DArTSNPbased genetic diversity analyses in cassava (Manihot esculenta) genotypes sourced from different regions revealed high level of diversity within population DOI

A. NeimSemman,

A. Abush Tesfaye,

Y. Ismael Rabbi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 18, 2024

Abstract Understanding the extent of genetic diversity is a pre requisite in cassava breeding program due to its, available broad base crop and have great opportunity for its improvement. This study was designed assess 184 germplasm sourced from International Institute Tropical Agriculture (IITA) previous collection Jimma Agricultural Research Center (JARC) by using DArTSNPs markers. The data were subjected imputation filtering minor allele frequency 0.01, 0.95 major TASSEL Beagle. resultants 9,310 informative SNPs retained used perform analysis molecular variance (AMOVA), diversity, population structure, dissimilarity-based clustering tested germplasm. results AMOVA revealed higher variation within (91.3%) than between (8.7%) populations. high average PIC (0.44), He (0.50), (0.61) (0.28) showed existence Population structure grouped panels into six structures with admixtures. Similarly, principal component analysis, factor cluster apparently divided clusters. Both introduced locally collected formed three clusters, each creating some mixes genotypes, indicating that alleles sharing common ancestral background. overall results, studied genotypes significant variations, which can render association mapping technical conservation purposes.

Language: Английский

Phylogenetic structure of tuna (Thunnus spp.) based on mitochondrial COI DNA in Indonesian and Australian waters DOI Creative Commons

Jean Claudia De Soysa,

Satrio Hani Samudra,

Siti Zanuba Aisyah

et al.

BIO Web of Conferences, Journal Year: 2025, Volume and Issue: 168, P. 01009 - 01009

Published: Jan. 1, 2025

Tuna ( Thunnus spp.) is a seafood commodity that significantly contributes to country’s foreign exchange. Given the increase in fishing activities, genetic studies have become vital ensure sustainable management. This study analyzed 65 mitochondrial cytochrome oxidase subunit I (COI) DNA sequences were obtained from GenBank and subjected phylogenetic analyses using Bootstrap Neighbor-Joining Model Kimura 2 Parameter Method. Phylogenetic analysis revealed spp. clustered into five clades. had bootstrap value of more than 50%, with largest distance recorded at 0.04 smallest 0.00. Regarding tuna species distribution zones, these findings imply there are no significant differences between Australia Indonesia indicating high connectivity regions.

Language: Английский

Citations

0
Prediction of the effects of the top 10 synonymous mutations from 26645 SARS-CoV-2 genomes of early pandemic phase DOI Creative Commons
Wan Xin Boon,

Boon Zhan Sia,

Chong Han Ng

et al.

F1000Research, Journal Year: 2024, Volume and Issue: 10, P. 1053 - 1053

Published: Sept. 18, 2024

Background The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had led to a global pandemic since December 2019. SARS-CoV-2 is single-stranded RNA virus, which mutates at higher rate. Multiple works been done study nonsynonymous mutations, change protein sequences. However, there little on the effects synonymous may affect viral fitness. This aims predict effect mutations genome. Methods A total 26645 genomic sequences retrieved from Global Initiative Sharing all Influenza Data (GISAID) database were aligned using MAFFT. Then, and their respective frequency identified. secondary structures prediction tools, namely RNAfold, IPknot++ MXfold2 applied structure base pair probabilities was estimated MutaRNA. Relative codon usage (RSCU) analysis also performed measure bias (CUB) SARS-CoV-2. Results 150 mutation identified with highest C3037U in nsp3 ORF1a. Of these top 10 C913U, C3037U, U16176C C18877U mutants show pronounced changes between wild type mutant 3 suggesting have some biological impact These four probabilities. All except more preferred codon, result translation efficiency. Conclusion Synonymous genome structure, changing possibly resulting lab experiments are required validate results obtained analysis.

Language: Английский

Citations

1
Prediction of the effects of the top 10 synonymous mutations from 26645 SARS-CoV-2 genomes DOI Creative Commons
Wan Xin Boon,

Boon Zhan Sia,

Chong Han Ng

et al.

F1000Research, Journal Year: 2024, Volume and Issue: 10, P. 1053 - 1053

Published: Feb. 29, 2024

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had led to a global pandemic since December 2019. SARS-CoV-2 is single-stranded RNA virus, which mutates at higher rate. Multiple works been done study nonsynonymous mutations, change protein sequences. However, there little on the effects synonymous may affect viral fitness. This aims predict effect mutations genome.

Language: Английский

Citations

0
DArTSNPbased genetic diversity analyses in cassava (Manihot esculenta) genotypes sourced from different regions revealed high level of diversity within population DOI

A. NeimSemman,

A. Abush Tesfaye,

Y. Ismael Rabbi

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 18, 2024

Abstract Understanding the extent of genetic diversity is a pre requisite in cassava breeding program due to its, available broad base crop and have great opportunity for its improvement. This study was designed assess 184 germplasm sourced from International Institute Tropical Agriculture (IITA) previous collection Jimma Agricultural Research Center (JARC) by using DArTSNPs markers. The data were subjected imputation filtering minor allele frequency 0.01, 0.95 major TASSEL Beagle. resultants 9,310 informative SNPs retained used perform analysis molecular variance (AMOVA), diversity, population structure, dissimilarity-based clustering tested germplasm. results AMOVA revealed higher variation within (91.3%) than between (8.7%) populations. high average PIC (0.44), He (0.50), (0.61) (0.28) showed existence Population structure grouped panels into six structures with admixtures. Similarly, principal component analysis, factor cluster apparently divided clusters. Both introduced locally collected formed three clusters, each creating some mixes genotypes, indicating that alleles sharing common ancestral background. overall results, studied genotypes significant variations, which can render association mapping technical conservation purposes.

Language: Английский

Citations

0