scholarly journals SSHSuite: an integrated software package for analysis of large-scale suppression subtractive hybridization data

BioTechniques ◽  
2004 ◽  
Vol 36 (6) ◽  
pp. 1043-1045 ◽  
Author(s):  
Stefan Weckx ◽  
Peter De Rijk ◽  
Christine Van Broeckhoven ◽  
Jurgen Del-Favero
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Software Package ◽  
Large Scale ◽  
Subtractive Hybridization ◽  
Hybridization Data ◽  
Integrated Software

scholarly journals RoboPV: An integrated software package for autonomous aerial monitoring of large scale PV plants

2022 ◽  
Vol 254 ◽  
pp. 115217
Author(s):  
A.M. Moradi Sizkouhi ◽  
S.M. Esmailifar ◽  
M. Aghaei ◽  
M. Karimkhani
Keyword(s):  
Software Package ◽  
Large Scale ◽  
Integrated Software

scholarly journals Towards sex identification of Asian Palmyra palm (Borassus flabelliferL.) by DNA fingerprinting, suppression subtractive hybridization andde novotranscriptome sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7268
Author(s):  
Kwanjai Pipatchartlearnwong ◽  
Piyada Juntawong ◽  
Passorn Wonnapinij ◽  
Somsak Apisitwanich ◽  
Supachai Vuttipongchaikij
Keyword(s):  
Dna Fingerprinting ◽  
Suppression Subtractive Hybridization ◽  
Transcriptome Sequencing ◽  
Large Scale ◽  
De Novo ◽  
Subtractive Hybridization ◽  
Pcr Analysis ◽  
Dna Fingerprints ◽  
Juvenile Period ◽  
Male And Female

BackgroundAsian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing.MethodsDNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries andde novotranscriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers.ResultsThrough extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Althoughde novotranscriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species.

scholarly journals Identification of New Potential Regulators of the Medicago truncatula—Sinorhizobium meliloti Symbiosis Using a Large-Scale Suppression Subtractive Hybridization Approach

2007 ◽  
Vol 20 (3) ◽  
pp. 321-332 ◽  
Author(s):  
Laurence Godiard ◽  
Andreas Niebel ◽  
Fabienne Micheli ◽  
Jérôme Gouzy ◽  
Thomas Ott ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Suppression Subtractive Hybridization ◽  
Medicago Truncatula ◽  
Large Scale ◽  
Sinorhizobium Meliloti ◽  
Zinc Finger Protein ◽  
Gene Clusters ◽  
Subtractive Hybridization ◽  
Symbiotic Interaction ◽  
Genes Encoding

We set up a large-scale suppression subtractive hybridization (SSH) approach to identify Medicago truncatula genes differentially expressed at different stages of the symbiotic interaction with Sinorhizobium meliloti, with a particular interest for regulatory genes. We constructed 7 SSH libraries covering successive stages from Nod factor signal transduction to S. meliloti infection, nodule organogenesis, and functioning. Over 26,000 clones were differentially screened by two rounds of macroarray hybridizations. In all, 3,340 clones, corresponding to genes whose expression was potentially affected, were selected, sequenced, and ordered into 2,107 tentative gene clusters, including 767 MtS clusters corresponding to new M. truncatula genes. In total, 52 genes encoding potential regulatory proteins, including transcription factors (TFs) and other elements of signal transduction cascades, were identified. The expression pattern of some of them was analyzed by quantitative reverse-transcription polymerase chain reaction in wild-type and in Nod¯ M. truncatula mutants blocked before or after S. meliloti infection. Three genes, coding for TFs of the bHLH and WRKY families and a C2H2 zinc-finger protein, respectively, were found to be upregulated, following S. meliloti inoculation, in the infection-defective mutant lin, whereas the bHLH gene also was expressed in the root-hair-curling mutant hcl. The potential role of these genes in early symbiotic steps is discussed.

scholarly journals Genomic Diversity of Burkholderia pseudomallei Clinical Isolates: Subtractive Hybridization Reveals a Burkholderia mallei-Specific Prophage in B. pseudomallei 1026b

2004 ◽  
Vol 186 (12) ◽  
pp. 3938-3950 ◽  
Author(s):  
David DeShazer
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Burkholderia Pseudomallei ◽  
Genomic Sequence ◽  
Subtractive Hybridization ◽  
Etiologic Agent ◽  
Polyclonal Antiserum ◽  
Genomic Diversity ◽  
Clinical Isolates ◽  
Immunogold Electron Microscopy ◽  
Burkholderia Mallei

ABSTRACT Burkholderia pseudomallei is the etiologic agent of the disease melioidosis and is a category B biological threat agent. The genomic sequence of B. pseudomallei K96243 was recently determined, but little is known about the overall genetic diversity of this species. Suppression subtractive hybridization was employed to assess the genetic variability between two distinct clinical isolates of B. pseudomallei, 1026b and K96243. Numerous mobile genetic elements, including a temperate bacteriophage designated φ1026b, were identified among the 1026b-specific suppression subtractive hybridization products. Bacteriophage φ1026b was spontaneously produced by 1026b, and it had a restricted host range, infecting only Burkholderia mallei. It possessed a noncontractile tail, an isometric head, and a linear 54,865-bp genome. The mosaic nature of the φ1026b genome was revealed by comparison with bacteriophage φE125, a B. mallei-specific bacteriophage produced by Burkholderia thailandensis. The φ1026b genes for DNA packaging, tail morphogenesis, host lysis, integration, and DNA replication were nearly identical to the corresponding genes in φE125. On the other hand, φ1026b genes involved in head morphogenesis were similar to head morphogenesis genes encoded by Pseudomonas putida and Pseudomonas aeruginosa bacteriophages. Consistent with this observation, immunogold electron microscopy demonstrated that polyclonal antiserum against φE125 reacted with the tail of φ1026b but not with the head. The results presented here suggest that B. pseudomallei strains are genetically heterogeneous and that bacteriophages are major contributors to the genomic diversity of this species. The bacteriophage characterized in this study may be a useful diagnostic tool for differentiating B. pseudomallei and B. mallei, two closely related biological threat agents.

scholarly journals Identification of up-regulated Ras-like GTPase, Rap1b, by suppression subtractive hybridization

2001 ◽  
Vol 60 (6) ◽  
pp. 2129-2141 ◽  
Author(s):  
Sun Lin ◽  
Sumant Chugh ◽  
Xiaomin Pan ◽  
Elisabeth I. Wallner ◽  
Jun Wada ◽  
...  
Keyword(s):  
Suppression Subtractive Hybridization ◽  
Subtractive Hybridization
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