KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences

Zhang, Zhang

doi:10.1101/2021.11.25.469998

Cited by 13 publications

(8 citation statements)

References 40 publications

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“…To validate the accuracy of the identification of the subgenome, we concatenated all individual alignments of orthologous gene triplets headto-tail to form microchromosomes and build no-root trees using PHYLIP v3.69 (https://evolution.gs.washington.edu/phylip.html). Then, we calculated the Ks values using KaKs_Calculator v2.0 (Zhang, 2022) and analyzed the Ks distributions of P. hallii and the broomcorn millet subgenomes on nine chromosome sets, which confirmed that the identification of the subgenomes was accurate. The divergence time of the subgenomes was estimated using the Ó 2022 Society for Experimental Biology and John Wiley & Sons Ltd., The Plant Journal, (2023), 113, 787-801 distribution of Ks of the homologous genes with the formula T = Ks/2μ, where T is the divergence time, Ks is the peak value of the synonymous substitution rate and μ is the neutral mutation rate of the species.…”

Section: Subgenome Identification and Estimation Of Tetraploidization...mentioning

confidence: 68%

Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome

et al. 2023

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SUMMARY Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops, and is a valuable resource to secure food diversity and combat drought stresses under the global warming scenario. However, due to the absence of extant diploid progenitors, the polyploidy genome of broomcorn millet remains poorly understood. Here, we report the chromosome‐scale genome assembly of broomcorn millet. We divided the broomcorn millet genome into two subgenomes using the genome sequence of Panicum hallii, a diploid relative of broomcorn millet. Our analyses revealed that the two subgenomes diverged at ~4.8 million years ago (Mya), while the allotetraploidization of broomcorn millet may have occurred about ~0.48 Mya, suggesting that broomcorn millet is a relatively recent allotetraploid. Comparative analyses showed that subgenome B was larger than subgenome A in size, which was caused by the biased accumulation of long terminal repeat retrotransposons in the progenitor of subgenome B before polyploidization. Notably, the accumulation of biased mutations in the transposable element‐rich subgenome B led to more gene losses. Although no significant dominance of either subgenome was observed in the expression profiles of broomcorn millet, we found the minimally expressed genes in P. hallii tended to be lost during diploidization of broomcorn millet. These results suggest that broomcorn millet is at the early stage of diploidization and that mutations likely occurred more on genes that were marked with lower expression levels.

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Section: Subgenome Identification and Estimation Of Tetraploidization...mentioning

confidence: 68%

Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome

et al. 2023

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“…The number of non‐synonymous substitutions per non‐synonymous site, dN, and the number of synonymous substitutions per synonymous site, dS, for each PDCoV S gene was calculated using NG, MS, GY‐HKY, and MA method in KaKs_Calculator 3.0 (Z. Zhang, 2022).…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of codon usage patterns of porcine deltacoronavirus and its host adaptability

Peng

Zhang

et al. 2022

Transbounding Emerging Dis

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The porcine deltacoronavirus (PDCoV) is a newly discovered pig enteric coronavirus that can infect cells from various species. In Haiti, PDCoV infections in children with acute undifferentiated febrile fever were recently reported. Considering the great potential of inter‐species transmission of PDCoV, we performed a comprehensive analysis of codon usage patterns and host adaptation profiles of 54 representative PDCoV strains with the spike (S) gene. Phylogenetic analysis of the PDCoV S gene indicates that the PDCoV strains can be divided into five genogroups. We found a certain codon usage bias existed in the S gene, in which the synonymous codons are often ended with U or A. Heat map analysis revealed that all the PDCoV strains shared a similar codon usage trend. The PDCoV S gene with a dN/dS ratio lower than 1 reveals a negative selection on the PDCoV S gene. Neutrality analysis showed that natural selection is the dominant force in shaping the codon usage bias of the PDCoV S gene. Unexpectedly, host adaptation analysis reveals a higher adaptation level of PDCoV to Homo sapiens and Gallus gallus than to Sus scrofa. Compared to the USA lineage, the PDCoV strains in the Early China lineage and Thailand lineage were less adapted to their hosts, which indicates that the evolutionary process plays an important role in the adaptation ability of PDCoV. These findings of this study add to our understanding of PDCoV's evolution, adaptability, and inter‐species transmission.

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“…Multiple sequence alignment within LFY a, LFY b and LFY c/d were performed with TranslatorX (Abascal et al, 2010) in combination with MUSCLE (Edgar, 2004), respectively. Pairwise Ka, Ks and Ka/Ks values were calculated using KaKs_Calculator 3.0 (Zhang, 2022).…”

Section: Methodsmentioning

confidence: 99%

The roles and evolution of the four LEAFY homologues in floral patterning and leaf development in woodland strawberry

Zhang

Kan

et al. 2022

Preprint

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The plant-specific transcription factor LEAFY (LFY), generally maintained as a single copy gene in most angiosperm species, plays critical roles in flower and leaf development. However, wild strawberry Fragaria vesca possesses four LFY homologues in the genome, their respective functions and evolution remain unknown. Through chemical mutagenesis screen, we identified two allelic mutations in one of the four LFY homologues, FveLFYa, in F. vesca, causing homeotic conversion of floral organs and reiterative outgrowth of ectopic florets. Both CRISPR-knockout and transgenic rescue confirmed the identity of FveLFYa. Ectopic expression of FveLFY homologues in Arabidopsis lfy-5 mutant revealed that only FveLFYa and FveLFYb can rescue the flower defects and induce solitary flowers in leaf axils. Disruption of FveLFYc, the second most abundantly expressed LFY homologue, caused no obvious morphology phenotypes in F. vesca. FveLFYb and FveLFYd are barely expressed. Expression of FveAP1, homologue of the well-known LFY target AtAP1, is not changed in the fvelfya flowers, possibly caused by an absence of any FveLFYa binding site in its promoter. Loss of Axillary Meristems encodes a GRAS transcription factor essential for stamen initiation. The ectopic florets are eliminated in fvelfya lam, suggesting that LAM is required for floret production. Moreover, approximately 30% of mature leaves have smaller or fewer leaflets in fvelfya. Among these homologues, only FveLFYa is syntenic to the homologues in other species. Overall, the detailed analyses of the four LFY homologues in woodland strawberry demonstrate that only FveLFYa plays crucial roles in floral patterning with rewired gene network.

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KaKs_Calculator 3.0: calculating selective pressure on coding and non-coding sequences

Cited by 13 publications

References 40 publications

Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome

Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome

Comprehensive analysis of codon usage patterns of porcine deltacoronavirus and its host adaptability

The roles and evolution of the four LEAFY homologues in floral patterning and leaf development in woodland strawberry

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