chakravarty
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Kartikeya Srivastava
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Radhe S Meena
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Ulhas Sopanrao Kadam
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Division of Life Science and Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Chandra P Srivastava
- Department of Entomology and Agricultural Zoology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221005, India
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Shamloo-Dashtpagerdi R, Shahriari AG, Tahmasebi A, Vetukuri RR. Potential role of the regulatory miR1119- MYC2 module in wheat ( Triticum aestivum L.) drought tolerance. Front Plant Sci 2023; 14:1161245. [PMID: 37324698 PMCID: PMC10266357 DOI: 10.3389/fpls.2023.1161245] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/26/2023] [Indexed: 06/17/2023]
Abstract
MicroRNA (miRNA)-target gene modules are essential components of plants' abiotic stress signalling pathways Little is known about the drought-responsive miRNA-target modules in wheat, but systems biology approaches have enabled the prediction of these regulatory modules and systematic study of their roles in responses to abiotic stresses. Using such an approach, we sought miRNA-target module(s) that may be differentially expressed under drought and non-stressed conditions by mining Expressed Sequence Tag (EST) libraries of wheat roots and identified a strong candidate (miR1119-MYC2). We then assessed molecular and physiochemical differences between two wheat genotypes with contrasting drought tolerance in a controlled drought experiment and assessed possible relationships between their tolerance and evaluated traits. We found that the miR1119-MYC2 module significantly responds to drought stress in wheat roots. It is differentially expressed between the contrasting wheat genotypes and under drought versus non-stressed conditions. We also found significant associations between the module's expression profiles and ABA hormone content, water relations, photosynthetic activities, H2O2 levels, plasma membrane damage, and antioxidant enzyme activities in wheat. Collectively, our results suggest that a regulatory module consisting of miR1119 and MYC2 may play an important role in wheat's drought tolerance.
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Affiliation(s)
| | - Amir Ghaffar Shahriari
- Department of Agriculture and Natural Resources, Higher Education Center of Eghlid, Eghlid, Iran
| | - Aminallah Tahmasebi
- Department of Agriculture, Minab Higher Education Center, University of Hormozgan, Bandar Abbas, Iran
| | - Ramesh R. Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Brhane H, Haileselassie T, Tesfaye K, Hammenhag C, Ortiz R, Abreha KB, Geleta M. Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars. Front Plant Sci 2021; 12:735610. [PMID: 34630485 PMCID: PMC8495221 DOI: 10.3389/fpls.2021.735610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/26/2021] [Indexed: 06/02/2023]
Abstract
Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (F ST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.
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Affiliation(s)
- Haftom Brhane
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Science and Technology, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kibrom B. Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Song Z, Li X. Recent Advances in Molecular Marker-Assisted Breeding for Quality Improvement of Traditional Chinese Medicine. Curr Pharm Biotechnol 2021; 22:867-875. [PMID: 32351179 DOI: 10.2174/1389201021666200430121013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The quality of Traditional Chinese Medicine (TCM), reflected by its bioactive compounds and associated contents, is directly linked to its clinical efficacy. Therefore, it is of great importance to improve the quality of TCM by increasing the bioactive compound content. METHODS Mapping the active component content-associated QTLs in TCM and further markerassisted breeding has enabled us to rapidly and effectively cultivate new varieties with high bioactive compound contents, which has opened the door for genetic breeding studies on medicinal plants. RESULTS In this paper, a strategy and technical molecular breeding method for TCM are discussed. The development of four methods and progress in functional marker development, as well as the applications of such markers in TCM, are reviewed. CONCLUSION The progress in, challenges of, and future of marker-assisted breeding for quality improvement of TCM are discussed, which provide valuable scientific references for future molecular breeding.
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Affiliation(s)
- Zhenqiao Song
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
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Sato M, Hasegawa Y, Mishima K, Takata K. Isolation and characterization of 22 EST-SSR markers for the genus Thujopsis (Cupressaceae). Appl Plant Sci 2015; 3:apps1400101. [PMID: 25699219 PMCID: PMC4332144 DOI: 10.3732/apps.1400101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/02/2014] [Indexed: 06/04/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed from Thujopsis dolabrata var. hondae (Cupressaceae) using Illumina sequencing to investigate the genetic diversity and population structure of the genus Thujopsis. • METHODS AND RESULTS Twenty-two primer pairs were developed from ESTs of T. dolabrata var. hondae. The primers amplified di- and trinucleotide repeat-containing sequences. Polymorphisms were assessed in 81 individuals from two T. dolabrata var. hondae populations and one T. dolabrata population. The number of alleles ranged from one to 17 per locus. The observed and expected heterozygosities ranged from 0.000 to 1.000 and from 0.000 to 0.926, respectively. • CONCLUSIONS These new EST-SSR markers will be useful in analyses of the genetic diversity and population structure of the genus Thujopsis.
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Affiliation(s)
- Miyako Sato
- Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876, Japan
| | - Yoichi Hasegawa
- Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876, Japan
| | - Kentaro Mishima
- Forestry and Forest Products Research Institute, Forest Tree Breeding Center, 3809-1 Ishi, Juo, Hitachi, Ibraraki 319-1301, Japan
| | - Katsuhiko Takata
- Institute of Wood Technology, Akita Prefectural University, 11-1 Kaieisaka, Noshiro, Akita 016-0876, Japan
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Ke T, Yu J, Dong C, Mao H, Hua W, Liu S. ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism. BMC Plant Biol 2015; 15:19. [PMID: 25604238 PMCID: PMC4312456 DOI: 10.1186/s12870-014-0399-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 12/22/2014] [Indexed: 05/29/2023]
Abstract
BACKGROUND Oil crop seeds are important sources of fatty acids (FAs) for human and animal nutrition. Despite their importance, there is a lack of an essential bioinformatics resource on gene transcription of oil crops from a comparative perspective. In this study, we developed ocsESTdb, the first database of expressed sequence tag (EST) information on seeds of four large-scale oil crops with an emphasis on global metabolic networks and oil accumulation metabolism that target the involved unigenes. DESCRIPTION A total of 248,522 ESTs and 106,835 unigenes were collected from the cDNA libraries of rapeseed (Brassica napus), soybean (Glycine max), sesame (Sesamum indicum) and peanut (Arachis hypogaea). These unigenes were annotated by a sequence similarity search against databases including TAIR, NR protein database, Gene Ontology, COG, Swiss-Prot, TrEMBL and Kyoto Encyclopedia of Genes and Genomes (KEGG). Five genome-scale metabolic networks that contain different numbers of metabolites and gene-enzyme reaction-association entries were analysed and constructed using Cytoscape and yEd programs. Details of unigene entries, deduced amino acid sequences and putative annotation are available from our database to browse, search and download. Intuitive and graphical representations of EST/unigene sequences, functional annotations, metabolic pathways and metabolic networks are also available. ocsESTdb will be updated regularly and can be freely accessed at http://ocri-genomics.org/ocsESTdb/ . CONCLUSION ocsESTdb may serve as a valuable and unique resource for comparative analysis of acyl lipid synthesis and metabolism in oilseed plants. It also may provide vital insights into improving oil content in seeds of oil crop species by transcriptional reconstruction of the metabolic network.
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Affiliation(s)
- Tao Ke
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
- Department of Life Science and Technology, Nanyang Normal University, Wolong Road, Nanyang, 473061, China.
| | - Jingyin Yu
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
| | - Caihua Dong
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
| | - Han Mao
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
| | - Wei Hua
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
| | - Shengyi Liu
- Key Laboratory for Oil Crops Biology, the Ministry of Agriculture, PR China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No.2 Xudong Second Road, Wuhan, 430062, China.
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Takahashi W, Miura Y, Sasaki T, Takamizo T. Identification of a novel major locus for gray leaf spot resistance in Italian ryegrass (Lolium multiflorum Lam.). BMC Plant Biol 2014; 14:303. [PMID: 25407403 PMCID: PMC4248433 DOI: 10.1186/s12870-014-0303-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/23/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Gray leaf spot (GLS), caused by Magnaporthe oryzae (anamorph Pyricularia oryzae), in ryegrasses is a very serious problem. Heavily infected small seedlings die within a matter of days, and stands of the grasses are seriously damaged by the disease. Thus, the development of GLS-resistant cultivars has become a concern in ryegrass breeding. RESULTS Phenotypic segregations in a single cross-derived F1 population of Italian ryegrass (Lolium multiflorum Lam.) indicated that the GLS resistance in the population was possibly controlled by one or two dominant genes with 66.5-77.9% of broad-sense heritability. In bulked segregant analyses, two simple sequence repeat (SSR) markers, which have so far been reported to locate on linkage group (LG) 3 of Italian ryegrass, showed specific signals in the resistant parent and resistant bulk, indicating that the resistance gene locus was possibly in the LG 3. We thus constructed a genetic linkage map of the LG 3 covering 133.6 centimorgan with other SSR markers of the LG 3 of Italian ryegrass and grass anchor probes that have previously been assigned to LG 3 of ryegrasses, and with rice expressed sequence tag (EST)-derived markers selected from a rice EST map of chromosome (Chr) 1 since LG 3 of ryegrasses are syntenic to rice Chr 1. Quantitative trait locus (QTL) analysis with the genetic linkage map and phenotypic data of the F1 population detected a major locus for GLS resistance. Proportions of phenotypic variance explained by the QTL at the highest logarithm of odds scores were 61.0-69.5%. CONCLUSIONS A resistance locus was confirmed as novel for GLS resistance, because its genetic position was different from other known loci for GLS resistance. Broad-sense heritability and the proportion of phenotypic variance explained by the QTL were similar, suggesting that most of the genetic factors for the resistance phenotype against GLS in the F1 population can be explained by a function of the single resistance locus. We designated the putative gene for the novel resistance locus as LmPi2. LmPi2 will be useful for future development of GLS-resistant cultivars in combination with other resistance genes.
