Complementary combination of multiplex high‐throughput DNA sequencing for molecular phylogeny
Article Swipe
Yoshihisa Suyama
,
Shun K. Hirota
,
Ayumi Matsuo
,
Yoshihiro Tsunamoto
,
Chika Mitsuyuki
,
Atsuki Shimura
,
Kunihiro Okano
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1111/1440-1703.12270
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1111/1440-1703.12270
The rapid development of DNA sequencing technology in recent years has provided new tools for phylogenetic data acquisition. By using high‐throughput DNA sequencing technology, molecular phylogenetic information can be obtained more quickly and economically. Here, we describe a complementary combination of two multiplex high‐throughput DNA sequencing methods. One is multiplexed phylogenetic marker sequencing (MPM‐seq), and the other is multiplexed inter‐simple sequence repeat (ISSR) genotyping by sequencing (MIG‐seq), whose protocol is improved over that of the original one. Both MPM‐seq and MIG‐seq begin with multiplex polymerase chain reaction (PCR), each amplifying multiple phylogenetic markers and genome‐wide ISSR regions, respectively. After another PCR using a second PCR primer set that is common in both methods, next‐generation sequencing is used to simultaneously detect DNA sequences of multiple regions from multiple samples in each method. In this case study, we performed a molecular phylogenetic analysis of Japanese fir ( Abies ) and the closely related Abies species. MPM‐seq revealed DNA sequences of three regions from chloroplast DNA and one nuclear internal transcribed spacer and created a partially informative phylogenetic tree for 13 Abies species. Whereas MIG‐seq detected 6700 single‐nucleotide polymorphisms and exhibited clear clustering of related species with 97%–100% bootstrap support for all branches of the phylogenetic tree. Hence, with a complementary combination, quick, simple, and economical analysis can be performed in a wide range of genomic studies, including molecular phylogeny, as well as for investigating genetic differentiation or genetic identification among species, hybrids, and populations, and even among clones and cultivars, as a DNA barcoding technique.
Related Topics
Concepts
Phylogenetic tree
Biology
DNA sequencing
Multiplex
Genetics
Multiplex polymerase chain reaction
Computational biology
Phylogenetics
Genome
Primer (cosmetics)
Evolutionary biology
Polymerase chain reaction
DNA
Gene
Organic chemistry
Chemistry
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1111/1440-1703.12270
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1440-1703.12270
- OA Status
- hybrid
- Cited By
- 141
- References
- 43
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3204654899
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3204654899Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1111/1440-1703.12270Digital Object Identifier
- Title
-
Complementary combination of multiplex high‐throughput
DNA sequencing for molecular phylogenyWork title - Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-10-07Full publication date if available
- Authors
-
Yoshihisa Suyama, Shun K. Hirota, Ayumi Matsuo, Yoshihiro Tsunamoto, Chika Mitsuyuki, Atsuki Shimura, Kunihiro OkanoList of authors in order
- Landing page
-
https://doi.org/10.1111/1440-1703.12270Publisher landing page
- PDF URL
-
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1440-1703.12270Direct link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/1440-1703.12270Direct OA link when available
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Phylogenetic tree, Biology, DNA sequencing, Multiplex, Genetics, Multiplex polymerase chain reaction, Computational biology, Phylogenetics, Genome, Primer (cosmetics), Evolutionary biology, Polymerase chain reaction, DNA, Gene, Organic chemistry, ChemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
141Total citation count in OpenAlex
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2025: 34, 2024: 48, 2023: 35, 2022: 23, 2021: 1Per-year citation counts (last 5 years)
- References (count)
-
43Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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