The DOI matches its Crossref record; 35 of the 35 references it cites were found in a registry or an index.
Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics
Open accessAbstract
The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species >15 kb and the remaining >10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr121 · Cited by 39,969
Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., Cooper, A., Markowitz, S., Duran, C., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts199 · Cited by 20,027
Biological identifications through DNA barcodes
Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.2002.2218 · Cited by 13,376
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · Gigascience · doi:10.1186/2047-217x-1-18 · Cited by 5,307
Self-citationChimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., Sodergren, E., et al. (2011) · Genome Research · doi:10.1101/gr.112730.110 · Cited by 3,473
Peng, Y., Leung, H. C. M., Yiu, S. M., & Chin, F. Y. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts174 · Cited by 2,989
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 1×
“0 (31,32) (-K 61, -k 45), SOAPdenovo-Trans (33) (-K 71, -L 100, -t 1) and IDBA-UD (34) (kMaxShortSequence = 256, –num threads 12), respectively.”
Self-citation
Cited by
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
Meng, G., Li, Y., Yang, C., & Liu, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz173 · Cited by 1,155
Self-citationLarge-scale ruminant genome sequencing provides insights into their evolution and distinct traits
Chen, L., Qiu, Q., Jiang, Y., Wang, K., Lin, Z., Li, Z., Bibi, F., Yang, Y., Wang, J., Nie, W., et al. (2019) · Science · doi:10.1126/science.aav6202 · Cited by 441
Scaling up: A guide to high‐throughput genomic approaches for biodiversity analysis
Porter, T. M., & Hajibabaei, M. (2018) · Molecular Ecology · doi:10.1111/mec.14478 · Cited by 305
Metadata
- Authors
- Tang, M., Tan, M., Meng, G., Yang, S., Su, X., Liu, S., Song, W., Li, Y., Wu, Q., Zhang, A., & Zhou, X.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-10-07
- Volume
- 42
- Issue
- 22
- Pages
- e166-e166
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2093343912
- Cited by
- 278
- References
- 35
- FWCI
- 10.46
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics. https://app.cochat.ai/papers/10.1093/nar/gku917
- The paper
- Tang, M., Tan, M., Meng, G., Yang, S., Su, X., Liu, S., Song, W., Li, Y., Wu, Q., Zhang, A., & Zhou, X. (2014). Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Research. https://doi.org/10.1093/nar/gku917
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
