scholarly journals Characterization of the Rosa roxbunghii Tratt transcriptome and analysis of MYB genes

2018 ◽  
Author(s):  
Xiaolong Huang ◽  
Huiqing Yan ◽  
Lisheng Zhai ◽  
Zhengting Yang ◽  
Yin Yi
Keyword(s):  
De Novo ◽  
Gc Content ◽  
Pcr Analysis ◽  
Mature Fruit ◽  
Illumina Hiseq ◽  
Rosaceae Family ◽  
Ssr Frequency ◽  
Myb Genes ◽  
Myb Proteins

AbstractRosa roxbunghii Tratt belongs to the Rosaceae family, and the fruit is flavorful, economic, and highly nutritious, providing health benefits. MYB proteins play key roles in R. roxbunghii’ fruit development and quality. However, the available genomic and transcriptomic information are extremely deficient. Here, a normalized cDNA library was constructed using five tissues, stem, leaf, flower, young fruit, and mature fruit, with three repetitions, and sequenced using the Illumina HiSeq 2500 platform. De novo assembly was performed, and 470.66 million clean reads were obtained. In total, 63,727 unigenes, with an average GC content of 42.08%, were determined and 59,358 were annotated. In addition, 9,354 unigenes were assigned the Gene Ontology category, and 20,202 unigenes were assigned to 25 Eukaryotic Ortholog Groups. Additionally, 19,507 unigenes were classified into 140 pathways of the Kyoto Encyclopedia of Genes and Genomes database. Using the transcriptome, 18 candidate MYB genes that were significantly expressed in mature fruit, compared with other tissues, were obtained. Among them, 10 R2R3 MYB and 1 R1 MYB were identified. The expression levels of 12 MYB genes randomly selected for qRT-PCR analysis were consistent with the RNA-seq results. A total of 37,545 microsatellites were detected, with an average EST-–SSR frequency of 0.59 (37,545/63,727). This transcriptome data will be valuable for identifying genes of interest and studying their expression and evolution.

scholarly journals Development and Characterization of SSR Markers in the Gossypium Barbadense Genome

2021 ◽  
Author(s):  
Wenjuan ZHONG ◽  
Can YUAN ◽  
Zhengjie CHEN ◽  
Yonghang ZHOU ◽  
Siwei Chen ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Low Cost ◽  
Fiber Quality ◽  
Gossypium Barbadense ◽  
Pcr Analysis ◽  
Genetic Studies ◽  
Genome Wide ◽  
User Friendly

Abstract BackgroundThe fiber quality and resistance traits of Gossypium barbadense are considerably better than that of other Gossypium species. Simple sequence repeats (SSRs) are user friendly, low cost markers widely used in genetic studies. However, most SSRs have been developed from G. hirsutum, G. arboreum, and G. raimondii; no genome-wide SSRs have been developed from G. barbadense.The de novo sequences of G. barbadense cv. Xinhai21 were utilized to develop SSR markers and scanned to detect SSRs using the MIcroSAtellite (http://pgrc.ipk-gatersleben.de/misa/) identification tool. And then in silico PCR analysis was conducted to evaluate these primers polymorphism in five Gossypium species.ResultsIn total, 85,582 SSRs were identified with different motifs. 153,560 primer pairs were successfully designed for 73,419 SSRs. In silico analysis, we found that 8,466 primer pairs of 3,288 SSRs yielded one product (monomorphic) simultaneously in five Gossypium species. two Gossypium species (30 G. hirsutum and 27 G. barbadense accessions) were successfully separated by 300 primer pairs with the polymorphism information content (PIC) ranging from 0.00 to 0.93. ConclusionThese newly developed SSR markers will be helpful for the construction of genetic linkage maps, genetic diversity analyses, QTL mapping, and molecular breeding of Gossypium species.

scholarly journals Genome description and inventory of immune-related genes of the endangered pen shell Pinna nobilis: a giant bivalve experiencing a mass mortality event

2019 ◽  
Author(s):  
Robert Bunet ◽  
Jean-Marc Prévot ◽  
Nardo Vicente ◽  
José Rafa García-March ◽  
Rajko Martinović ◽  
...  
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Gc Content ◽  
Innate Immune ◽  
Trna Genes ◽  
Ecological Value ◽  
Illumina Hiseq ◽  
Late 20Th Century ◽  
Pinna Nobilis ◽  
Pen Shell