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Affiliation(s)
- Wataru Takahashi
- />Forage Crop Research Division, NARO Institute of Livestock and Grassland Science, 768 Senbonmatsu, Nasushiobara, Tochigi 329-2793 Japan
| | - Yuichi Miura
- />Kyushu Experiment Station, Japan Grassland Agriculture and Forage Seed Association, 1740 Takaba, Koshi, Kumamoto 861-1114 Japan
- />Present address: Snow Brand Seed Co., Ltd, Hokkaido Research Station, 1066 Horonai, Naganuma-cho, Yubari-gun, Hokkaido 069-1464 Japan
| | - Tohru Sasaki
- />Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed Association, 388-5 Higashiakada, Nasushiobara, Tochigi 329-2742 Japan
- />Present address: Hokkaido Branch, Japan Grassland Agriculture and Forage Seed Association, 406 Higashi-Nopporo, Ebetsu, Hokkaido 069-0822 Japan
| | - Tadashi Takamizo
- />Forage Crop Research Division, NARO Institute of Livestock and Grassland Science, 768 Senbonmatsu, Nasushiobara, Tochigi 329-2793 Japan
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Sakaguchi S, Ito M. Development and characterization of EST-SSR markers for the Solidago virgaurea complex (Asteraceae) in the Japanese archipelago. Appl Plant Sci 2014; 2:apps1400035. [PMID: 25202641 PMCID: PMC4103478 DOI: 10.3732/apps.1400035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/27/2014] [Indexed: 05/29/2023]
Abstract
PREMISE OF THE STUDY We developed simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) for the Solidago virgaurea complex, an ecologically and morphologically diverse species complex in the Japanese archipelago, to elucidate population genetic structure and examine taxonomic boundaries. • METHODS AND RESULTS Utilizing the RNA sequencing data obtained by next-generation sequencing techniques, 15 polymorphic EST-SSR markers with three to 14 alleles were developed, most of which were transferable to different Solidago species native to Eurasia and North America. • CONCLUSIONS The EST-SSR markers developed in this study may be useful for elucidating the population structure and taxonomic delimitation of the species complex, as well as for investigating the population genetics and reproductive ecology of Solidago species.
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Affiliation(s)
- Shota Sakaguchi
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, Meguro, Tokyo 153-0041, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Chiyoda, Tokyo 102-8472, Japan
| | - Motomi Ito
- Laboratory of Plant Evolution and Biodiversity, Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, Meguro, Tokyo 153-0041, Japan
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Zhu G, Zhong D, Cao J, Zhou H, Li J, Liu Y, Bai L, Xu S, Wang MH, Zhou G, Chang X, Gao Q, Yan G. Transcriptome profiling of pyrethroid resistant and susceptible mosquitoes in the malaria vector, Anopheles sinensis. BMC Genomics 2014; 15:448. [PMID: 24909924 PMCID: PMC4070547 DOI: 10.1186/1471-2164-15-448] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 05/28/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Anopheles sinensis is a major malaria vector in China and other Southeast Asian countries, and it is becoming increasingly resistant to the insecticides used for agriculture, net impregnation, and indoor residual spray. Very limited genomic information on this species is available, which has hindered the development of new tools for resistance surveillance and vector control. We used the 454 GS FLX system and generated expressed sequence tag (EST) databases of various life stages of An. sinensis, and we determined the transcriptional differences between deltamethrin resistant and susceptible mosquitoes. RESULTS The 454 GS FLX transcriptome sequencing yielded a total of 624,559 reads (average length of 290 bp) with the pooled An. sinensis mosquitoes across various development stages. The de novo assembly generated 33,411 contigs with average length of 493 bp. A total of 8,057 ESTs were generated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. A total of 2,131 ESTs were differentially expressed between deltamethrin resistant and susceptible mosquitoes collected from the same field site in Jiangsu, China. Among these differentially expressed ESTs, a total of 294 pathways were mapped to the KEGG database, with the predominant ESTs belonging to metabolic pathways. Furthermore, a total of 2,408 microsatellites and 15,496 single nucleotide polymorphisms (SNPs) were identified. CONCLUSIONS The annotated EST and transcriptome databases provide a valuable genomic resource for further genetic studies of this important malaria vector species. The differentially expressed ESTs associated with insecticide resistance identified in this study lay an important foundation for further functional analysis. The identified microsatellite and SNP markers will provide useful tools for future population genetic and comparative genomic analyses of malaria vectors.
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Affiliation(s)
- Guoding Zhu
- />Department of Parasitology, Medical College of Soochow University, Suzhou, 215123 PR China
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Daibin Zhong
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Jun Cao
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Huayun Zhou
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Julin Li
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Yaobao Liu
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Liang Bai
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Sui Xu
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Mei-Hui Wang
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Guofa Zhou
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Xuelian Chang
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
| | - Qi Gao
- />Department of Parasitology, Medical College of Soochow University, Suzhou, 215123 PR China
- />Jiangsu Institute of Parasitic Diseases, Key Laboratory of Parasitic Disease Control and Prevention (Ministry of Health), Jiangsu Provincial Key Laboratory of Parasite Molecular Biology, Wuxi, Jiangsu Province 214064 PR China
| | - Guiyun Yan
- />Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA 92697 USA
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Licciardello C, D’Agostino N, Traini A, Recupero GR, Frusciante L, Chiusano ML. Characterization of the glutathione S-transferase gene family through ESTs and expression analyses within common and pigmented cultivars of Citrus sinensis (L.) Osbeck. BMC Plant Biol 2014; 14:39. [PMID: 24490620 PMCID: PMC3922800 DOI: 10.1186/1471-2229-14-39] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/20/2013] [Indexed: 05/05/2023]
Abstract
BACKGROUND Glutathione S-transferases (GSTs) represent a ubiquitous gene family encoding detoxification enzymes able to recognize reactive electrophilic xenobiotic molecules as well as compounds of endogenous origin. Anthocyanin pigments require GSTs for their transport into the vacuole since their cytoplasmic retention is toxic to the cell. Anthocyanin accumulation in Citrus sinensis (L.) Osbeck fruit flesh determines different phenotypes affecting the typical pigmentation of Sicilian blood oranges. In this paper we describe: i) the characterization of the GST gene family in C. sinensis through a systematic EST analysis; ii) the validation of the EST assembly by exploiting the genome sequences of C. sinensis and C. clementina and their genome annotations; iii) GST gene expression profiling in six tissues/organs and in two different sweet orange cultivars, Cadenera (common) and Moro (pigmented). RESULTS We identified 61 GST transcripts, described the full- or partial-length nature of the sequences and assigned to each sequence the GST class membership exploiting a comparative approach and the classification scheme proposed for plant species. A total of 23 full-length sequences were defined. Fifty-four of the 61 transcripts were successfully aligned to the C. sinensis and C. clementina genomes. Tissue specific expression profiling demonstrated that the expression of some GST transcripts was 'tissue-affected' and cultivar specific. A comparative analysis of C. sinensis GSTs with those from other plant species was also considered. Data from the current analysis are accessible at http://biosrv.cab.unina.it/citrusGST/, with the aim to provide a reference resource for C. sinensis GSTs. CONCLUSIONS This study aimed at the characterization of the GST gene family in C. sinensis. Based on expression patterns from two different cultivars and on sequence-comparative analyses, we also highlighted that two sequences, a Phi class GST and a Mapeg class GST, could be involved in the conjugation of anthocyanin pigments and in their transport into the vacuole, specifically in fruit flesh of the pigmented cultivar.
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Affiliation(s)
- Concetta Licciardello
- Consiglio per la Ricerca e la sperimentazione in Agricoltura - Centro di ricerca per l'Agrumicoltura e le Colture Mediterranee (CRA-ACM), Corso Savoia 190, 95024 Acireale, Catania, Italy
| | - Nunzio D’Agostino
- Consiglio per la Ricerca e la sperimentazione in Agricoltura - Centro di ricerca per l'Orticoltura (CRA-ORT), via Cavalleggeri 25, 84098 Pontecagnano, Salerno, Italy
| | | | - Giuseppe Reforgiato Recupero
- Consiglio per la Ricerca e la sperimentazione in Agricoltura - Centro di ricerca per l'Agrumicoltura e le Colture Mediterranee (CRA-ACM), Corso Savoia 190, 95024 Acireale, Catania, Italy
| | - Luigi Frusciante
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Via Università, 100, 80055 Portici, Naples, Italy
| | - Maria Luisa Chiusano
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Via Università, 100, 80055 Portici, Naples, Italy
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11
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Lozinsky S, Yang H, Forseille L, Cook GR, Ramirez-Erosa I, Smith MA. Characterization of an oleate 12-desaturase from Physaria fendleri and identification of 5'UTR introns in divergent FAD2 family genes. Plant Physiol Biochem 2014; 75:114-22. [PMID: 24429134 DOI: 10.1016/j.plaphy.2013.12.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 12/20/2013] [Indexed: 05/08/2023]
Abstract
Mining of an EST sequence collection representing genes expressed during seed development in Physaria fendleri identified abundant sequences encoding apparent homologues of the Arabidopsis oleate 12-desaturase (AtFAD2 At3g12120). Of the 62 sequenced clones, 59 were identified as encoding the previously characterized bifunctional oleate 12-hydroxylase/desaturase (LFAH12/PfFAH12). The remaining 3 clones encoded a second FAD2 homologue. Isolation of a full length ORF and heterologous expression in yeast revealed that this sequence, designated PfFAD2, is the first full length sequence from any Physaria species that encodes an oleate 12-desaturase. PfFAD2 was expressed in both leaf and developing seed with activity on palmitate (16:1(Δ9)) and oleate (18:1(Δ9)). Sequence comparison revealed that PfFAD2 shares 93% amino acid identity with Arabidopsis FAD2 and only 84% identity with PfFAH12. By comparison of EST and genomic sequences it was revealed that the PfFAD2 gene encodes a transcript with a single intron of 1120 bp in the 5'-untranslated region (5'UTR). A short intron, 81 bp in length, was also discovered in the 5'UTR of the PfFAH12 gene, 16 bp upstream of the translation initiation codon. In silico examination of FAD2 like genes from the genome of castor (Ricinus communis) identified putative 5'UTR introns in genes encoding the castor oleate 12-desaturase (RcFAD2) and oleate 12-hydroxylase (CFAH12). By sequencing of genomic DNA the presence of single 5'UTR introns in each gene, and the size of these introns, was confirmed. These findings suggest that 5'UTR introns may be a characteristic feature of FAD2 genes and also of divergent FAD2 genes encoding fatty acid modifying enzymes, and that the selection pressure maintaining these introns is very different.
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Affiliation(s)
- Sharla Lozinsky
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Hui Yang
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Li Forseille
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Gillian R Cook
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Irving Ramirez-Erosa
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Mark A Smith
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
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12
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Panda D, Dehury B, Sahu J, Barooah M, Sen P, Modi MK. Computational identification and characterization of conserved miRNAs and their target genes in garlic (Allium sativum L.) expressed sequence tags. Gene 2014; 537:333-42. [PMID: 24434367 DOI: 10.1016/j.gene.2014.01.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 12/03/2013] [Accepted: 01/04/2014] [Indexed: 01/22/2023]
Abstract
The endogenous small non-coding functional microRNAs (miRNAs) are short in size, range from ~21 to 24 nucleotides in length, play a pivotal role in gene expression in plants and animals by silencing genes either by destructing or blocking of translation of homologous mRNA. Although various high-throughput, time consuming and expensive techniques like forward genetics and direct cloning are employed to detect miRNAs in plants but comparative genomics complemented with novel bioinformatic tools pave the way for efficient and cost-effective identification of miRNAs through homologous sequence search with previously known miRNAs. In this study, an attempt was made to identify and characterize conserved miRNAs in garlic expressed sequence tags (ESTs) through computational means. For identification of novel miRNAs in garlic, a total 3227 known mature miRNAs of plant kingdom Viridiplantae were searched for homology against 21,637 EST sequences resulting in identification of 6 potential miRNA candidates belonging to 6 different miRNA families. The psRNATarget server predicted 33 potential target genes and their probable functions for the six identified miRNA families in garlic. Most of the garlic miRNA target genes seem to encode transcription factors as well as genes involved in stress response, metabolism, plant growth and development. The results from the present study will shed more light on the understanding of molecular mechanisms of miRNA in garlic which may aid in the development of novel and precise techniques to understand some post-transcriptional gene silencing mechanism in response to stress tolerance.
