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Markee A, Godfrey RK, Frandsen PB, Weng YM, Triant DA, Kawahara AY. De Novo Long-Read Genome Assembly and Annotation of the Luna Moth (Actias luna) Fully Resolves Repeat-Rich Silk Genes. Genome Biol Evol 2024; 16:evae148. [PMID: 38957923 PMCID: PMC11258402 DOI: 10.1093/gbe/evae148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
We present the first long-read de novo assembly and annotation of the luna moth (Actias luna) and provide the full characterization of heavy chain fibroin (h-fibroin), a long and highly repetitive gene (>20 kb) essential in silk fiber production. There are >160,000 described species of moths and butterflies (Lepidoptera), but only within the last 5 years have we begun to recover high-quality annotated whole genomes across the order that capture h-fibroin. Using PacBio HiFi reads, we produce the first high-quality long-read reference genome for this species. The assembled genome has a length of 532 Mb, a contig N50 of 16.8 Mb, an L50 of 14 contigs, and 99.4% completeness (BUSCO). Our annotation using Bombyx mori protein and A. luna RNAseq evidence captured a total of 20,866 genes at 98.9% completeness with 10,267 functionally annotated proteins and a full-length h-fibroin annotation of 2,679 amino acid residues.
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Affiliation(s)
- Amanda Markee
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | | | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Yi-Ming Weng
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Deborah A Triant
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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Qazi IH, Yuan T, Yang S, Angel C, Liu J. Molecular characterization and phylogenetic analyses of MetAP2 gene and protein of Nosema bombycis isolated from Guangdong, China. Front Vet Sci 2024; 11:1429169. [PMID: 39005720 PMCID: PMC11239577 DOI: 10.3389/fvets.2024.1429169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Background Pebrine, caused by microsporidium Nosema bombycis, is a devastating disease that causes serious economic damages to the sericulture industry. Studies on development of therapeutic and diagnostic options for managing pebrine in silkworms are very limited. Methionine aminopeptidase type 2 (MetAP2) of microsporidia is an essential gene for their survival and has been exploited as the cellular target of drugs such as fumagillin and its analogues in several microsporidia spp., including Nosema of honeybees. Methods In the present study, using molecular and bioinformatics tools, we performed in-depth characterization and phylogenetic analyses of MetAP2 of Nosema bombycis isolated from Guangdong province of China. Results The full length of MetAP2 gene sequence of Nosema bombycis (Guangdong isolate) was found to be 1278 base pairs (bp), including an open reading frame of 1,077 bp, encoding a total of 358 amino acids. The bioinformatics analyses predicted the presence of typical alpha-helix structural elements, and absence of transmembrane domains and signal peptides. Additionally, other characteristics of a stable protein were also predicted. The homology-based 3D models of MetAP2 of Nosema bombycis (Guangdong isolate) with high accuracy and reliability were developed. The MetAP2 protein was expressed and purified. The observed molecular weight of MetAP2 protein was found to be ~43-45 kDa. The phylogenetic analyses showed that MetAP2 gene and amino acids sequences of Nosema bombycis (Guangdong isolate) shared a close evolutionary relationship with Nosema spp. of wild silkworms, but it was divergent from microsporidian spp. of other insects, Aspergillus spp., Saccharomyces cerevisiae, and higher animals including humans. These analyses indicated that the conservation and evolutionary relationships of MetAP2 are closely linked to the species relationships. Conclusion This study provides solid foundational information that could be helpful in optimization and development of diagnostic and treatment options for managing the threat of Nosema bombycis infection in sericulture industry of China.
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Affiliation(s)
- Izhar Hyder Qazi
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Ting Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Sijia Yang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Christiana Angel
- Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Pakistan
| | - Jiping Liu
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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Subrahmanyam G, Thirupathaiah Y, Vijay N, Debnath R, Arunkumar KP, Gadwala M, Sangannavar PA, Manthira Moorthy S, Chutia M. Contrasting gut bacteriomes unveiled between wild Antheraea assamensis Helfer (Lepidoptera: Saturniidae) and domesticated Bombyx mori L. (Lepidoptera: Bombycidae) silkworms. Mol Biol Rep 2024; 51:666. [PMID: 38777963 DOI: 10.1007/s11033-024-09629-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Insect gut microbiomes play a fundamental role in various aspects of insect physiology, including digestion, nutrient metabolism, detoxification, immunity, growth and development. The wild Muga silkworm, Antheraea assamensis Helfer holds significant economic importance, as it produces golden silk. METHODS AND RESULTS In the current investigation, we deciphered its intricate gut bacteriome through high-throughput 16S rRNA amplicon sequencing. Further, to understand bacterial community dynamics among silkworms raised under outdoor environmental conditions, we compared its gut bacteriomes with those of the domesticated mulberry silkworm, Bombyx mori L. Most abundant bacterial phyla identified in the gut of A. assamensis were Proteobacteria (78.1%), Bacteroidetes (8.0%) and Firmicutes (6.6%), whereas the most-abundant phyla in B. mori were Firmicutes (49-86%) and Actinobacteria (10-36%). Further, Gammaproteobacteria (57.1%), Alphaproteobacteria (10.47%) and Betaproteobacteria (8.28%) were the dominant bacterial classes found in the gut of A. assamensis. The predominant bacterial families in A. assamensis gut were Enterobacteriaceae (27.7%), Comamonadaceae (9.13%), Pseudomonadaceae (9.08%) Flavobacteriaceae (7.59%) Moraxellaceae (7.38%) Alteromonadaceae (6.8%) and Enterococcaceae (4.46%). In B. mori, the most-abundant bacterial families were Peptostreptococcaceae, Enterococcaceae, Lactobacillaceae and Bifidobacteriaceae, though all showed great variability among the samples. The core gut bacteriome of A. assamensis consisted of Pseudomonas, Acinetobacter, Variovorax, Myroides, Alteromonas, Enterobacter, Enterococcus, Sphingomonas, Brevundimonas, Oleispira, Comamonas, Oleibacter Vagococcus, Aminobacter, Marinobacter, Cupriavidus, Aeromonas, and Bacillus. Comparative gut bacteriome analysis revealed a more complex gut bacterial diversity in wild A. assamensis silkworms than in domesticated B. mori silkworms, which contained a relatively simple gut bacteriome as estimated by OTU richness. Predictive functional profiling of the gut bacteriome suggested that gut bacteria in A. assamensis were associated with a wide range of physiological, nutritional, and metabolic functions, including biodegradation of xenobiotics, lipid, amino acid, carbohydrate metabolism, and biosynthesis of secondary metabolites and amino acids. CONCLUSIONS These results showed great differences in the composition and diversity of gut bacteria between the two silkworm species. Both insect species harbored core bacterial taxa commonly found in insects, but the relative abundance and composition of these taxa varied markedly.
