scholarly journals Genome-wide analysis of the aquaporin genes in melon (Cucumis melo L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alvaro Lopez-Zaplana ◽  
Juan Nicolas-Espinosa ◽  
Micaela Carvajal ◽  
Gloria Bárzana
Keyword(s):  
Cucumis Melo ◽  
Evolutionary Relationship ◽  
Physiological Importance ◽  
Genome Wide ◽  
Related Plant ◽  
Complete Set ◽  
The Individual ◽  
Almost All ◽  
Relationship Of ◽  
Cucumis Melo L

AbstractMelon (Cucumis melo L.) is a very important crop throughout the world and has great economic importance, in part due to its nutritional properties. It prefers well-drained soil with low acidity and has a strong demand for water during fruit set. Therefore, a correct water balance—involving aquaporins—is necessary to maintain the plants in optimal condition. This manuscript describes the identification and comparative analysis of the complete set of aquaporins in melon. 31 aquaporin genes were identified, classified and analysed according to the evolutionary relationship of melon with related plant species. The individual role of each aquaporin in the transport of water, ions and small molecules was discussed. Finally, qPCR revealed that almost all melon aquaporins in roots and leaves were constitutively expressed. However, the high variations in expression among them point to different roles in water and solute transport, providing important features as that CmPIP1;1 is the predominant isoform and CmTIP1;1 is revealed as the most important osmoregulator in the tonoplast under optimal conditions. The results of this work pointing to the physiological importance of each individual aquaporin of melon opening a field of knowledge that deserves to be investigated.

scholarly journals Genome-wide variations of SARS-CoV-2 infer evolution relationship and transmission route

2020 ◽  
Author(s):  
Lehai Zhang ◽  
Shifu Wang ◽  
Qian Ren ◽  
Junjie Yang ◽  
Yanqin Lu ◽  
...  
Keyword(s):  
Molecular Detection ◽  
Detection Efficiency ◽  
Evolutionary Relationship ◽  
Clinical Manifestations ◽  
Coding Region ◽  
Gene Coding ◽  
Genome Wide ◽  
Group A ◽  
Group B ◽  
Relationship Of

AbstractIn the epidemic evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the issues of mutation, origin, typing and the effect of mutation on molecular detection remain to be unrevealed. In order to identify the evolutionary relationship of SARS-CoV-2 and evaluate the detection efficiency of primers that are currently used in different countries, we retrieved genomic sequences of 373 SARS-CoV-2 strains from multiple databases and performed genome-wide variation analysis. According to the nucleotide C28144T variation, the SARS-CoV-2 can be divided into group A (117 strains) and group B (256 strains). The spike protein gene (S gene) coding region 1841 (total 23403) A1841G, formed a B1 subgroup (40 strains) in group B, of which 30 strains were from European and American countries in March (especially Washington, USA). These mutations are likely to be influenced by the environment or the immunization selection pressure of different populations. Although the mutation is not in the receptor binding region (RBD) and alkaline cleavage region, it may also affect the ability of transmission and pathogenicity; however, the significance is not yet clear. As the ratio of A / B strains in the epidemic months showed an increasing trend (0.35: 1 in January, 0.62: 1 in February and 0.76: 1 in March), it seems that the transmissibility of group A strains becomes stronger with time. Based on the variation of 11 nucleotide sites during the epidemic process, it is speculated that the Washington strain is more like an ancestor type, and the Wuhan strain is the offspring of the group A virus strain. By comparing the detection capabilities of primers in different countries, the SARS-CoV-2 nucleotide variation may only affect molecular detection of very few strains. The differences in the transmissibility, pathogenicity and clinical manifestations of different types of strains require further investigations.

Genome-wide identification, characterization, and expression analysis related to autotoxicity of the GST gene family in Cucumis melo L.

2020 ◽  
Vol 155 ◽  
pp. 59-69
Author(s):  
Jingrong Wang ◽  
Zhengda Zhang ◽  
Jinghua Wu ◽  
Xiaoyun Han ◽  
Gefu Wang-Pruski ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Cucumis Melo ◽  
Genome Wide ◽  
Cucumis Melo L

Genome-wide characterization of two-component system (TCS) genes in melon (Cucumis melo L.)

2020 ◽  
Vol 151 ◽  
pp. 197-213 ◽  
Author(s):  
Panjing Liu ◽  
Shuoshuo Wang ◽  
Xiangfei Wang ◽  
Xiaoyu Yang ◽  
Qiang Li ◽  
...  
Keyword(s):  
Cucumis Melo ◽  
Two Component System ◽  
Component System ◽  
Genome Wide ◽  
Two Component ◽  
Cucumis Melo L

scholarly journals Genome-Wide GRAS Gene Family Analysis Reveals the Classification, Expression Profiles in Melon (Cucumis melo L.)