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Affiliation(s)
- Debashis Panda
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Budheswar Dehury
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Jagajjit Sahu
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Priyabrata Sen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Mahendra K Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India.
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13
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Fang P, Niu S, Yuan H, Li Z, Zhang Y, Yuan L, Li W. Development and characterization of 25 EST-SSR markers in Pinus sylvestris var. mongolica (Pinaceae). Appl Plant Sci 2014; 2:apps1300057. [PMID: 25202597 PMCID: PMC4123385 DOI: 10.3732/apps.1300057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/22/2013] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY A set of novel expressed sequence tag (EST) microsatellite markers was developed in Pinus sylvestris var. mongolica to promote further genetic studies in this species. • METHODS AND RESULTS One hundred seventy-five EST-simple sequence repeat (SSR) primers were designed and synthesized for 31,653 isotigs based on P. tabuliformis EST sequences. The primer pairs were used to identify 25 polymorphic loci in 48 individuals. The number of alleles ranged from two to eight with observed and expected heterozygosity values of 0.0435 to 0.8125 and 0.0430 to 0.7820, respectively. • CONCLUSIONS These new polymorphic EST-SSR markers will be useful for assessing genetic diversity, molecular breeding and genetic improvement, and conservation of P. sylvestris var. mongolica.
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Affiliation(s)
- Pan Fang
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Shihui Niu
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Huwei Yuan
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Zhexin Li
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Yuncheng Zhang
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Lu Yuan
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
| | - Wei Li
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
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14
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Yu Y, Liang Y, Lv M, Wu J, Lu G, Cao J. Genome-wide identification and characterization of polygalacturonase genes in Cucumis sativus and Citrullus lanatus. Plant Physiol Biochem 2014; 74:263-275. [PMID: 24321876 DOI: 10.1016/j.plaphy.2013.11.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 11/20/2013] [Indexed: 06/03/2023]
Abstract
Polygalacturonase (PG, EC3.2.1.15), one of the hydrolytic enzymes associated with the modification of pectin network in plant cell wall, has an important role in various cell-separation processes that are essential for plant development. PGs are encoded by a large gene family in plants. However, information on this gene family in plant development remains limited. In the present study, 53 and 62 putative members of the PG gene family in cucumber and watermelon genomes, respectively, were identified by genome-wide search to explore the composition, structure, and evolution of the PG family in Cucurbitaceae crops. The results showed that tandem duplication could be an important factor that contributes to the expansion of the PG genes in the two crops. The phylogenetic and evolutionary analyses suggested that PGs could be classified into seven clades, and that the exon/intron structures and intron phases were conserved within but divergent between clades. At least 24 ancestral PGs were detected in the common ancestor of Arabidopsis and Cucumis sativus. Expression profile analysis by quantitative real-time polymerase chain reaction demonstrated that most CsPGs exhibit specific or high expression pattern in one of the organs/tissues. The 16 CsPGs associated with fruit development could be divided into three subsets based on their specific expression patterns and the cis-elements of fruit-specific, endosperm/seed-specific, and ethylene-responsive exhibited in their promoter regions. Our comparative analysis provided some basic information on the PG gene family, which would be valuable for further functional analysis of the PG genes during plant development.
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Affiliation(s)
- Youjian Yu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Ying Liang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Meiling Lv
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Jian Wu
- Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, OH 43210, USA
| | - Gang Lu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
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15
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Ma L, Gu SH, Liu ZW, Wang SN, Guo YY, Zhou JJ, Zhang YJ. Molecular characterization and expression profiles of olfactory receptor genes in the parasitic wasp, Microplitis mediator (Hymenoptera: Braconidae). J Insect Physiol 2014; 60:118-126. [PMID: 24291166 DOI: 10.1016/j.jinsphys.2013.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 06/02/2023]
Abstract
Olfactory receptors (OR) are believed to fulfil an indispensable role in insects host-seeking, mating and ovipositing. We obtained 4785 high-quality expressed sequencing tags (EST) from the antennal cDNA library of the parasitic wasp Microplitis mediator, a natural enemy of crop pests. After assembling, 786 contigs and 2130 singletons were generated. Using BLAST searches, a number of olfactory-related genes were identified, including ESTs encoding for 25 ORs. 14 full-length OR genes were cloned and their expression profiles in the wasp olfactory organs were quantified by real-time qRT-PCR. The results indicated a diverse distribution between the tissues and genders, yet the majority of OR genes are highly expressed in antennae. Three OR genes (Or2, Or12 and Or13) are highly expressed in female antennae, eight OR genes (ORco, Or3, Or4, Or5, Or7, Or8, Or9 and Or11) are highly expressed in male antennae. This is the first report on tissue-specific expression of wasp OR genes. Our study provides a foundational knowledge to explore and understand the molecular basis of odorant reception in this parasitic wasp and for the study of trophic interactions of natural enemy.
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Affiliation(s)
- Long Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Shao-Hua Gu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ze-Wen Liu
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Shan-Ning Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yu-Yuan Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK.
| | - Yong-Jun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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16
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Wang YL, Li Q, Xie J, Zhu M, Sun WJ, He L, Wang Q. Involvement of the single Cul4 gene of Chinese mitten crab Eriocheir sinensis in spermatogenesis. Gene 2013; 536:9-17. [PMID: 24334119 DOI: 10.1016/j.gene.2013.11.099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 11/13/2013] [Accepted: 11/13/2013] [Indexed: 12/21/2022]
Abstract
The Cullin-RING finger ligases (CRLs) are involved in the ubiquitin-mediated degradation of cell cycle regulators and play an important role in gametogenesis. Cullin 4 (CUL4) is a conserved core component of a new class of ubiquitin E3 ligase, and participates in the proteolysis of several regulatory proteins through the ubiquitin-proteasome pathway. The mammals encode two paralogs of CUL4, CUL4A and CUL4B, and the two Cul4 genes are functionally redundant. However, Drosophila or other metazoans only contain one Cul4 gene. Here we cloned the Cul4 gene and confirmed that there is only one protein of CUL4 in Eriocheir sinensis, a full length Cul4 comprised of 2777 nucleotides, an open-reading frame of 2373bp encoding 790 amino acid residues. The expression level of Cul4 mRNAs, as demonstrated by quantitative real-time PCR, varied significantly during testis development, with the greatest transcript levels found at an early stage. Localization analysis using antibodies against CUL4A/4B in the reproductive system showed that EsCUL4 mainly distribute in spermatogonia and primary spermatocytes, and gradually reduced during the development and maturation of sperm. The results indicated that a single CUL4 protein may play a role in spermatogenesis in E. sinensis.
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Affiliation(s)
- Yuan-Li Wang
- School of Life Science, East China Normal University, Shanghai, China
| | - Qing Li
- School of Life Science, East China Normal University, Shanghai, China
| | - Jing Xie
- School of Life Science, East China Normal University, Shanghai, China
| | - Ming Zhu
- School of Life Science, East China Normal University, Shanghai, China
| | - Wen-Juan Sun
- School of Life Science, East China Normal University, Shanghai, China
| | - Lin He
- School of Life Science, East China Normal University, Shanghai, China.
| | - Qun Wang
- School of Life Science, East China Normal University, Shanghai, China.
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17
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Han J, Li A, Liu H, Wen X, Zhao M, Korir NB, Korir NK, Wang C, Fang J. Computational identification of microRNAs in the strawberry (Fragaria x ananassa) genome sequence and validation of their precise sequences by miR-RACE. Gene 2013; 536:151-62. [PMID: 24333854 DOI: 10.1016/j.gene.2013.11.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 11/06/2013] [Accepted: 11/12/2013] [Indexed: 12/20/2022]
Abstract
In plants, microRNAs (miRNAs) play significant roles in post-transcriptional gene regulation and have been found to control many genes involved in different biological and metabolic processes. Extensive studies were carried out to discover miRNAs and analyze their functions in model plant species, such as in Arabidopsis and rice that have been reported. In this research, we used bioinformatics to predict microRNAs in an important strawberry rootstock cultivar to discover and validate precise sequences of microRNAs in strawberry. By adopting a range of filtering criteria, we obtained 59 potential miRNAs belonging to 40 miRNA families from the Fragaria vesca genome. Using two specific 5' and 3' miRNA RACE PCR reactions and a sequence-directed cloning method, we accurately determined 34 precise sequences of candidate miRNAs, while six other sequences exhibited some minor divergence in their termini nucleotides, and 19 miRNAs that could not be cloned owing to expression abundance may be too low or these mirRNAs predicted could not be existing in strawberry. Potential target genes were further predicted for the miRNAs above. The expression of the 16 miRNAs unreported and having exact sequences and their targets by experiment could be detected in different tissues of strawberry ranging from roots, stems, leaves, flowers and fruits by qRT-PCR and some of them showed differential expression in various tissues. The functional analysis of 16 miRNAs and their targets was carried out. Finally, we conclude that there are 34 mirRNAs in strawberry and their targets play vital roles not only in growth and development, but also in diverse physiological processes. These results show that regulatory miRNAs exist in agronomically important strawberry and might have an important function in strawberry growth and development.
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Affiliation(s)
- Jian Han
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Aying Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Liu
- Department of Horticulture, Nanjing Jinling Institute of Technology, Nanjing 210038, China
| | - Xicheng Wen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mizhen Zhao
- Department of Horticulture, Nanjing Jinling Institute of Technology, Nanjing 210038, China
| | | | - Nicholas Kibet Korir
- Department of Agricultural Technology, Kenyatta University, P.O. Box, 43844-00100 Nairobi, Kenya
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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18
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Rocha AJ, Soares EL, Costa JH, Costa WLG, Soares AA, Nogueira FCS, Domont GB, Campos FAP. Differential expression of cysteine peptidase genes in the inner integument and endosperm of developing seeds of Jatropha curcas L. (Euphorbiaceae). Plant Sci 2013; 213:30-37. [PMID: 24157205 DOI: 10.1016/j.plantsci.2013.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 06/02/2023]
Abstract
In several plant tissues, programmed cell death (PCD) is mediated by the combined action of cysteine peptidases, namely KDEL-tailed cysteine peptidases (KDEL-CysEP) and vacuolar processing enzymes (VPE). Here, we performed a search of the draft genome of Jatropha curcas L. (Euphorbiaceae) and identified 2 genes for KDEL-CysEP (Jc-CysEP1 and Jc-CysEP2) and 3 genes for VPE (Jc-βVPE, Jc-γVPE and Jc-δVPE) and determined the expression patterns of these genes by RT-qPCR in integument and cellular endosperm of seeds collected at seven different developmental stages. We were able to demonstrate that the expression of Jc-CysEP1, Jc-CysEP2, Jc-βVPE and Jc-γVPE proceeded rapidly from Stage IV, with Jc-CysEP2 displaying the highest relative expression; expression of Jc-δVPE could not be detected in any of the tissues/developmental stages analyzed. Additionally, we showed that the expression pattern of these peptidases correlates with anatomical changes in integument and cellular endosperm, thus suggesting a role for both classes of peptidases in PCD and in protein processing, both of which occur simultaneously in each of these tissues.
