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Gautam D, Sindhu A, Vats A, Rajput S, Rana C, De S. Evolutionary insights of interferon lambda genes in tetrapods. J Evol Biol 2024; 37:1101-1112. [PMID: 39066611 DOI: 10.1093/jeb/voae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/07/2024] [Accepted: 07/25/2024] [Indexed: 07/28/2024]
Abstract
Type III interferon (IFN), also known as IFN-λ, is an innate antiviral protein. We retrieved the sequences of IFN-λ and their receptors from 42 tetrapod species and conducted a computational evolutionary analysis to understand the diversity of these genes. The copy number variation (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 mammals have 2 IFN-λ loci, while marsupials, monotremes, and birds have a single IFN-λ locus. Some placental mammals and amphibians exhibit multiple IFN-λ genes, including both intron-less and intron-containing forms. Placental mammals typically possess 3-4 functional IFN-λ genes, some of them lack signal peptides. IFN-λ of these tetrapod species formed 3 major clades. Mammalian IFN-λ4 appears as an ancestral form, with syntenic conservation in most mammalian species. The intron-less IFN-λ1 and both 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 revealed that IFN-λ3 and IFN-λ4 have more than 1 copy in buffalo (Murrah) and 6 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.
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Affiliation(s)
- Devika Gautam
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, Haryana, India
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonipat, Haryana, India
| | - Anil Sindhu
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonipat, Haryana, India
| | - Ashutosh Vats
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Shiveeli Rajput
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Chanchal Rana
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, Haryana, India
| | - Sachinandan De
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute (NDRI), Karnal, Haryana, India
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Dubey H, Pradeep AR, Neog K, Debnath R, Aneesha PJ, Shah SK, Kamatchi I, Ponnuvel KM, Ramesha A, Vijayan K, Nongthomba U, Bora U, Vankadara S, VijayaKumari KM, Arunkumar KP. Genome sequencing and assembly of Indian golden silkmoth, Antheraea assamensis Helfer (Saturniidae, Lepidoptera). Genomics 2024; 116:110841. [PMID: 38599255 DOI: 10.1016/j.ygeno.2024.110841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/19/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
Muga silkworm (Antheraea assamensis), one of the economically important wild silkmoths, is unique among saturniid silkmoths. It is confined to the North-eastern part of India. Muga silk has the highest value among the other silks. Unlike other silkmoths, A. assamensis has a low chromosome number (n = 15), and ZZ/ZO sex chromosome system. Here, we report the first high-quality draft genome of A. assamensis, assembled by employing the Illumina and PacBio sequencing platforms. The assembled genome of A. assamensis is 501.18 Mb long, with 2697 scaffolds and an N50 of 683.23 Kb. The genome encompasses 18,385 protein-coding genes, 86.29% of which were functionally annotated. Phylogenetic analysis of A. assamensis revealed its divergence from other Antheraea species approximately 28.7 million years ago. Moreover, an investigation into detoxification-related gene families, CYP450, GST, and ABC-transporter, revealed a significant expansion in A. assamensis as compared to the Bombyx mori. This expansion is comparable to Spodoptera litura, suggesting adaptive responses linked to the polyphagous behavior observed in these insects. This study provides valuable insights into the molecular basis of evolutionary divergence and adaptations in muga silkmoth. The genome assembly reported in this study will significantly help in the functional genomics studies on A. assamensis and other Antheraea species along with comparative genomics analyses of Bombycoidea insects.
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Affiliation(s)
- Himanshu Dubey
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - A R Pradeep
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - Kartik Neog
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India
| | - Rajal Debnath
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India; Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India
| | - P J Aneesha
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - Suraj Kumar Shah
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India
| | - Indumathi Kamatchi
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - K M Ponnuvel
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | - A Ramesha
- Seribiotech Research Laboratory, Central Silk Board, Kodathi, Bangalore, India
| | | | - Upendra Nongthomba
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Utpal Bora
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, India
| | | | - K M VijayaKumari
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India
| | - Kallare P Arunkumar
- Central Muga Eri Research and Training Institute, Central Silk Board, Jorhat, India.
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Zhang X, Hu Y, Cheng Z, Archibald JM. HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes. STAR Protoc 2023; 4:102014. [PMID: 36633953 PMCID: PMC9852648 DOI: 10.1016/j.xpro.2022.102014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Many tools have been developed to measure the degree of similarity between gene duplicates within and between species. Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene sets, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2021)1 and Zhang et al. (2022).2.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Yining Hu
- Department of Computer Science, Western University, London, ON N6A 5B7, Canada
| | - Zhenyu Cheng
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada; Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Institute for Comparative Genomics, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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Lebedeva MA, Gancheva MS, Kulaeva OA, Zorin EA, Dobychkina DA, Romanyuk DA, Sulima AS, Zhukov VA, Lutova LA. Identification and Expression Analysis of the C-TERMINALLY ENCODED PEPTIDE Family in Pisum sativum L. Int J Mol Sci 2022; 23:14875. [PMID: 36499210 PMCID: PMC9739355 DOI: 10.3390/ijms232314875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The C-TERMINALLY ENCODED PEPTIDE(CEP) peptides play crucial roles in plant growth and response to environmental factors. These peptides were characterized as positive regulators of symbiotic nodule development in legume plants. However, little is known about the CEP peptide family in pea. Here, we discovered in pea genome 21 CEP genes (PsCEPs), among which three genes contained additional conserved motifs corresponding to the PIP (PAMP-induced secreted peptides) consensus sequences. We characterized the expression patterns of pea PsCEP genes based on transcriptomic data, and for six PsCEP genes with high expression levels in the root and symbiotic nodules the detailed expression analysis at different stages of symbiosis and in response to nitrate treatment was performed. We suggest that at least three PsCEP genes, PsCEP1, PsCEP7 and PsCEP2, could play a role in symbiotic nodule development, whereas the PsCEP1 and PsCEP13 genes, downregulated by nitrate addition, could be involved in regulation of nitrate-dependent processes in pea. Further functional studies are required to elucidate the functions of these PsCEP genes.
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Affiliation(s)
- Maria A. Lebedeva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
| | - Maria S. Gancheva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
| | - Olga A. Kulaeva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Evgeny A. Zorin
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Daria A. Dobychkina
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
| | - Daria A. Romanyuk
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Anton S. Sulima
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Vladimir A. Zhukov
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
- Laboratory of Genetics of Plant-Microbe Interactions, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Podbelsky Sh. 3, Saint Petersburg 196608, Russia
| | - Lyudmila A. Lutova
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya emb.7/9, Saint Petersburg 199034, Russia
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Zhang X, Smith DR. An overview of online resources for intra-species detection of gene duplications. Front Genet 2022; 13:1012788. [PMID: 36313461 PMCID: PMC9606816 DOI: 10.3389/fgene.2022.1012788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Gene duplication plays an important role in evolutionary mechanism, which can act as a new source of genetic material in genome evolution. However, detecting duplicate genes from genomic data can be challenging. Various bioinformatics resources have been developed to identify duplicate genes from single and/or multiple species. Here, we summarize the metrics used to measure sequence identity among gene duplicates within species, compare several computational approaches that have been used to predict gene duplicates, and review recent advancements of a Basic Local Alignment Search Tool (BLAST)-based web tool and database, allowing future researchers to easily identify intra-species gene duplications. This article is a quick reference guide for research tools used for detecting gene duplicates.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
| | - David Roy Smith
- Department of Biology, Western University, London, ON, Canada
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