scholarly journals Complete genome sequencing of SARS-CoV-2 strains: A pilot survey in Palestine reveals spike mutation H245N

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Amer Al-Jawabreh ◽  
Suheir Ereqat ◽  
Kamal Dumaidi ◽  
Hanan Al-Jawabreh ◽  
Abedelmajeed Nasereddin
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genome Sequencing ◽  
Rna Virus ◽  
Haplotype Network ◽  
Health Concern ◽  
Diversity Analysis ◽  
High Genetic Diversity ◽  
Genetic Diversity Analysis ◽  
First Time

Abstract Objectives SARS-CoV-2, severe respiratory syndrome coronavirus-2, is an RNA virus that emerged from China sweeping the globe in the form of a pandemic that became an international public health concern. This pilot study aimed to describe the genetic variation and molecular epidemiology of SARS-CoV-2 in Palestine in fall 2020. Results To achieve these aims, whole genome sequencing of SARS-CoV-2, phylogenetic analysis, haplotype networking and genetic diversity analysis were performed. These analyses revealed a unique spike mutation H245N that has never been reported before. The phylogenetic analysis depicted that three clusters existed in Palestinian SARS-CoV-2 genome sequences, in which cluster-I comprised the majority of clusters by 90%. Congruently, the haplotype network analysis depicted the same three clusters with a total of 39 haplotypes. The genetic diversity analysis showed that Cluster-I is highly diverse as confirmed by statistically significant mutation rate indices, Tajima’s D and Fu-Li’s-F tests (− 2.11 and 2.74, respectively), highest number of mutations (Eta = 120), highest number of haplotypes (h = 17), and highest average number of nucleotide differences between any two sequences (S = 118). The study confirmed the high genetic diversity among the Palestinian of SARS-CoV-2 which possessed high number of mutations including one which was reported for the first time.

scholarly journals Molecular diversity analysis of genotypes from four Aegilops species based on retrotransposon–microsatellite amplified polymorphism (REMAP) markers

2020 ◽  
Author(s):  
Justyna Leśniowska-Nowak ◽  
Sylwia Okoń ◽  
Aleksandra Wieremczuk
Keyword(s):  
Genetic Diversity ◽  
Molecular Diversity ◽  
Crop Improvement ◽  
Diversity Analysis ◽  
Aegilops Species ◽  
Powerful Method ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Genetic Diversity Analysis ◽  
Valuable Source

Abstract Genetic diversity analysis is an important tool in crop improvement. Species with high genetic diversity are a valuable source of variation used in breeding programs. The aim of this study was to assess the genetic diversity of four species belonging to the genus Aegilops, which are often used to expand the genetic variability of wheat and triticale. Forty-five genotypes belonging to the genus Aegilops were investigated. Within- and among-species genetic diversity was calculated based on REMAP (retrotransposon–microsatellite amplified polymorphism) molecular markers. Obtained results showed that REMAP markers are a powerful method for genetic diversity analysis, which produces a high number of polymorphic bands (96.09% of total bands were polymorphic). Among tested genotypes, Ae. crassa and Ae. vavilovii showed the highest genetic diversity and should be chosen as a valuable source of genetic variation.

scholarly journals Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis

PLoS ONE ◽  
2011 ◽  
Vol 6 (7) ◽  
pp. e21743 ◽  
Author(s):  
Maximo Rivarola ◽  
Jeffrey T. Foster ◽  
Agnes P. Chan ◽  
Amber L. Williams ◽  
Danny W. Rice ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Sequencing ◽  
Castor Bean ◽  
Diversity Analysis ◽  
Genetic Diversity Analysis ◽  
Organelle Genome

scholarly journals Genetic diversity analysis of daluga (Cyrtosperma merkusii) using Sequence-Related Amplified Polymorphism in Siau, Sangihe and Talaud Islands, North Sulawesi, Indonesia

2018 ◽  
Vol 19 (6) ◽  
pp. 2374-2380
Author(s):  
INA ERLINAWATI ◽  
ABINAWANTO ABINAWANTO ◽  
ANDI SALAMAH ◽  
RUGAYAH RUGAYAH
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Nutritional Value ◽  
Island Population ◽  
Diversity Analysis ◽  
Mean Values ◽  
Genetic Diversity Analysis ◽  
North Sulawesi ◽  
Polymorphic Bands ◽  
First Time

Erlinawati I, Abinawanto, Salamah A, Rugayah. 2018. Genetic diversity analysis of daluga (Cyrtosperma merkusii) using Sequence-Related Amplified Polymorphism in Siau, Sangihe and Talaud Islands, North Sulawesi, Indonesia. Biodiversitas 19: 2374-2380. Daluga or the giant swamp taro (Cyrtosperma merkusii (Hassk.) Schott, a member of Araceae, is one of the minor tuber crops in Indonesia. It has high nutritional value for alternative food. Sequences-Related Amplified Polymorphism (SRAP) primers combinations were used for the first time to assess the genetic diversity among 36 of daluga accessions from several locations in Siau, Sangihe and Talaud islands, North Sulawesi, Indonesia. All of the samples were successfully extracted from silica-gel dried leaves using CTAB methods with minor modifications. Using six SRAP primer combinations, a total of 80 DNA fragments were yielded, varied from 75-1500 bp. The scoring of the fragments resulted in 68 (85.03%) polymorphic bands. Amongst four populations studied, Siau Island population has the highest level of genetic variation with mean values of Na = 1.9375±0.2436, Ne = 1.6409 ± 0.3255, PPL = 93.75%, H = 0.3614 ± 0.1516 and I = 0.5299 ± 0.1978. Meanwhile, Salibabu, Talaud Island population has the lowest level of genetic variation with mean values of Na = 1.5125 ± 0.5030, Ne = 1.3075 ± 0.3723 , PPL = 51.25%, H = 0.1800 ± 0.1989 and I = 0.2700 ± 0.2855. The high of polymorphic bands were generated by SRAP markers suitable for further analysis method in applied and basic of the genetic study on Cyrtosperma species and also related genera. This new genetic information can be used for baseline data for further research especially to improving the variation of daluga and for the conservation of daluga in the future.

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

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