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Affiliation(s)
- Antônio J Rocha
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, CE, Brazil
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19
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Ballerini ES, Mockaitis K, Arnold ML. Transcriptome sequencing and phylogenetic analysis of floral and leaf MIKC(C) MADS-box and R2R3 MYB transcription factors from the monocot Iris fulva. Gene 2013; 531:337-46. [PMID: 23994293 DOI: 10.1016/j.gene.2013.08.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/21/2013] [Accepted: 08/21/2013] [Indexed: 02/03/2023]
Abstract
The Louisiana Irises serve as an important system for the study of the evolutionary processes of speciation, including reproductive isolation, hybridization, and adaptation. Sequencing methods today allow for the generation of resources key to elucidating the genetic basis of these phenomena. Here we describe the transcriptomes of floral and young leaf tissue from Iris fulva generated by massively parallel pyrosequencing. In order to identify potential candidates for the study of reproductive isolation and adaptation in the Louisiana Irises we phylogenetically analyzed the type II MIKC(C) MADS-box and R2R3 MYB transcription factors expressed in these tissues. A total of 25 Iris MIKC(C) MADS-box genes in 9 clades and 42 Iris R2R3 MYB genes in 19 clades were identified. Through the identification of eudicot and monocot specific clades, these analyses contribute to our understanding of the evolution of these prominent transcription factor families in the angiosperms.
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20
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Gojanovich GS, Ross P, Holmer SR, Holmes JC, Hess PR. Characterization and allelic variation of the transporters associated with antigen processing (TAP) genes in the domestic dog (Canis lupus familiaris). Dev Comp Immunol 2013; 41:578-586. [PMID: 23892057 PMCID: PMC3846772 DOI: 10.1016/j.dci.2013.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/15/2013] [Accepted: 07/21/2013] [Indexed: 06/02/2023]
Abstract
The function of the transporters associated with antigen processing (TAP) complex is to shuttle antigenic peptides from the cytosol to the endoplasmic reticulum to load MHC class I molecules for CD8(+) T-cell immunosurveillance. Here we report the promoter and coding regions of the canine TAP1 and TAP2 genes, which encode the homologous subunits forming the TAP heterodimer. By sampling genetically divergent breeds, polymorphisms in both genes were identified, although there were few amino acid differences between alleles. Splice variants were also found. When aligned to TAP genes of other species, functional regions appeared conserved, and upon phylogenetic analysis, canine sequences segregated appropriately with their orthologs. Transfer of the canine TAP2 gene into a murine TAP2-defective cell line rescued surface MHC class I expression, confirming exporter function. This data should prove useful in investigating the association of specific TAP defects or alleles with immunity to intracellular pathogens and cancer in dogs.
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Affiliation(s)
- Gregory S. Gojanovich
- Immunology Program, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607 USA
| | - Peter Ross
- Immunology Program, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607 USA
| | - Savannah R. Holmer
- Immunology Program, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607 USA
| | - Jennifer C. Holmes
- Immunology Program, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607 USA
| | - Paul R. Hess
- Immunology Program, Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607 USA
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21
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Lin P, Cheng T, Jin S, Jiang L, Wang C, Xia Q. Structural, evolutionary and functional analysis of APN genes in the Lepidoptera Bombyx mori. Gene 2014; 535:303-11. [PMID: 24286860 DOI: 10.1016/j.gene.2013.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/07/2013] [Accepted: 11/09/2013] [Indexed: 12/27/2022]
Abstract
Aminopeptidases N (APNs), the receptors of Bacillus thuringiensis (Bt) toxin in the lepidopteran midgut, are involved in the Bt pathogen infection mechanism. In the present work, we screened 102 APNs from SilkDB, ButterflyBase and MonarchBase; 16 APNs were identified from the silkworm (Bombyx mori) and 24 from the monarch butterfly (Danaus plexippus). Syntenic and phylogenetic tree analysis showed that APN genes have developed multi-family genes before evolutionary divergence of the Lepidoptera. The tissue-expression pattern shows some BmAPNs are specifically or highly expressed in the midgut. Bacillus bombysepticus (Bb) is a specific pathogen of B. mori, leading to acute fuliginosa septicemia of the larva. BmAPNs were modulated by real time quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis after Bb or Bt oral infection. There were different patterns of induced expression between Bb and Bt challenges, suggesting that B. mori has different responses to infection by the specific pathogen Bb and the nonspecific pathogen Bt. Research on BmAPNs will help us to better understand the evolutionary conservation and functions in Bb or Bt pathogen interaction with the host and to apply this knowledge in agricultural and forestry pest control.
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Ding M, Jiang Y, Cao Y, Lin L, He S, Zhou W, Rong J. Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development. Gene 2013; 535:273-85. [PMID: 24279997 DOI: 10.1016/j.gene.2013.11.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 11/02/2013] [Accepted: 11/13/2013] [Indexed: 12/14/2022]
Abstract
Ligon lintless-1 (Li1) is a monogenic dominant mutant of Gossypium hirsutum (upland cotton) with a phenotype of impaired vegetative growth and short lint fibers. Despite years of research involving genetic mapping and gene expression profile analysis of Li1 mutant ovule tissues, the gene remains uncloned and the underlying pathway of cotton fiber elongation is still unclear. In this study, we report the whole genome-level deep-sequencing analysis of leaf tissues of the Li1 mutant. Differentially expressed genes in leaf tissues of mutant versus wild-type (WT) plants are identified, and the underlying pathways and potential genes that control leaf and fiber development are inferred. The results show that transcription factors AS2, YABBY5, and KANDI-like are significantly differentially expressed in mutant tissues compared with WT ones. Interestingly, several fiber development-related genes are found in the downregulated gene list of the mutant leaf transcriptome. These genes include heat shock protein family, cytoskeleton arrangement, cell wall synthesis, energy, H2O2 metabolism-related genes, and WRKY transcription factors. This finding suggests that the genes are involved in leaf morphology determination and fiber elongation. The expression data are also compared with the previously published microarray data of Li1 ovule tissues. Comparative analysis of the ovule transcriptomes of Li1 and WT reveals that a number of pathways important for fiber elongation are enriched in the downregulated gene list at different fiber development stages (0, 6, 9, 12, 15, 18dpa). Differentially expressed genes identified in both leaf and fiber samples are aligned with cotton whole genome sequences and combined with the genetic fine mapping results to identify a list of candidate genes for Li1.
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Affiliation(s)
- Mingquan Ding
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Yurong Jiang
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Yuefen Cao
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Lifeng Lin
- Nanosphere Inc., 4088 Commercial Drive, Northbrook, IL 60062, USA
| | - Shae He
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Wei Zhou
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China
| | - Junkang Rong
- School of Agriculture and Food Science, Zhejiang A&F University, Linan, Hangzhou, Zhejiang 311300, China; The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, China.
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23
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Abstract
Host defense peptides (HDPs) are important effector molecules of the innate immune system of vertebrates. These antimicrobial peptides are also present in invertebrates, plants and fungi. HDPs display broad-spectrum antimicrobial activities and fulfill an important role in the first line of defense of many organisms. It is becoming increasingly clear that in the animal kingdom the functions of HDPs are not confined to direct antimicrobial actions. Research in mammals has indicated that HDPs have many immunomodulatory functions and are also involved in other physiological processes ranging from development to wound healing. During the past five years our knowledge about avian HDPs has increased considerably. This review addresses our current knowledge on the evolution, regulation and biological functions of HDPs of birds.
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Affiliation(s)
- Tryntsje Cuperus
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
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24
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Ren L, Zhang D, Jiang XN, Gai Y, Wang WM, Reed BM, Shen XH. Peroxidation due to cryoprotectant treatment is a vital factor for cell survival in Arabidopsis cryopreservation. Plant Sci 2013; 212:37-47. [PMID: 24094052 DOI: 10.1016/j.plantsci.2013.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/16/2013] [Accepted: 07/20/2013] [Indexed: 05/25/2023]
Abstract
Cryopreservation can be a safe and cost-effective tool for the long-term storage of plant germplasm. In Arabidopsis, the ability to recover from cryogenic treatment was lost as growth progressed. Growth could be restored in 48-h seedlings, whereas 72-h seedlings died after cryogenic treatment. Why seedling age and survival are negatively correlated is an interesting issue. A comparative transcriptomics was performed to screen differentially expressed genes between 48- and 72-h seedlings after exposure to cryoprotectant. Among differentially expressed genes, oxidative stress response genes played important roles in cryoprotectant treatment, and peroxidation was a key factor related to cell survival. Seedlings underwent more peroxidation at 72-h than at 48-h. A comprehensive analysis indicated that peroxidation injured membrane systems leading to photophosphorylation and oxidative phosphorylation damage. Furthermore, the apoptosis-like events were found in cryogenic treatment of Arabidopsis seedlings. 48- and 72-h seedlings underwent different degrees of membrane lipid peroxidation during cryoprotectant treatment, and reducing the injury of oxidative stress was an important factor to successful cryopreservation. This study provided a novel insight of genetic regulatory mechanisms in cryopreservation, and established an excellent model to test and evaluate the effect of exogenous antioxidants and conventional cryoprotectants in plant cryopreservation.
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Affiliation(s)
- Li Ren
- Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, No. 800, Rd. Dong Chuan, Shanghai, PR China.