Abstract Background: The noble pen shell Pinna nobilis is a Mediterranean endemic and emblematic giant bivalve. Already registered as an endangered species in the late 20th century, it is facing a dramatic and rapidly expanding epizooty that decimates its populations since mid-2016. The ecological value of P. nobilis has urged important investigations for conservation purposes. In light of this, we report here the first draft genome of this animal. Results: The whole-genome sequencing has been performed on an Illumina HiSeq X platform using a single paired-end library of short fragments (2x150 bp). The de novo contig assembly accounted for a total size of 584 Mb (96,738 contigs, N50 = 7.6 kb, with 0.4% of “N” nucleotides), representing 77.5% of the predicted genome size of 754 Mb. The pen shell genome is very AT-rich, with a GC-content of 35.6 %. Heterozygosity was found to be in the range of other sequenced bivalves (1%). Over one third (36.2 %) of the genome consisted of repeated elements with a surprising larger number of SINEs elements compared to other molluscan genomes. We were also able to reconstruct the full mitochondrial genome (~19 kb, with 12 protein-coding genes, 2 rRNA and 22 tRNA genes). In relation with the outbreak that affects P. nobilis, we paid a special attention on the innate immune and stress-related genes found in the sequence. We revealed that P. nobilis disposes of a complete chemical defensome, and a relatively sophisticated innate immune system. Conclusion: In addition to offering a valuable resource for further research in comparative biology and evolution, access to the draft genome sequence is central to deepen our understanding of the vulnerability of P. nobilis to new diseases, which are likely to occur more often in the current scenario of a rapidly changing environment.

scholarly journals Mining MYB transcription factors from the genomes of orchids (Phalaenopsis and Dendrobium) and characterization of an orchid R2R3-MYB gene involved in water-soluble polysaccharide biosynthesis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chunmei He ◽  
Jaime A. Teixeira da Silva ◽  
Haobin Wang ◽  
Can Si ◽  
Mingze Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Water Soluble ◽  
Polysaccharide Biosynthesis ◽  
Myb Gene ◽  
Wide Range ◽  
Soluble Polysaccharide ◽  
Myb Genes ◽  
Myb Proteins ◽  
R2r3 Myb

Abstract Members of the MYB superfamily act as regulators in a wide range of biological processes in plants. Despite this, the MYB superfamily from the Orchidaceae has not been identified, and MYB genes related to bioactive water-soluble polysaccharide (WSP) biosynthesis are relatively unknown. In this study, we identified 159 and 165 MYB genes from two orchids, Phalaenopsis equestris and Dendrobium officinale, respectively. The MYB proteins were classified into four MYB classes in both orchids: MYB-related (MYBR), R2R3-MYB, 3R-MYB and atypical MYB proteins. The MYBR proteins in both orchids were classified into five subfamilies and 12 genes were strongly up-regulated in response to cold stress in D. officinale. The R2R3-MYB proteins were both divided into 31 clades in P. equestris and D. officinale. Among these clades, nine contained MYB TFs related to secondary cell wall biosynthesis or testa mucilage biosynthesis in Arabidopsis thaliana. In D. officinale, 10 candidate genes showed an expression pattern corresponding to changes in the WSP content. Overexpression of one of these candidate genes (DoMYB75) in A. thaliana increased seed WSP content by about 14%. This study provides information about MYB genes in two orchids that will further help to understand the transcriptional regulation of WSP biosynthesis in these orchids as well as other plant species.

scholarly journals The whole-genome sequence analysis of Morchella sextelata

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mei-Han ◽  
Qingshan-Wang ◽  
Baiyintala ◽  
Wuhanqimuge
Keyword(s):  
De Novo ◽  
Gc Content ◽  
Gene Clusters ◽  
Essential Amino Acids ◽  
Biologically Active ◽  
Whole Genome Sequence ◽  
Daily Consumption ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Morphological Studies

