DOI: 10.5061/dryad.q2bvq83ts
title: Data from: Evolutionary insights of interferon Lambda genes in Tetrapods

description: 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.
description: 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.
description: # 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.