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25
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Vimolmangkang S, Zheng D, Han Y, Khan MA, Soria-Guerra RE, Korban SS. Transcriptome analysis of the exocarp of apple fruit identifies light-induced genes involved in red color pigmentation. Gene 2013; 534:78-87. [PMID: 24140126 DOI: 10.1016/j.gene.2013.10.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 09/27/2013] [Accepted: 10/02/2013] [Indexed: 10/26/2022]
Abstract
Although the mechanism of light regulation of color pigmentation of apple fruit is not fully understood, it has been shown that light can regulate expression of genes in the anthocyanin biosynthesis pathway by inducing transcription factors (TFs). Moreover, expression of genes encoding enzymes involved in this pathway may be coordinately regulated by multiple TFs. In this study, fruits on trees of apple cv. Red Delicious were covered with paper bags during early stages of fruit development and then removed prior to maturation to analyze the transcriptome in the exocarp of apple fruit. Comparisons of gene expression profiles of fruit covered with paper bags (dark-grown treatment) and those subjected to 14 h light treatment, following removal of paper bags, were investigated using an apple microarray of 40,000 sequences. Expression profiles were investigated over three time points, at one week intervals, during fruit development. Overall, 736 genes with expression values greater than two-fold were found to be modulated by light treatment. Light-induced products were classified into 19 categories with highest scores in primary metabolism (17%) and transcription (12%). Based on the Arabidopsis gene ontology annotation, 18 genes were identified as TFs. To further confirm expression patterns of flavonoid-related genes, these were subjected to quantitative RT-PCR (qRT-PCR) using fruit of red-skinned apple cv. Red Delicious and yellow-skinned apple cv. Golden Delicious. Of these, two genes showed higher levels of expression in 'Red Delicious' than in 'Golden Delicious', and were likely involved in the regulation of fruit red color pigmentation.
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Affiliation(s)
- Sornkanok Vimolmangkang
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1201 W. Gregory, Urbana, IL 61801, USA; Department of Pharmacognosy, Faculty of Pharmaceutical Science, Chulalongkorn University, Bangkok 10330, Thailand
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26
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Ahn YK, Tripathi S, Kim JH, Cho YI, Lee HE, Kim DS, Woo JG, Cho MC. Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery. Gene 2014; 533:494-9. [PMID: 24125952 DOI: 10.1016/j.gene.2013.09.095] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 09/26/2013] [Indexed: 11/22/2022]
Abstract
Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae) is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster, using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 'isogroups' and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variant analysis identified a total of 9701 and 12,741 potential SNPs which eventually resulted in 1025 and 1059 genotype specific SNPs, for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.
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27
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Rossi A, Ross EJ, Jack A, Sánchez Alvarado A. Molecular cloning and characterization of SL3: a stem cell-specific SL RNA from the planarian Schmidtea mediterranea. Gene 2013; 533:156-67. [PMID: 24120894 DOI: 10.1016/j.gene.2013.09.101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 08/26/2013] [Accepted: 09/26/2013] [Indexed: 01/03/2023]
Abstract
Spliced leader (SL) trans-splicing is a biological phenomenon, common among many metazoan taxa, consisting in the transfer of a short leader sequence from a small SL RNA to the 5' end of a subset of pre-mRNAs. While knowledge of the biochemical mechanisms driving this process has accumulated over the years, the functional consequences of such post-transcriptional event at the organismal level remain unclear. In addition, the fact that functional analyses have been undertaken mainly in trypanosomes and nematodes leaves a somehow fragmented picture of the possible biological significance and evolution of SL trans-splicing in eukaryotes. Here, we analyzed the spatial expression of SL RNAs in the planarian flatworm Schmidtea mediterranea, with the goal of identifying novel developmental paradigms for the study of trans-splicing in metazoans. Besides the previously identified SL1 and SL2, S. mediterranea expresses a third SL RNA described here as SL3. While, SL1 and SL2 are collectively expressed in a broad range of planarian cell types, SL3 is highly enriched in a subset of the planarian stem cells engaged in regenerative responses. Our findings provide new opportunities to study how trans-splicing may regulate the phenotype of a cell.
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Affiliation(s)
- Alessandro Rossi
- Stowers Institute for Medical Research, 1000 E 50th St., Kansas City, MO 64110, USA.
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28
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Li P, Deng WQ, Li TH, Song B, Shen YH. Illumina-based de novo transcriptome sequencing and analysis of Amanita exitialis basidiocarps. Gene 2013; 532:63-71. [PMID: 24050899 DOI: 10.1016/j.gene.2013.09.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 01/24/2023]
Abstract
Amanita exitialis is a lethal mushroom that was first discovered in Guangdong Province, China. The high content of amanitin in its basidiocarps makes it lethal to humans. To comprehensively characterize the A. exitialis transcriptome and analyze the Amanita toxins as well as their related gene family, transcriptome sequencing of A. exitialis was performed using Illumina HiSeq 2000 technology. A total of 25,563,688 clean reads were collected and assembled into 62,137 cDNA contigs with an average length of 481 bp and N50 length of 788 bp. A total of 27,826 proteins and 39,661 unigenes were identified among the assembled contigs. All of the unigenes were classified into 166 functional categories for understanding the gene functions and regulation pathways. The genes contributing to toxic peptide biosynthesis were analyzed. From this set, eleven gene sequences encoding the toxins or related cyclic peptides were discovered in the transcriptome. Three of these sequences matched the peptide toxins α-amanitin, β-amanitin, and phallacidin, while others matched amanexitide and seven matched unknown peptides. All of the genes encoding peptide toxins were confirmed by polymerase chain reaction (PCR) in A. exitialis, and the phylogenetic relationships among these proprotein sequences were discussed. The gene polymorphism and degeneracy of the toxin encoding sequences were found and analyzed. This study provides the first primary transcriptome of A. exitialis, which provided comprehensive gene expression information on the lethal amanitas at the transcriptional level, and could lay a strong foundation for functional genomics studies in those fungi.
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Affiliation(s)
- Peng Li
- School of Bioscience & Bioengineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Applied Microbiology, South China (The Ministry-Province Joint Development), Guangdong Institute of Microbiology, Guangzhou 510070, China
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29
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Heavner ME, Gueguen G, Rajwani R, Pagan PE, Small C, Govind S. Partial venom gland transcriptome of a Drosophila parasitoid wasp, Leptopilina heterotoma, reveals novel and shared bioactive profiles with stinging Hymenoptera. Gene 2013; 526:195-204. [PMID: 23688557 PMCID: PMC3905606 DOI: 10.1016/j.gene.2013.04.080] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/25/2013] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
Analysis of natural host-parasite relationships reveals the evolutionary forces that shape the delicate and unique specificity characteristic of such interactions. The accessory long gland-reservoir complex of the wasp Leptopilina heterotoma (Figitidae) produces venom with virus-like particles. Upon delivery, venom components delay host larval development and completely block host immune responses. The host range of this Drosophila endoparasitoid notably includes the highly-studied model organism, Drosophila melanogaster. Categorization of 827 unigenes, using similarity as an indicator of putative homology, reveals that approximately 25% are novel or classified as hypothetical proteins. Most of the remaining unigenes are related to processes involved in signaling, cell cycle, and cell physiology including detoxification, protein biogenesis, and hormone production. Analysis of L. heterotoma's predicted venom gland proteins demonstrates conservation among endo- and ectoparasitoids within the Apocrita (e.g., this wasp and the jewel wasp Nasonia vitripennis) and stinging aculeates (e.g., the honey bee and ants). Enzyme and KEGG pathway profiling predicts that kinases, esterases, and hydrolases may contribute to venom activity in this unique wasp. To our knowledge, this investigation is among the first functional genomic studies for a natural parasitic wasp of Drosophila. Our findings will help explain how L. heterotoma shuts down its hosts' immunity and shed light on the molecular basis of a natural arms race between these insects.
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Affiliation(s)
- Mary E Heavner
- Biology Department, The City College, City University of New York, 138th Street and Convent Avenue, New York, NY 10031, USA
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30
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Huang M, Song X, Zhao J, Mu C, Wang L, Zhang H, Zhou Z, Liu X, Song L. A C-type lectin (AiCTL-3) from bay scallop Argopecten irradians with mannose/galactose binding ability to bind various bacteria. Gene 2013; 531:31-8. [PMID: 24008017 DOI: 10.1016/j.gene.2013.08.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 07/20/2013] [Accepted: 08/13/2013] [Indexed: 11/22/2022]
Abstract
C-type lectins are a family of Ca(2+)-dependent carbohydrate-binding proteins playing crucial roles in innate immunity of vertebrates and invertebrates. In the present study, the cDNA of a C-type lectin with one carbohydrate-recognition domain (CRD) of 127 amino acids was cloned from bay scallop Argopecten irradians (designated AiCTL-3) by rapid amplification of cDNA end (RACE) techniques based on expressed sequence tag (EST) analysis. The mRNA transcripts of AiCTL-3 could be detected in all the tested tissues including hepatopancreas, gonad, adductor muscle, heart, hemocytes, mantle and gill, with the highest expression level in hepatopancreas. After the challenges with Vibrio anguillarum and Micrococcus luteus, the mRNA expression level of AiCTL-3 was obviously up-regulated and reached the maximum level at 9h (11.87fold, P<0.01, and 20.02-fold, P<0.05, respectively). The recombinant AiCTL-3 (designated as rAiCTL-3) could bind LPS, PGN, and glucan in vitro, but could not bind mannan. And it also bound Gram-positive bacteria Staphylococcus aureus as well as Gram-negative bacteria Escherichia coli and V. anguillarum. With a Ca(2+) binding site 2 EPN (Glu-Pro-Asn) motif, rAiCTL-3 could bind both mannose and galactose which was quite different from those in vertebrate. Meanwhile, it could significantly enhance the phagocytosis of scallop hemocytes in vitro. The results clearly suggested that AiCTL-3 could serve not only as a PRR participated in the immune response against various PAMPs and bacteria in non-self recognition via mannose/galactose binding specificity but an opsonin playing an important part in clearance of invaders.
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31
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Rigouin C, Vermeire JJ, Nylin E, Williams DL. Characterization of the phytochelatin synthase from the human parasitic nematode Ancylostoma ceylanicum. Mol Biochem Parasitol 2013; 191:1-6. [PMID: 23916800 PMCID: PMC3823645 DOI: 10.1016/j.molbiopara.2013.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/18/2013] [Accepted: 07/19/2013] [Indexed: 11/21/2022]
Abstract
Hookworm disease is a debilitating worm infection that affects hundreds of millions of people. Despite the existence of anthelmintic drugs, reports have testified of a decrease in efficacy of these drugs. Therefore, it is imperative to find new drugs and drug targets for hookworm disease treatment. In this study we identify the gene encoding the phytochelatin synthase in the human hookworm, Ancylostoma ceylanicum (AcePCS). Phytochelatin synthase catalyzes the production of metal chelating peptides, the phytochelatins, from glutathione (GSH). In plants, algae, and fungi phytochelatin production is important for metal tolerance and detoxification. Phytochelatin synthase proteins also function in the elimination of xenobiotics by processing GSH S-conjugates. We found that in vitro AcePCS could both synthesize phytochelatins and hydrolyze a GSH S-conjugate. Interestingly, the enzyme works through a thiol-dependent and, notably, metal-independent mechanism for both transpeptidase (phytochelatin synthesis) and peptidase (hydrolysis of GSH S-conjugates) activities. AcePCS mRNAs are expressed in vivo throughout the life cycle of A. ceylanicum. Mature adult male hookworms isolated from the small intestines of their hosts displayed significantly enhanced expression of AcePCS with transcript levels 5-fold greater than other developmental forms. Although the role of AcePCS in A. ceylanicum biology has yet to be fully investigated the results reported here provide encouraging evidence of the potential that this enzyme holds as a target for new chemotherapeutic intervention.