Phyton ◽  
2021 ◽  
Vol 90 (4) ◽  
pp. 1161-1175
Author(s):  
Yanfei Bi ◽  
Bin Wei ◽  
Ying Meng ◽  
Zhongzhao Li ◽  
Zhenghui Tang ◽  
...  
Keyword(s):  
Gene Family ◽  
Cucumis Melo ◽  
Expression Profiles ◽  
Genome Wide ◽  
Family Analysis ◽  
Cucumis Melo L ◽  
Gras Gene

scholarly journals Genome-wide protein phylogenies for four African cichlid species

2017 ◽  
Author(s):  
Ajay Ramakrishnan Varadarajan ◽  
Rohini Mopuri ◽  
J. Todd Streelman ◽  
Patrick T. McGrath
Keyword(s):  
Protein Function ◽  
Evolutionary Relationship ◽  
Trait Variation ◽  
Cichlid Species ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Astatotilapia Burtoni ◽  
African Cichlids ◽  
Relationship Of

ABSTRACTBackgroundThe thousands of species of closely related cichlid fishes in the great lakes of East Africa are a powerful model for understanding speciation and the genetic basis of trait variation. Recently, the genomes of five species of African cichlids representing five distinct lineages were sequenced and used to predict protein products at a genome-wide level. Here we characterize the evolutionary relationship of each cichlid protein to previously sequenced animal species.ResultsWe used the Treefam database, a set of preexisting protein phylogenies built using 109 previously sequenced genomes, to identify Treefam families for each protein annotated from four cichlid species: Metriaclima zebra, Astatotilapia burtoni, Pundamilia nyererei and Neolamporologus brichardi. For each of these Treefam families, we built new protein phylogenies containing each of the cichlid protein hits. Using these new phylogenies we identified the evolutionary relationship of each cichlid protein to its nearest human and zebrafish protein. This data is available either through download or through a webserver we have implemented.ConclusionThese phylogenies will be useful for any cichlid researchers trying to predict biological and protein function for a given cichlid gene, understanding the evolutionary history of a given cichlid gene, identifying recently duplicated cichlid genes, or performing genome-wide analysis in cichlids that relies on using databases generated from other species.

scholarly journals Hubungan Filogenetik Intraspesies Cucumis melo L. berdasarkan DNA Barcode Gen matK

2018 ◽  
Vol 2 (2) ◽  
Author(s):  
Dewi Retnaningati
Keyword(s):  
Maximum Parsimony ◽  
Cucumis Melo ◽  
Dna Barcode ◽  
Evolutionary Relationship ◽  
Evolutionary Genetics ◽  
Barcode Dna ◽  
Cucumis Melo L

Rekonstruksi hubungan evolusi (evolutionary relationship) dari kelompok organisme, salah satunya yaitu hubungan filogenetik, merupakan hal penting dalam kajian sistematika yang dapat digunakan sebagai landasan untuk melakukan penelitian-penelitian komparatif. Pemikiran dasar penggunaan sekuen DNA dalam studi filogenetika (DNA Barcode) adalah bahwa terjadi perubahan basa nukleotida menurut waktu, sehingga akan dapat diperkirakan kecepatan evolusi yang terjadi dan akan dapat direkonstruksi hubungan evolusi antara satu kelompok organisme dengan yang lainnya. Gen MatK adalah gen populer yang digunakan dalam DNA Barcode tanaman di dunia, maka penyusunan DNA barcode berdasarkan gen MatK diharapkan dapat menunjukkan karakter molekuler yang spesifik dari melon. Analisis filogenetik dilakukan oleh paket perangkat lunak MEGA (Molecular Evolutionary Genetics Analysis) berdasarkan metode Maximum Parsimony (MP). Gen matK dalam melon mengandung lebih banyak basa A dan T daripada basa G dan C. Hasil analisis menunjukkan ada 43 situs variatif dan 6 situs Parsimony dari 576 bp gen matK yang diaggregasi. Indeks konsistensi adalah (0,777778), indeks retensi adalah (0,777778), dan indeks komposit adalah 0,744681 (0,604938) untuk semua situs dan situs parsimoni-informatif (dalam kurung). Genus Cucumis adalah kelompok monofiletik. Analisis karakter molekuler berdasarkan barcode DNA dari gen matK menunjukkan bahwa gen ini mampu membedakan variasi intraspesies dalam melon.

On the occurrence, distribution, taxonomy and genepool relationship of Cucumis callosus (Rottler) Cogn., the wild progenitor of Cucumis melo L. from India

2012 ◽  
Vol 60 (3) ◽  
pp. 1037-1046 ◽  
Author(s):  
K. Joseph John ◽  
Sheen Scariah ◽  
V. A. Muhammed Nissar ◽  
M. Latha ◽  
S. Gopalakrishnan ◽  
...  
Keyword(s):  
Cucumis Melo ◽  
Wild Progenitor ◽  
Relationship Of ◽  
Cucumis Melo L
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