Insights into Immune Gene Prediction and Function Through the Evolutionary History of ADF Gene Family
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Abstract
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ACTIN DEPOLYMERIZING FACTORS (ADFs) are key regulators of actin cytoskeletal dynamics and plant immunity.
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We predicted the potential immune-associated function of 38 genes from Arabidopsis using gene expression values from 24,123 RNA-Seq datasets and 34 single-cell datasets through machine learning algorithms.
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The evolutionary relationships of ADF family members from 38 eukaryotic species were evaluated, including an assessment of the sub-function(s) of these members.
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Our results show that the ADF clade in plant and other kingdoms are separated, with ADF3, 5, 7, 9, and 10 possessing collinear relationships within species, and ADF 2,3,4,6,7, and 10 possessing evolved, new, sub-functions related to response to Fe, copper-deficiency, and ABA signaling in Arabidopsis . Expanded, multiple, roles for ADF1,4, and 6 were also identified.
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This study not only provides an analysis of the expanded role for the ADF family of genes/proteins, but also provides insight into, and a framework for, the identification and study of the evolutionary history of genes having putative roles in immune signaling.
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Introduction
This is an interesting deep dive into the ADF family, particularly in Arabidopsis! There's a ton of data and I appreciate the open code!
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Dataset S1
Are these datasets provided somewhere? I might have missed them, but couldn't find them!
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Fig
Are motifs 3 and 6 related since they're both green?
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The longest genome sequence is ADF (AT3G45990; Putative), at 3,359bp, and the shortest is 945 bp (ADF11). The average length is 1,490 bp for all ADFs. Next, we analyzed the physicochemical properties of ADF proteins, including amino acid length, molecular weight (MW), theoretical pI, aliphatic index, and the grand average of hydropathy (GRAVY) (Table 1). The amino acids length of each ADF was found to be similar, ranging from 133 to 150. The molecular weight varied from 15,820 kDa (AtADF7) to 17.942 kDa (ADF2), while the GRAVY of all ADF genes were below zero. The maximum aliphatic index value was 83.53 (AtADF4), and the minimum value was 70.07 (AtADF6). The results of hydrophilicity and hydrophobicity analysis indicated that all ADF family proteins are hydrophilic proteins.
Can you draw any sort of hypotheses from this analysis? It's …
The longest genome sequence is ADF (AT3G45990; Putative), at 3,359bp, and the shortest is 945 bp (ADF11). The average length is 1,490 bp for all ADFs. Next, we analyzed the physicochemical properties of ADF proteins, including amino acid length, molecular weight (MW), theoretical pI, aliphatic index, and the grand average of hydropathy (GRAVY) (Table 1). The amino acids length of each ADF was found to be similar, ranging from 133 to 150. The molecular weight varied from 15,820 kDa (AtADF7) to 17.942 kDa (ADF2), while the GRAVY of all ADF genes were below zero. The maximum aliphatic index value was 83.53 (AtADF4), and the minimum value was 70.07 (AtADF6). The results of hydrophilicity and hydrophobicity analysis indicated that all ADF family proteins are hydrophilic proteins.
Can you draw any sort of hypotheses from this analysis? It's a lot of data and I'm just wondering exactly what it all means in the context of the rest!
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cantates
I think this is maybe supposed to be "candidates"?
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ADF subclass I in Arabidopsis includes ADF1, ADF2, ADF3, and ADF4,
Is it known if any of these ADF proteins have overlapping functions? Can they compensate for another if needed?
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As shown in Fig 2b,
I don't see a Fig 2b.
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divided into three clusters, as shown in Fig. 3a
The clusters aren't super obvious to me, could you maybe highlight the 3 clusters in the figure?
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ADF genes with other homologous genes,
I'm curious how similar these genes are within organisms and between organisms. Do you have sequence alignments or sequence identities you could share to give an idea?
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38 eukaryotic species with 1 bacteria species as outgroup. The protein sequence data of selected species, which presents each phylum of eukaryotes, were download from Ensembl and Ensembl Plants database
Apart from choosing one to represent each phylum of eukaryotes, how did you pick these specific species? You might have this somewhere up ahead, but it could also be nice to have a table of these species and the other set of 8 species.
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With 25,498 predicted protein-coding genes, 69% of these have predicted functions based on sequence comparisons and similarities to known proteins. However, approximately only 9% of the genes have been studied or characterized through experimental methods. The remaining 30% remain without any predicted function (Wigge and Weigel, 2001).
I really like the inclusion of the stats to highlight the need for characterization of these proteins! This is no big deal but the last sentence of this chunk (The remaining 30% remain without any...) has slightly odd wording. Maybe something like "the remaining 30% lack functional annotation or characterization"?
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