Abstract Morchella are macrofungi and are also called morels, as they exhibit a morel-like upper cap structure. Morels contain abundant essential amino acids, vitamins and biologically active compounds, which provide substantial health benefits. Approximately 80 species of Morchella have been reported, and even more species have been isolated. However, the lack of wild Morchella resources and the difficulties associated with culturing Morchella have caused a shortage in the morels available for daily consumption. Additionally, in-depth genomic and morphological studies are still needed. In this study, to provide genomic data for further investigations of culturing techniques and the biological functions of Morchella sextelata (M. sextelata), de novo genome sequencing was carried out on the Illumina HiSeq. 4000 platform using both the Illumina 150 and PacBio systems. The final estimated genome size of M. sextelata was 52.93 Mb, containing 59 contigs and a GC content of 47.37%. A total of 9,550 protein-coding genes were annotated. In addition, the repeat sequences, gene components and gene functions were analyzed using various databases. Furthermore, the secondary metabolite gene clusters and the predicted structures of their products were analyzed. Finally, a genomic comparison of different species of Morchella was performed.

Characterization of Partial Gene Deletions in Type III von Willebrand Disease with Alloantibody Inhibitors

1994 ◽  
Vol 72 (02) ◽  
pp. 180-185 ◽  
Author(s):  
David J Mancuso ◽  
Elodee A Tuley ◽  
Ricardo Castillo ◽  
Norma de Bosch ◽  
Pler M Mannucci ◽  
...  
Keyword(s):  
Von Willebrand Factor ◽  
Von Willebrand Disease ◽  
Pcr Analysis ◽  
Gene Deletions ◽  
Factor Gene ◽  
Type Iii ◽  
Large Deletions ◽  
Von Willebrand ◽  
Willebrand Factor

Summaryvon Willebrand factor gene deletions were characterized in four patients with severe type III von Willebrand disease and alloantibodies to von Willebrand factor. A PCR-based strategy was used to characterize the boundaries of the deletions. Identical 30 kb von Willebrand factor gene deletions which include exons 33 through 38 were identified in two siblings of one family by this method. A small 5 base pair insertion (CCTGG) was sequenced at the deletion breakpoint. PCR analysis was used to detect the deletion in three generations of the family, including two family members who are heterozygous for the deletion. In a second family, two type III vWD patients, who are distant cousins, share an -56 kb deletion of exons 22 through 43. The identification and characterization of large vWF gene deletions in these type III vWD patients provides further support for the association between large deletions in both von Willebrand factor alleles and the development of inhibitory alloantibodies.

Acanthamoeba Species in Tap Water, Egypt

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Ahmad Z Al-Herrawy ◽  
Mohamed A Marouf ◽  
Mahmoud A. Gad
Keyword(s):  
Water Samples ◽  
Tap Water ◽  
Pcr Analysis ◽  
Pulmonary Infections ◽  
Clinical Syndromes ◽  
Acanthamoeba Species ◽  
Amebic Encephalitis ◽  
Acanthamoeba Culbertsoni ◽  
Autumn And Winter

Genus Acanthamoeba causes 3 clinical syndromes amebic keratitis, granulomatous amebic encephalitis and disseminated granulomatous amebic disease (eg, sinus, skin and pulmonary infections). A total of 144 tap water samples were collected from Giza governorate, Egypt. Samples were processed for detection of Acanthamoeba species using non-nutrient agar (NNA) and were incubated at 30oC. The isolates of Acanthamoeba were identified to species level based on the morphologic criteria. Molecular characterization of the Acanthamoeba isolates to genus level was performed by using PCR. The obtained results showed that the highest occurrence percentage of Acanthamoeba species in water samples was observed in summer season (38.9%), then it decreased to be 30.6% in spring and 25% in each of autumn and winter. PCR analysis showed that 100% of 43 Acanthamoeba morphologically positive samples were positive by genus specific primer. In the present study eight species of Acanthamoeba can be morphologically recognized namely Acanthamoeba triangularis, Acanthamoeba echinulata, Acanthamoeba astronyxis, Acanthamoeba comandoni, Acanthamoeba griffini, Acanthamoeba culbertsoni, Acanthamoeba quina and Acanthamoeba lenticulata. In conclusion, the most common Acanthamoeba species in tap water was Acanthamoeba comandoni

scholarly journals Characterization of De Novo Synthesized GPCRs Supported in Nanolipoprotein Discs

PLoS ONE ◽  
2012 ◽  
Vol 7 (9) ◽  
pp. e44911 ◽  
Author(s):  
Tingjuan Gao ◽  
Jitka Petrlova ◽  
Wei He ◽  
Thomas Huser ◽  
Wieslaw Kudlick ◽  
...  
Keyword(s):  
De Novo

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

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