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Affiliation(s)
- Gangavarapu Subrahmanyam
- Seri-biotech Research Laboratory, Central Silk Board, Ministry of Textiles, Govt. of India, Kodathi, Carmelram Post, Bangalore, Karnataka, 560035, India.
| | - Yeruva Thirupathaiah
- Central Sericultural Research & Training Institute, Central Silk Board, Manandawadi Road, Srirampura, Mysore, Karnataka, 570008, India
| | - N Vijay
- Central Muga Eri Research & Training Institute, Central Silk Board, Ministry of Textiles, Govt. of India, Lahdoigarh, Jorhat, Assam, 785700, India
| | - Rajal Debnath
- Seri-biotech Research Laboratory, Central Silk Board, Ministry of Textiles, Govt. of India, Kodathi, Carmelram Post, Bangalore, Karnataka, 560035, India
| | - K P Arunkumar
- Central Muga Eri Research & Training Institute, Central Silk Board, Ministry of Textiles, Govt. of India, Lahdoigarh, Jorhat, Assam, 785700, India
| | - Mallikarjuna Gadwala
- Central Sericultural Research & Training Institute, Central Silk Board, Manandawadi Road, Srirampura, Mysore, Karnataka, 570008, India
| | - Prashant A Sangannavar
- Central Silk Board, Ministry of Textiles, Govt. of India, B.T.M. Layout, Madivala, Bangalore, Karnataka, 560068, India
| | - S Manthira Moorthy
- Seri-biotech Research Laboratory, Central Silk Board, Ministry of Textiles, Govt. of India, Kodathi, Carmelram Post, Bangalore, Karnataka, 560035, India
| | - Mahananda Chutia
- Muga Eri Silkworm Seed Organization, Central Silk Board, Reshom Nagar, Khanapara, Guwahati, Assam, 781022, India
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Kiani-Azad K, Bagheri M, Sadeghi M, Nematollahian S, Zahmatkesh A, Moharrami M, Miraie-Ashtiani SR. Molecular Characterization of a New Nosema bombycis Strain Detected in Iranian Silkworm Farms. Acta Parasitol 2022; 67:1364-1371. [PMID: 35857274 DOI: 10.1007/s11686-022-00592-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/01/2022] [Indexed: 11/01/2022]
Abstract
PURPOSE Pebrine as the most dangerous disease of silkworm mostly caused by Nosema species has caused huge economic losses. There is no information on the species and the genomic sequences of the pebrine-causing microsporidia in Iran. METHODS In the present research, we tried to determine the sequences of two regions of rDNA using molecular methods. First, infected larvae and mother moths were collected from several farms in the north of Iran for identification and molecular characterization of microsporidian isolates. After extracting the spores and genomic DNA from the collected samples, two fragments of internal transcribed spacer (ITS) rDNA and small subunit (SSU) rDNA were amplified and sequenced, and registered in NCBI database and then, the phylogenetic tree was drawn. RESULTS Results showed the obtained sequences (ITS rDNA: Accession No. MZ322002 and SSU rDNA: Accession No. MZ314703) represent a new strain of Nosema bombycis, which differs from the sequences deposited in the NCBI. CONCLUSION The new N. bombycis strain identified in our study will help in control and management of the pebrine disease by specific detection of the infectious agent.
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Affiliation(s)
- Kimia Kiani-Azad
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, 31976-19751, Iran.,Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Masoumeh Bagheri
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, 31976-19751, Iran.
| | - Mostafa Sadeghi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Shahla Nematollahian
- Iran Silkworm Research Center (ISRC) Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran
| | - Azadeh Zahmatkesh
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, 31976-19751, Iran
| | - Mojtaba Moharrami
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, 31976-19751, Iran
| | - Seyed Reza Miraie-Ashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
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