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Lee YC, Ke HM, Liu YC, Lee HH, Wang MC, Tseng YC, Kikuchi T, Tsai IJ. Single-worm long-read sequencing reveals genome diversity in free-living nematodes. Nucleic Acids Res 2023; 51:8035-8047. [PMID: 37526286 PMCID: PMC10450198 DOI: 10.1093/nar/gkad647] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.
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Affiliation(s)
- Yi-Chien Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan
| | - Huei-Mien Ke
- Department of Microbiology, Soochow University, Taipei, Taiwan
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Min-Chen Wang
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Yung-Che Tseng
- Marine Research Station (MRS), Institute of Cellular and Organismic Biology, Academia Sinica, 262 I-Lan County, Taiwan
| | - Taisei Kikuchi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
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Rao CS, Sirisha G, Raju KB, Raju NVG. Method for identification of 10 SSR markers from monkey genomes and its Statistical inference with One & Two-way ANOVA. MethodsX 2022; 9:101833. [PMID: 36117677 PMCID: PMC9474309 DOI: 10.1016/j.mex.2022.101833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/21/2022] [Indexed: 11/16/2022] Open
Affiliation(s)
- Chinta Someswara Rao
- Department of CSE, SRKR Engineering College, Bhimavaram, AP, India
- Corresponding author.
| | - G.N.V.G. Sirisha
- Department of CSE, SRKR Engineering College, Bhimavaram, AP, India
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The first draft genome assembly and data analysis of the Malaysian mahseer (Tor tambroides). AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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