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Affiliation(s)
- Coraline Rigouin
- Department of Immunology/Microbiology, Rush University Medical Center, 1735 West Harrison Street, Chicago, IL 60612, United States
| | - Jon J. Vermeire
- Program in International Child Health and Department of Pediatrics, Yale University School of Medicine, New Haven, CT, United States
| | - Elyse Nylin
- Department of Immunology/Microbiology, Rush University Medical Center, 1735 West Harrison Street, Chicago, IL 60612, United States
| | - David L. Williams
- Department of Immunology/Microbiology, Rush University Medical Center, 1735 West Harrison Street, Chicago, IL 60612, United States
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32
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Zhang LF, Li WF, Han SY, Yang WH, Qi LW. cDNA cloning, genomic organization and expression analysis during somatic embryogenesis of the translationally controlled tumor protein (TCTP) gene from Japanese larch (Larix leptolepis). Gene 2013; 529:150-8. [PMID: 23933269 DOI: 10.1016/j.gene.2013.07.076] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 07/01/2013] [Accepted: 07/22/2013] [Indexed: 11/22/2022]
Abstract
A full-length cDNA and genomic sequences of a translationally controlled tumor protein (TCTP) gene were isolated from Japanese larch (Larix leptolepis) and designated LaTCTP. The length of the cDNA was 1, 043 bp and contained a 504 bp open reading frame that encodes a predicted protein of 167 amino acids, characterized by two signature sequences of the TCTP protein family. Analysis of the LaTCTP gene structure indicated four introns and five exons, and it is the largest of all currently known TCTP genes in plants. The 5'-flanking promoter region of LaTCTP was cloned using an improved TAIL-PCR technique. In this region we identified many important potential cis-acting elements, such as a Box-W1 (fungal elicitor responsive element), a CAT-box (cis-acting regulatory element related to meristem expression), a CGTCA-motif (cis-acting regulatory element involved in MeJA-responsiveness), a GT1-motif (light responsive element), a Skn-1-motif (cis-acting regulatory element required for endosperm expression) and a TGA-element (auxin-responsive element), suggesting that expression of LaTCTP is highly regulated. Expression analysis demonstrated ubiquitous localization of LaTCTP mRNA in the roots, stems and needles, high mRNA levels in the embryonal-suspensor mass (ESM), browning embryogenic cultures and mature somatic embryos, and low levels of mRNA at day five during somatic embryogenesis. We suggest that LaTCTP might participate in the regulation of somatic embryo development. These results provide a theoretical basis for understanding the molecular regulatory mechanism of LaTCTP and lay the foundation for artificial regulation of somatic embryogenesis.
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33
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Shoji K, Kiuchi T, Hara K, Kawamoto M, Kawaoka S, Arimura SI, Tsutsumi N, Sugano S, Suzuki Y, Shimada T, Katsuma S. Characterization of a novel chromodomain-containing gene from the silkworm, Bombyx mori. Gene 2013; 527:649-54. [PMID: 23850730 DOI: 10.1016/j.gene.2013.06.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 06/07/2013] [Accepted: 06/24/2013] [Indexed: 01/04/2023]
Abstract
Heterochromatin protein 1 (HP1) is an evolutionarily conserved protein across different eukaryotic species, and is crucial in the establishment and maintenance of heterochromatin. HP1 proteins have two distinct functional domains, an N-terminal chromodomain (CD) and a C-terminal chromoshadow domain (CSD), which are required for the selective binding of HP1 proteins to modified histones. During our screen for HP1-like proteins in the Bombyx mori genome, we found a novel silkworm gene, Bombyx mori chromodomain protein 1 (BmCdp1), encoding a putative chromobox protein with only two CDs. The BmCdp1 family proteins are closely related to the HP1 proteins, and most of them belong to insect lineages. qRT-PCR analysis indicated that BmCdp1 mRNA was most abundantly expressed in early embryos, and relatively higher expression was observed in larval testes, hemocytes, and pupal ovaries. Western blot and immunostaining experiments showed that BmCdp1 was localized mainly in the nucleus of BmN4 cells. We searched BmCdp1-bound loci in the Bombyx genome by ChIP-seq analysis using Flag-tagged BmCdp1-expressing BmN4 cells. Combined with ChIP-qPCR experiments, we identified two reliable BmCdp1-bound loci in the genome. siRNA-mediated knockdown of BmCdp1 in BmN4 cells and early embryos did not affect the expression of the gene located close to the BmCdp1-bound locus.
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Affiliation(s)
- Keisuke Shoji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Lu J, Bushel PR. Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling. Gene 2013; 527:616-23. [PMID: 23845781 DOI: 10.1016/j.gene.2013.06.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 06/11/2013] [Accepted: 06/19/2013] [Indexed: 10/26/2022]
Abstract
RNA sequencing (RNA-Seq) allows for the identification of novel exon-exon junctions and quantification of gene expression levels. We show that from RNA-Seq data one may also detect utilization of alternative polyadenylation (APA) in 3' untranslated regions (3' UTRs) known to play a critical role in the regulation of mRNA stability, cellular localization and translation efficiency. Given the dynamic nature of APA, it is desirable to examine the APA on a sample by sample basis. We used a Poisson hidden Markov model (PHMM) of RNA-Seq data to identify potential APA in human liver and brain cortex tissues leading to shortened 3' UTRs. Over three hundred transcripts with shortened 3' UTRs were detected with sensitivity >75% and specificity >60%. Tissue-specific 3' UTR shortening was observed for 32 genes with a q-value ≤ 0.1. When compared to alternative isoforms detected by Cufflinks or MISO, our PHMM method agreed on over 100 transcripts with shortened 3' UTRs. Given the increasing usage of RNA-Seq for gene expression profiling, using PHMM to investigate sample-specific 3' UTR shortening could be an added benefit from this emerging technology.
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Affiliation(s)
- Jun Lu
- Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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35
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Cifarelli RA, D’Onofrio O, Grillo R, Mango T, Cellini F, Piarulli L, Simeone R, Giancaspro A, Colasuonno P, Blanco A, Gadaleta A. Development of a new wheat microarray from a durum wheat totipotent cDNA library used for a powdery mildew resistance study. Cell Mol Biol Lett 2013; 18:231-48. [PMID: 23515937 PMCID: PMC6275905 DOI: 10.2478/s11658-013-0086-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 03/14/2013] [Indexed: 01/10/2023] Open
Abstract
Totipotent cDNA libraries representative of all the potentially expressed sequences in a genome would be of great benefit to gene expression studies. Here, we report on an innovative method for creating such a library for durum wheat (Triticum turgidum L. var. durum) and its application for gene discovery. The use of suitable quantities of 5-azacytidine during the germination phase induced the demethylation of total DNA, and the resulting seedlings potentially express all of the genes present in the genome. A new wheat microarray consisting of 4925 unigenes was developed from the totipotent cDNA library and used to screen for genes that may contribute to differences in the disease resistance of two near-isogenic lines, the durum wheat cultivar Latino and the line 5BIL-42, which are respectively susceptible and resistant to powdery mildew. Fluorescently labeled cDNA was prepared from the RNA of seedlings of the two near-isogenic wheat lines after infection with a single powdery mildew isolate under controlled conditions in the greenhouse. Hybridization to the microarray identified six genes that were differently expressed in the two lines. Four of the sequences could be assigned putative functions based on their similarity to known genes in public databases. Physical mapping of the six genes localized them to two regions of the genome: the centromeric region of chromosome 5B, where the Pm36 resistance gene was previously localized, and chromosome 6B.
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Affiliation(s)
- Rosa Anna Cifarelli
- Metapontum Agrobios, S.S. Jonica 106, 75010 Metaponto di Bernalda, Province of Matera, Italy
| | - Olimpia D’Onofrio
- Metapontum Agrobios, S.S. Jonica 106, 75010 Metaponto di Bernalda, Province of Matera, Italy
| | - Rosalba Grillo
- Metapontum Agrobios, S.S. Jonica 106, 75010 Metaponto di Bernalda, Province of Matera, Italy
| | - Teresa Mango
- Metapontum Agrobios, S.S. Jonica 106, 75010 Metaponto di Bernalda, Province of Matera, Italy
| | - Francesco Cellini
- Metapontum Agrobios, S.S. Jonica 106, 75010 Metaponto di Bernalda, Province of Matera, Italy
| | - Luciana Piarulli
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Angelica Giancaspro
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Pasqualina Colasuonno
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126 Bari, Italy
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Badal M, Xamena N, Cabré O. FB-NOF is a non-autonomous transposable element, expressed in Drosophila melanogaster and present only in the melanogaster group. Gene 2013; 526:459-63. [PMID: 23685284 DOI: 10.1016/j.gene.2013.04.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 04/04/2013] [Accepted: 04/24/2013] [Indexed: 11/17/2022]
Abstract
Most foldback elements are defective due to the lack of coding sequences but some are associated with coding sequences and may represent the entire element. This is the case of the NOF sequences found in the FB of Drosophila melanogaster, formerly considered as an autonomous TE and currently proposed as part of the so-called FB-NOF element, the transposon that would be complete and fully functional. NOF is always associated with FB and never seen apart from the FB inverted repeats (IR). This is the reason why the FB-NOF composite element can be considered the complete element. At least one of its ORFs encodes a protein that has always been considered its transposase, but no detailed studies have been carried out to verify this. In this work we test the hypothesis that FB-NOF is an active transposon nowadays. We search for its expression product, obtaining its cDNA, and propose the ORF and the sequence of its potential protein. We found that the NOF protein is not a transposase as it lacks any of the motifs of known transposases and also shows structural homology with hydrolases, therefore FB-NOF cannot belong to the superfamily MuDR/foldback, as up to now it has been classified, and can be considered as a non-autonomous transposable element. The alignment with the published genomes of 12 Drosophila species shows that NOF presence is restricted only to the 6 Drosophila species belonging to the melanogaster group.
