Data from: Evolutionary insights of interferon Lambda genes in Tetrapods
Data files
Jul 30, 2024 version files 3.09 MB
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JEB-2024-0086R.2.zip
3.09 MB
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README.md
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Abstract
Type III interferon, also known as interferon lambda is an innate antiviral protein. We retrieved the IFN-λ and their receptors’ sequences belonging to forty-two tetrapod species and conducted computational evolutionary analysis to understand the gene’s diversity. The CNV of IFN-λ was determined through qPCR in Indian cattle and buffalo. The tetrapod species feature intron-containing type-III IFN genes. Some reptiles and placental mammal have two IFN-λ loci. While marsupials, monotremes, and birds have a single IFN-λ locus. Some of the placental mammals and amphibians exhibit multiple IFN-λ genes as intron-less and intron-containing. Placental mammals typically possess three to four functional IFN-λ genes, some of them lack signal peptides. IFN-λ of these tetrapod species formed three major clades. Mammalian IFN-λ4 appears as an ancestral form, with syntenic conservation in most mammalian species. The intron-less IFN-λ1 and both the type III IFN receptors have conserved synteny in tetrapod. Purifying selection was noted in their evolutionary analysis that plays a crucial role in minimizing genetic diversity and maintaining the integrity of biological function. This indicates that these proteins have successfully retained their biological function and indispensability, even in the presence of the type I IFNs. The expansion of IFN-λ genes in amphibians and camels have led to the evolution of multiple IFN-λ. The CNV can arise from gene duplication and conversion events. The qPCR-based absolute quantification resulted that IFN-λ3 and IFN-λ4 have more than one copy in buffalo (Murrah) and six cattle breeds (Sahiwal, Tharparkar, Kankrej, Red Sindhi, Jersey and Holstein Friesian). Overall, these findings highlight the evolutionary diversity and functional significance of IFN-λ in tetrapod species.
README: Data from: Evolutionary Insights of Interferon Lambda Genes in Tetrapods
#Abbreviations used in JEB-2024-0086.R2 sypplementary Domain prediction.csv, JEB-2024-0086.R2 sypplementary Gene details.csv, JEB-2024-0086.R2 Supplementary Signal peptide prediction.csv
IFNL/IFN-λ- interferon lambda
IFNLR1- Interferon Lambda Receptor 1
IL10-R2/β- Interleukin 10 Receptor subunit beta
IL28A- interleukin 28A domain
Brief description of the analysis:
The Type III Interferon (interferon lambda) gene encoding Protein and nucleotide sequences of tetrapods were collected
from the public databases like NCBI, UCSC genome browser, and Ensembl (sequence details are relegated in ###JEB-2024-0086.R2 sypplementary Gene details.csv). The tetrapod species included in this study belonged
to amphibians (African clawed frog, Tropical clawed frogs, and common toad), reptiles (Chinese alligator, green anole,
American alligator, Chinese soft-shelled turtle, Pond turtle, and painted turtle), birds (Chicken and Pheasant), and mammals
[monotreme (Platypus); marsupials (Opossum, common brush tail, and common wombat); and placental (human, rhesus monkey, gorilla,
chimpanzee, mouse, rats, cats, tigers, hyaena, arctic fox, dogs, pigs, camels, horses, donkeys, African elephant, rhinoceros,
Indian flying foxes, round leaf bats, mouse-eared bat, taurine cattle, buffalo, indigenous cattle, oryx, sheep, and goats] as mentioned in method section of the manuscript.
Some of the sequences were annotated using FGENESH program. The evolutionary analysis of IFNL in tetrapods included phylogenetic
analysis, synteny analysis, duplication analysis, selection pressure analysis and copy number variotion analysis in some species through PCR as mentioned in method section of the manuscript.
File list and description
JEB-2024-0086.R2 sypplementary Domain prediction.csv
Conserved domain found in type III IFN sequences as mentioned in the manuscript is relegated to JEB-2024-0086.R2 sypplementary Domain prediction.csv.
JEB-2024-0086.R2 sypplementary Gene details.csv
The type III interferon protein and nucleotide sequences retrieved from the public database ans used for the evolutionary study of Interferon Lambda Genes in Tetrapods are relagated in JEB-2024-0086.R2 sypplementary Gene details.csv.
n/a = not applicable
JEB-2024-0086.R2 Supplementary Signal peptide prediction.csv
The type III interferon protein's signal peptide predicted in SignalP6.0 is relegated in JEB-2024-0086.R2 Supplementary Signal peptide prediction.csv
n/a = not applicable
JEB-2024-00086.R2 Supplementary.PDF
The supplementary material of Evolutionary Insights of Interferon Lambda Genes in Tetrapods is relegated in JEB-2024-00086.R2 Supplementary.PDF.
The phylogenetic tree of IFNLR1 and IL10R2 using the sequences presented in JEB-2024-0086.R2 sypplementary Gene details.csv are presented as Figure S1 and Figure S2.
The Figure S1 and Figure S2 represents the selection pressure acting on type III interferon and their receptor analysed in PAML, FEL, and FUBAR using their domain (EB-2024-0086.R2 sypplementary Domain prediction.csv).
Supplementary Table S1 and table S2: selecton pressure analysis of type III interferon and its receptor genes using PAML and Selecton Pressure analysis of type III IFN and its receptor using FEL and FUBAR of Data Monkey Server.
The Figure S5 represents the synteny of IFNLR1 and IL10-RB using informations from JEB-2024-0086.R2 sypplementary Gene details.csv.
The Figure S6 represents the duplication of type III interferon genes in tetrapods constructed in MEGA Duplication Wizard using informations from JEB-2024-0086.R2 sypplementary Gene details.csv.
The Figure S7 represents the standard plots standard curves of IFN-λ3, IFN-λ4, CSN2 (single copy reference), and IFN-β, details are presented in the results in the manuscript ' Evolutionary Insights of Interferon Lambda Genes in Tetrapods'. The primers used for copy number variation analysis is presented in Table S3.
The Supplementary text 1 represents the multple sequence alignment of Type III Interferon proteins of 38 tetrapod species.
Supplementary Text describs the Genomic DNA preparation, Determination of absolute copy number through standard curve method, Construction of standard curve,and Quantitative PCR to determine the copy number of unknown sample.
The Table S4 shows the Duplication analysis in DupGen_finder for cattle and buffalo genes IFN-λ genes, to correlate with copy number variation.
##The sequences used for this analysis is relegated to JEB-2024-0086.R2 Dryad.zip.
Methods
The Type III Interferon (interferon lambda) gene encoding Protein and nucleotide sequences of tetrapods were collected from the public databases like NCBI, UCSC genome browser, and Ensembl. The tetrapod species included in this study belonged to amphibians (African clawed frog, Tropical clawed frogs, and common toad), reptiles (Chinese alligator, green anole, American alligator, Chinese soft-shelled turtle, Pond turtle, and painted turtle), birds (Chicken and Pheasant), and mammals [monotreme (Platypus); marsupials (Opossum, common brush tail, and common wombat); and placental (human, rhesus monkey, gorilla, chimpanzee, mouse, rats, cats, tigers, hyaena, arctic fox, dogs, pigs, camels, horses, donkeys, African elephant, rhinoceros, Indian flying foxes, round leaf bats, mouse-eared bat, taurine cattle, buffalo, indigenous cattle, oryx, sheep, and goats]. Some of the sequences were annotated using FGENESH program. The evolutionary analysis of IFNL in tetrapods included phylogenetic analysis, synteny analysis, duplication analysis, selection pressure analysis and copy number variotion analysis in some species through PCR.