This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
ddRAD Sequencing: A Novel Arsenal Added to the Biosecurity Toolbox to Trace the Origin of Brown Marmorated Stink Bug, Halyomorpha Halys (Hemiptera: Pentatomidae)
Dongmei Li
Ministry for Primary Industries
Corresponding Author
ORCiD: https://orcid.org/0000-0002-0509-3221
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. It is a polyphagous insect pest and causing significant economic losses to agriculture worldwide. Knowledge on the genetic diversity among BMSB populations is scarce but is essential to understand the patterns of colonization and invasion history of local populations. Efforts have been made to assess the genetic diversity of BMSB using partial mitochondrial DNA sequences but genetic divergence on mitochondria is not high enough to precisely identify and distinguish various BMSB populations. Therefore, in this study, we applied a ddRAD (double digest restriction-site associated DNA) sequencing approach to ascertain the genetic diversity of BMSB populations collected from 12 countries (2 native and 10 invaded) across four continents with the ultimate aim to trace the origin of BMSBs intercepted during border inspections and post-border surveillance.
Result
A total of 1775 high confidence single nucleotide polymorphisms (SNPs) were identified from ddRAD sequencing data collected from 389 BMSB individuals. Principal component analysis (PCA) of the identified SNPs indicated the existence of two main distinct genetic clusters representing individuals sampled from regions where BMSB is native to, China and Japan, respectively, and one broad cluster comprised individuals sampled from countries which have been invaded by BMSB. The population genetic structure analysis further discriminated the genetic diversity among the BMSB populations at a higher resolution and distinguished them into five potential genetic clusters.
Conclusion
The study revealed hidden genetic diversity among the studied BMSB populations across the continents. The BMSB populations from Japan were genetically distant from the other studied populations. Similarly, the BMSB populations from China were also separated from the Japanese and other populations. Further genetic structure analysis revealed the presence of at least three genetic clusters of BMSB in the invaded countries, possibly originating from multiple invasions. Furthermore, this study has produced novel set of SNP markers to enhance knowledge of genetic diversity among BMSB populations and demonstrate a great potential to trace the origin of BMSB individuals for future invasion events.
Keywords
BMSB, SNP, population genetics, invasion, biosecurity, ddRADSeq, restriction digestion
Figure 1
Figure 2
Figure 3
Figure 4
This is a list of supplementary files associated with this preprint. Click to download.
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 21 Sep, 2020
No community comments so far
Editorial decision: Major revision
On 02 Nov, 2020
Review #2 received
Received 01 Nov, 2020
Review #1 received
Received 26 Oct, 2020
Reviewer #2 agreed
On 12 Oct, 2020
Reviewer #1 agreed
On 10 Oct, 2020
Reviewers invited
Invitations sent on 05 Oct, 2020
Editor assigned
On 08 Sep, 2020
Submission checks complete
On 07 Sep, 2020
Editor invited
On 07 Sep, 2020
First submitted
On 25 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
Learn more about our company.
This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
ddRAD Sequencing: A Novel Arsenal Added to the Biosecurity Toolbox to Trace the Origin of Brown Marmorated Stink Bug, Halyomorpha Halys (Hemiptera: Pentatomidae)
Dongmei Li
Ministry for Primary Industries
Corresponding Author
ORCiD: https://orcid.org/0000-0002-0509-3221
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 1
Posted 21 Sep, 2020
No community comments so far
Editorial decision: Major revision
On 02 Nov, 2020
Review #2 received
Received 01 Nov, 2020
Review #1 received
Received 26 Oct, 2020
Reviewer #2 agreed
On 12 Oct, 2020
Reviewer #1 agreed
On 10 Oct, 2020
Reviewers invited
Invitations sent on 05 Oct, 2020
Editor assigned
On 08 Sep, 2020
Submission checks complete
On 07 Sep, 2020
Editor invited
On 07 Sep, 2020
First submitted
On 25 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background
Brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. It is a polyphagous insect pest and causing significant economic losses to agriculture worldwide. Knowledge on the genetic diversity among BMSB populations is scarce but is essential to understand the patterns of colonization and invasion history of local populations. Efforts have been made to assess the genetic diversity of BMSB using partial mitochondrial DNA sequences but genetic divergence on mitochondria is not high enough to precisely identify and distinguish various BMSB populations. Therefore, in this study, we applied a ddRAD (double digest restriction-site associated DNA) sequencing approach to ascertain the genetic diversity of BMSB populations collected from 12 countries (2 native and 10 invaded) across four continents with the ultimate aim to trace the origin of BMSBs intercepted during border inspections and post-border surveillance.
Result
A total of 1775 high confidence single nucleotide polymorphisms (SNPs) were identified from ddRAD sequencing data collected from 389 BMSB individuals. Principal component analysis (PCA) of the identified SNPs indicated the existence of two main distinct genetic clusters representing individuals sampled from regions where BMSB is native to, China and Japan, respectively, and one broad cluster comprised individuals sampled from countries which have been invaded by BMSB. The population genetic structure analysis further discriminated the genetic diversity among the BMSB populations at a higher resolution and distinguished them into five potential genetic clusters.
Conclusion
The study revealed hidden genetic diversity among the studied BMSB populations across the continents. The BMSB populations from Japan were genetically distant from the other studied populations. Similarly, the BMSB populations from China were also separated from the Japanese and other populations. Further genetic structure analysis revealed the presence of at least three genetic clusters of BMSB in the invaded countries, possibly originating from multiple invasions. Furthermore, this study has produced novel set of SNP markers to enhance knowledge of genetic diversity among BMSB populations and demonstrate a great potential to trace the origin of BMSB individuals for future invasion events.
Figure 1
Figure 2
Figure 3
Figure 4