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Affiliation(s)
- Martí Badal
- Grup de Mutagènesi, Departament de Genètica i de Microbiologia, Facultat de Biociències, Edifici C, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Spain
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Lv Y, Zuo Z, Xu X. Global detection and identification of developmental stage specific transcripts in mouse brain using subtractive cross-screening algorithm. Genomics 2013; 102:229-36. [PMID: 23676619 DOI: 10.1016/j.ygeno.2013.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 04/18/2013] [Accepted: 05/06/2013] [Indexed: 02/05/2023]
Abstract
BACKGROUND Pre-mRNA splicing is a crucial step for genetic regulation and accounts largely for downstream translational diversity. The current time of biological research is characterized by advances in functional genomics study and the understanding of the pre-mRNA splicing process has thus become a major portal for biologists to gain insights into the complex gene regulatory mechanism. The intranuclear alternative splicing process can form a variety of genomic transcripts that modulate the growth and development of an organism, particularly in the immune and neural systems. METHODS In the current study, we investigated and identified alternative splicing transcripts at different stages of embryonic mouse brain morphogenesis using subtractive cross-screening algorithm. RESULTS A total of 195 candidate transcripts were found during organogenesis; 1629 identified at fetus stage, 116 in juvenile and 148 transcripts from adulthood. To document our findings, we developed a database named DMBAS, which can be accessed through the link: http://173.234.48.5/DMBAS. We further investigated the alternative splicing products obtained in our experiment and noted the existence of chromosome preference between prenatal and postnatal transcripts. Additionally, the distribution of splicing sites and the splicing types were found to have distinct genomic features at varying stages of brain development. The majority of identified alternative splices (72.3%) at fetus stage were confirmed later using separate RNA-seq data sets. CONCLUSION This study is a comprehensive profiling of alternative splicing transcripts of mouse brain morphogenesis using advanced computational algorithm. A series of developmental stage specific transcripts, as well as their splicing sites and chromosome preferences were revealed in the current study. Our findings and the related online database would form a solid foundation for studies of broader biological significance and paved the way for future investigations in relevant human brain diseases.
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Affiliation(s)
- Yi Lv
- College of Life Sciences, Central China Normal University, Wuhan, PR China.
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Li C, Zhu Y, Guo X, Sun C, Luo H, Song J, Li Y, Wang L, Qian J, Chen S. Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C. A. Meyer. BMC Genomics 2013; 14:245. [PMID: 23577925 PMCID: PMC3637502 DOI: 10.1186/1471-2164-14-245] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 04/02/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence tags is still the most powerful tool for large-scale gene discovery. The global expressed sequence tags from P. ginseng tissues, especially those isolated from stems, leaves and flowers, are still limited, hindering in-depth study of P. ginseng. RESULTS Two 454 pyrosequencing runs generated a total of 2,423,076 reads from P. ginseng roots, stems, leaves and flowers. The high-quality reads from each of the tissues were independently assembled into separate and shared contigs. In the separately assembled database, 45,849, 6,172, 4,041 and 3,273 unigenes were only found in the roots, stems, leaves and flowers database, respectively. In the jointly assembled database, 178,145 unigenes were observed, including 86,609 contigs and 91,536 singletons. Among the 178,145 unigenes, 105,522 were identified for the first time, of which 65.6% were identified in the stem, leaf or flower cDNA libraries of P. ginseng. After annotation, we discovered 223 unigenes involved in ginsenoside backbone biosynthesis. Additionally, a total of 326 potential cytochrome P450 and 129 potential UDP-glycosyltransferase sequences were predicted based on the annotation results, some of which may encode enzymes responsible for ginsenoside backbone modification. A BLAST search of the obtained high-quality reads identified 14 potential microRNAs in P. ginseng, which were estimated to target 100 protein-coding genes, including transcription factors, transporters and DNA binding proteins, among others. In addition, a total of 13,044 simple sequence repeats were identified from the 178,145 unigenes. CONCLUSIONS This study provides global expressed sequence tags for P. ginseng, which will contribute significantly to further genome-wide research and analyses in this species. The novel unigenes identified here enlarge the available P. ginseng gene pool and will facilitate gene discovery. In addition, the identification of microRNAs and the prediction of targets from this study will provide information on gene transcriptional regulation in P. ginseng. Finally, the analysis of simple sequence repeats will provide genetic makers for molecular breeding and genetic applications in this species.
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Affiliation(s)
- Chunfang Li
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Yingjie Zhu
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Xu Guo
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Chao Sun
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Hongmei Luo
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Jingyuan Song
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Ying Li
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Lizhi Wang
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Jun Qian
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
| | - Shilin Chen
- Chinese Academy of Medical Sciences & Peking Union Medical College, Institute of Medicinal Plant Development, Beijing, 100094, China
- China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing, 100700, China
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Abstract
Rho family small GTPases are involved in the spatio-temporal regulation of several physiological processes. They operate as molecular switches based on their GTP- or GDP-bound state. Their GTPase activator proteins (Rho/Rac GAPs) are able to increase the GTP hydrolysis of small GTPases, which turns them to an inactive state. This regulatory step is a key element of signal termination. According to the human genome project the potential number of Rho family GAPs is approximately 70. Despite their significant role in cellular signaling our knowledge on their expression pattern is quite incomplete. In this study we tried to reveal the tissue-distribution of Rho/Rac GAPs based on expressed sequence tag (EST) database from healthy and tumor tissues and microarray experiments. Our accumulated data sets can provide important starting information for future research. However, the nomenclature of Rho family GAPs is quite heterogeneous. Therefore we collected the available names, abbreviations and aliases of human Rho/Rac GAPs in a useful nomenclature table. A phylogenetic tree and domain structure of 65 human RhoGAPs are also presented.
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Uchiyama K, Fujii S, Ishizuka W, Goto S, Tsumura Y. Development of 32 EST-SSR markers for Abies firma (Pinaceae) and their transferability to related species. Appl Plant Sci 2013; 1:apps1200464. [PMID: 25202517 PMCID: PMC4105371 DOI: 10.3732/apps.1200464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/03/2012] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY We developed simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) for Abies firma, a conifer endemic in Japan, to facilitate evaluation of the population genetic structure in this species. • METHODS AND RESULTS We designed primers for 153 EST-SSRs identified from 486322 ESTs from A. sachalinensis ESTs, and tested 96 of them for PCR amplification. Thirty-two primers provided clear amplification, and 14 of those 32 displayed clear polymorphic patterns in multiple populations of A. firma and in two closely related species. The number of alleles per locus and mean expected heterozygosity ranged from one to six and 0 to 0.476, respectively. • CONCLUSIONS The EST-SSR markers developed in this study may be useful for phylogeography and population genetic studies of A. firma. Successful amplifications were obtained for two other Abies species, suggesting that these markers may also be useful for similar applications in other fir species.
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Affiliation(s)
- Kentaro Uchiyama
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
| | - Sayaka Fujii
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Ministry of Environment, Godochosha No. 5, Kasumigaseki 1-2-2, Chiyoda-ku, Tokyo 100-8975, Japan
| | - Wataru Ishizuka
- Department of General Systems Studies, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Susumu Goto
- University of Tokyo Forests, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshihiko Tsumura
- Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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Xie W, Lei Y, Fu W, Yang Z, Zhu X, Guo Z, Wu Q, Wang S, Xu B, Zhou X, Zhang Y. Tissue-specific transcriptome profiling of Plutella xylostella third instar larval midgut. Int J Biol Sci 2012; 8:1142-55. [PMID: 23091412 PMCID: PMC3477684 DOI: 10.7150/ijbs.4588] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 08/11/2012] [Indexed: 11/06/2022] Open
Abstract
The larval midgut of diamondback moth, Plutella xylostella, is a dynamic tissue that interfaces with a diverse array of physiological and toxicological processes, including nutrient digestion and allocation, xenobiotic detoxification, innate and adaptive immune response, and pathogen defense. Despite its enormous agricultural importance, the genomic resources for P. xylostella are surprisingly scarce. In this study, a Bt resistant P. xylostella strain was subjected to the in-depth transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes in the P. xylostella larval midgut. Using Illumina deep sequencing, we obtained roughly 40 million reads containing approximately 3.6 gigabases of sequence data. De novo assembly generated 63,312 ESTs with an average read length of 416 bp, and approximately half of the P. xylostella sequences (45.4%, 28,768) showed similarity to the non-redundant database in GenBank with a cut-off E-value below 10(-5). Among them, 11,092 unigenes were assigned to one or multiple GO terms and 16,732 unigenes were assigned to 226 specific pathways. In-depth analysis identified genes putatively involved in insecticide resistance, nutrient digestion, and innate immune defense. Besides conventional detoxification enzymes and insecticide targets, novel genes, including 28 chymotrypsins and 53 ABC transporters, have been uncovered in the P. xylostella larval midgut transcriptome; which are potentially linked to the Bt toxicity and resistance. Furthermore, an unexpectedly high number of ESTs, including 46 serpins and 7 lysozymes, were predicted to be involved in the immune defense.As the first tissue-specific transcriptome analysis of P. xylostella, this study sheds light on the molecular understanding of insecticide resistance, especially Bt resistance in an agriculturally important insect pest, and lays the foundation for future functional genomics research. In addition, current sequencing effort greatly enriched the existing P. xylostella EST database, and makes RNAseq a viable option in the future genomic analysis.
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Affiliation(s)
- Wen Xie
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Yanyuan Lei
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Wei Fu
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Zhongxia Yang
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Xun Zhu
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Zhaojiang Guo
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Qingjun Wu
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Shaoli Wang
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Baoyun Xu
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Xuguo Zhou
- 2. Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Youjun Zhang
- 1. Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
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Förster F, Beisser D, Grohme MA, Liang C, Mali B, Siegl AM, Engelmann JC, Shkumatov AV, Schokraie E, Müller T, Schnölzer M, Schill RO, Frohme M, Dandekar T. Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. Bioinform Biol Insights 2012; 6:69-96. [PMID: 22563243 PMCID: PMC3342025 DOI: 10.4137/bbi.s9150] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.
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Affiliation(s)
- Frank Förster
- Dept. of Bioinformatics, Biocenter University of Würzburg, 97074 Würzburg, Germany
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Singh S, Gupta S, Mani A, Chaturvedi A. Mining and gene ontology based annotation of SSR markers from expressed sequence tags of Humulus lupulus. Bioinformation 2012; 8:114-22. [PMID: 22368382 PMCID: PMC3283882 DOI: 10.6026/97320630008114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 01/17/2012] [Indexed: 12/03/2022] Open
Abstract
Humulus lupulus is commonly known as hops, a member of the family moraceae. Currently many projects are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. The genetically characterized domains in these databases are limited due to non-availability of reliable molecular markers. The large data of EST sequences are available in hops. The simple sequence repeat markers extracted from EST data are used as molecular markers for genetic characterization, in the present study. 25,495 EST sequences were examined and assembled to get full-length sequences. Maximum frequency distribution was shown by mononucleotide SSR motifs i.e. 60.44% in contig and 62.16% in singleton where as minimum frequency are observed for hexanucleotide SSR in contig (0.09%) and pentanucleotide SSR in singletons (0.12%). Maximum trinucleotide motifs code for Glutamic acid (GAA) while AT/TA were the most frequent repeat of dinucleotide SSRs. Flanking primer pairs were designed in-silico for the SSR containing sequences. Functional categorization of SSRs containing sequences was done through gene ontology terms like biological process, cellular component and molecular function.
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Affiliation(s)
- Swati Singh
- Center of Bioinformatics,University of Allahabad,Allahabad, India-211002
| | - Sanchita Gupta
- Anoop Chaturvedi, Department of Statistics,University of Allahabad,Allahabad, India-211002
| | - Ashutosh Mani
- Center of Bioinformatics,University of Allahabad,Allahabad, India-211002
| | - Anoop Chaturvedi
- Department of Statistics,University of Allahabad,Allahabad, India-211002
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Muvva C, Tewari L, Aruna K, Ranjit P, MD ZS, MD KAM, Veeramachaneni H. In silico identification of miRNAs and their targets from the expressed sequence tags of Raphanus sativus. Bioinformation 2012; 8:98-103. [PMID: 22359443 PMCID: PMC3282264 DOI: 10.6026/97320630008098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/07/2012] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRNAs) are a novel growing family of endogenous, small, non- coding, single-stranded RNA molecules directly involved in regulating gene expression at the posttranscriptional level. High conservation of miRNAs in plant provides the foundation for identification of new miRNAs in other plant species through homology alignment. Here, previous known plant miRNAs were BLASTed against the Expressed Sequence Tag (EST) database of Raphanus sativus, and according to a series of filtering criteria, a total of 48 miRNAs belonging to 9 miRNA families were identified, and 16 potential target genes of them were subsequently predicted, most of which seemed to encode transcription factors or enzymes participating in regulation of development, growth and other physiological processes. Overall, our findings lay the foundation for further researches of miRNAs function in R.sativus.
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Affiliation(s)
- Charuvaka Muvva
- Muvva Biosolutions Pvt.Ltd, Bioinformatics Division, #301, No: 7-1-414/21, Kaushik Sai Rama Residency, Srinivasa colony (East)
S.R.Nagar, Hyderabad-500038, India
- Charuvaka Muvva: Phone: 040-32584321
| | - Lata Tewari
- Department of Bioscience and Biotechnology, Banasthali University, P.O.Banasthali
Vidyapith, Rajasthan- 304022, India
| | - Kasoju Aruna
- Department of Biotechnology, JNTU College of Engineering, Pulivendula, Kadapa (Dist),
Andhra Pradesh, India-516390
| | - Pabbati Ranjit
- Department of Biotechnology, JNTU College of Engineering, Pulivendula, Kadapa (Dist),
Andhra Pradesh, India-516390
| | - Zahoorullah S MD
- Department of Biotechnology, Joginpally B R Engineering College, Yenkapally, Moinabad, Ranga
Reddy (Dist), Andhra Pradesh, India-500075
| | - K A Matheen MD
- Department of Biotechnology, Chaitanya Bharathi Institute of Technology, Gandipet,
Hyderabad-500075, India
| | - Hemanth Veeramachaneni
- Muvva Biosolutions Pvt.Ltd Bioinformatics Division, #301, No: 7-1-414/21, Kaushik Sai Rama
Residency, Srinivasa colony (E), S.R.Nagar, Hyderabad-500038, India
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Abstract
The unicellular green alga Dunaliella salina (Dunal) Teodor. is a novel model photosynthetic eukaryote for studying photosystems, high salinity acclimation, and carotenoid accumulation. In spite of such significance, there have been limited studies on the Dunaliella genome transcriptome and proteome. To further investigate D. salina, a cDNA library was constructed and sequenced. Here, we present the analysis of the 2,282 expressed sequence tags (ESTs) generated together with 3,990 ESTs from dbEST. A total of 4,148 unique sequences (UniSeqs) were identified, of which 56.1% had sequence similarity with Uniprot entries, suggesting that a large number of unique genes may be harbored by Dunaliella. Additionally, protein family domains were identified to further characterize these sequences. Then, we also compared EST sequences with different complete eukaryotic genomes from several animals, plants, and fungi. We observed notable differences between D. salina and other organisms. This EST collection and its annotation provided a significant resource for basic and applied research on D. salina and laid the foundation for a systematic analysis of the transcriptome basis of green algae development and diversification.
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Affiliation(s)
- Rui Zhao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China, 610064
| | - Yu Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China, 610064
| | - Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China, 610064
| | - Linfeng Lv
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China, 610064
| | - Dairong Qiao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China, 610064
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China, 610064
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Seok JW, Lee YS, Moon EK, Lee JY, Jha BK, Kong HH, Chung DI, Hong Y. Expressed sequence tag analysis of the erythrocytic stage of Plasmodium berghei. Korean J Parasitol 2011; 49:221-8. [PMID: 22072821 PMCID: PMC3210838 DOI: 10.3347/kjp.2011.49.3.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/01/2011] [Accepted: 06/02/2011] [Indexed: 11/23/2022]
Abstract
Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploiting the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clusters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene Ontology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presently-collected ESTs and its bioinformatic analysis will be useful resources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.
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Affiliation(s)
- Ji-Woong Seok
- Department of Parasitology, Kyungpook National University School of Medicine, Daegu 700-422, Korea
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Shin D, Jin L, Lobo NF, Severson DW. Transcript profiling of the meiotic drive phenotype in testis of Aedes aegypti using suppressive subtractive hybridization. J Insect Physiol 2011; 57:1220-1226. [PMID: 21708167 PMCID: PMC3167017 DOI: 10.1016/j.jinsphys.2011.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 05/20/2011] [Accepted: 05/24/2011] [Indexed: 05/31/2023]
Abstract
The meiotic drive gene in Aedes aegypti is tightly linked with the sex determination locus on chromosome 1, and causes highly male-biased sex ratios. We prepared cDNA libraries from testes from the Ae. aegypti T37 strain (driving) and RED strain (non-driving), and used suppressive subtraction hybridization techniques to enrich for T37 testes-specific transcripts. Expressed sequence tags (ESTs) were obtained from a total of 2784 randomly selected clones from the subtracted T37 (subT37) library as well as the primary libraries for each strain (pT37 and pRED). Sequence analysis identified a total of 171 unique genes in the subT37 library and 299 unique genes among the three libraries. The majority of genes enriched in the subT37 library were associated with signal transduction, development, reproduction, metabolic process and cell cycle functions. Further, as observed with meiotic drive systems in Drosophila and mouse, a number of these genes were associated with signaling cascades that involve the Ras superfamily of regulatory small GTPases. Differential expression of several of these genes was verified in Ae. aegypti pupal testes using qRT-PCR. This study increases our understanding of testes gene expression enriched in adult males from the meiotic drive strain as well as insights into the basic testes transcriptome in Ae. aegypti.
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Affiliation(s)
- Dongyoung Shin
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556-5645, USA.
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Euling SY, White LD, Kim AS, Sen B, Wilson VS, Keshava C, Keshava N, Hester S, Ovacik MA, Ierapetritou MG, Androulakis IP, Gaido KW. Use of genomic data in risk assessment case study: II. Evaluation of the dibutyl phthalate toxicogenomic data set. Toxicol Appl Pharmacol 2011; 271:349-62. [PMID: 21745491 DOI: 10.1016/j.taap.2011.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 06/03/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
Abstract
An evaluation of the toxicogenomic data set for dibutyl phthalate (DBP) and male reproductive developmental effects was performed as part of a larger case study to test an approach for incorporating genomic data in risk assessment. The DBP toxicogenomic data set is composed of nine in vivo studies from the published literature that exposed rats to DBP during gestation and evaluated gene expression changes in testes or Wolffian ducts of male fetuses. The exercise focused on qualitative evaluation, based on a lack of available dose-response data, of the DBP toxicogenomic data set to postulate modes and mechanisms of action for the male reproductive developmental outcomes, which occur in the lower dose range. A weight-of-evidence evaluation was performed on the eight DBP toxicogenomic studies of the rat testis at the gene and pathway levels. The results showed relatively strong evidence of DBP-induced downregulation of genes in the steroidogenesis pathway and lipid/sterol/cholesterol transport pathway as well as effects on immediate early gene/growth/differentiation, transcription, peroxisome proliferator-activated receptor signaling and apoptosis pathways in the testis. Since two established modes of action (MOAs), reduced fetal testicular testosterone production and Insl3 gene expression, explain some but not all of the testis effects observed in rats after in utero DBP exposure, other MOAs are likely to be operative. A reanalysis of one DBP microarray study identified additional pathways within cell signaling, metabolism, hormone, disease, and cell adhesion biological processes. These putative new pathways may be associated with DBP effects on the testes that are currently unexplained. This case study on DBP identified data gaps and research needs for the use of toxicogenomic data in risk assessment. Furthermore, this study demonstrated an approach for evaluating toxicogenomic data in human health risk assessment that could be applied to future chemicals.
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Affiliation(s)
- Susan Y Euling
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington, DC, USA.
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Abstract
The power of eukaryote genomics relies strongly on taxon sampling. This point was underlined in a recent analysis of red algal genome evolution in which we tested the Plantae hypothesis that posits the monophyly of red, green (including plants) and glaucophyte algae. The inclusion of novel genome data from two mesophilic red algae enabled us to robustly demonstrate the sisterhood of red and green algae in the tree of life. Perhaps more exciting was the finding that >1,800 putative genes in the unicellular red alga Porphyridium cruentum showed evidence of gene-sharing with diverse lineages of eukaryotes and prokaryotes. Here we assessed the correlation between the putative functions of these shared genes and their susceptibility to transfer. It turns out that genes involved in complex interactive networks such as biological regulation and transcription/translation are less susceptible to endosymbiotic or horizontal gene transfer, when compared to genes with metabolic and transporter functions.
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Affiliation(s)
- Cheong Xin Chan
- Department of Ecology, Evolution and Natural Resources; and Institute of Marine and Coastal Sciences; Rutgers University; New Brunswick, NJ USA
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Zwenger SR, Alsaggaf R, Basu C. Does an expressed sequence tag (EST) library of Salsola iberica (tumbleweed) help to understand plant responses to environmental stresses? Plant Signal Behav 2010; 5:1330-1335. [PMID: 20935479 PMCID: PMC3115229 DOI: 10.4161/psb.5.11.12837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2010] [Accepted: 06/29/2010] [Indexed: 05/30/2023]
Abstract
Weeds play an important role in agriculture and molecular techniques are useful to help understand traits that contribute to weediness and weeds' interactions with the environment. A total of 377 expressed sequence tags (ESTs) from a modest library were arranged into 227 unique fragments and 61 contigs, which consisted of two or more ESTs. From blastx results, we mapped and annotated unigenes using the gene ontology vocabulary according to biological process, cellular component and molecular function. These were then compared to a reference set of Arabidopsis thaliana sequences for statistically significant over- or underrepresented genes. The sequences were also compared against multiple protein databases for similarity of functional domains. Overall, the S. iberica sequences showed high similarity to response to stress, which included salt-induced proteins, betaine aldehydehyde dehydrogenase and calcium binding proteins. Only a modest number of transcripts were sequenced; however, the results presented here demonstrate the metabolic versatility of S. iberica in sub-optimal conditions that are likely to contribute to its cosmopolitan distribution. Here we propose that an EST library of an economically important weed species could be used to understand the weed's interactions with the environment.
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Affiliation(s)
- Sam R Zwenger
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
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