1
|
Tay WT, Court LN, Macfadyen S, Jacomb F, Vyskočilová S, Colvin J, De Barro PJ. A high-throughput amplicon sequencing approach for population-wide species diversity and composition survey. Mol Ecol Resour 2021; 22:1706-1724. [PMID: 34918473 DOI: 10.1111/1755-0998.13576] [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: 11/28/2019] [Revised: 11/16/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
Management of agricultural pests requires an understanding of pest species diversity, their interactions with beneficial insects and spatial-temporal patterns of pest abundance. Invasive and agriculturally important insect pests can build up very high populations, especially in cropping landscapes. Traditionally, sampling effort for species identification involves small sample sizes and is labour intensive. Here, we describe a multi-primer high throughput sequencing (HTS) metabarcoding method and associated analytical workflow for a rapid, intensive, high-volume survey of pest species compositions. We demonstrate our method using the taxonomically challenging Bemisia pest cryptic species complex as examples. The whiteflies Bemisia including the 'tabaci' species are agriculturally important capable of vectoring diverse plant viruses that cause diseases and crop losses. Our multi-primer metabarcoding HTS amplicon approach simultaneously process high volumes of whitefly individuals, with efficiency to detect rare (i.e., 1%) test-species, while our improved whitefly primers for metabarcoding also detected beneficial hymenopteran parasitoid species from whitefly nymphs. Field-testing our redesigned Bemisia metabarcoding primer sets across the Tanzania, Uganda and Malawi cassava cultivation landscapes, we identified the sub-Saharan Africa 1 Bemisia putative species as the dominant pest species, with other cryptic Bemisia species being detected at various abundances. We also provide evidence that Bemisia species compositions can be affected by host crops and sampling techniques that target either nymphs or adults. Our multi-primer HTS metabarcoding method incorporated two over-lapping amplicons of 472bp and 518bp that spanned the entire 657bp 3' barcoding region for Bemisia, and is particularly suitable to molecular diagnostic surveys of this highly cryptic insect pest species complex that also typically exhibited high population densities in heavy crop infestation episodes. Our approach can be adopted to understand species biodiversity across landscapes, with broad implications for improving trans-boundary biosecurity preparedness, thus contributing to molecular ecological knowledge and the development of control strategies for high-density, cryptic, pest-species complexes.
Collapse
Affiliation(s)
- W T Tay
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - L N Court
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - S Macfadyen
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - F Jacomb
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - S Vyskočilová
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia.,Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Maritime Kent, ME4 4TB, United Kingdom
| | - J Colvin
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Maritime Kent, ME4 4TB, United Kingdom
| | | |
Collapse
|
2
|
Khatun MF, Shim JK, Lee KY. Genetic diversity and host relationships of endosymbiotic bacteria in the Asian cryptic species of Bemisia tabaci from Bangladesh. Symbiosis 2019. [DOI: 10.1007/s13199-019-00622-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
3
|
Genetic diversity and host relationships of endosymbiotic bacteria in the Asian cryptic species of Bemisia tabaci from Bangladesh. Symbiosis 2019. [DOI: 10.1007/s13199-019-00625-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
4
|
Khatun MF, Jahan SMH, Lee S, Lee KY. Genetic diversity and geographic distribution of the Bemisia tabaci species complex in Bangladesh. Acta Trop 2018; 187:28-36. [PMID: 30055176 DOI: 10.1016/j.actatropica.2018.07.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/21/2018] [Accepted: 07/24/2018] [Indexed: 11/17/2022]
Abstract
Bemisia tabaci (Gennadius) is a species complex consisting of at least 40 cryptic species. Although the genetic diversity of B. tabaci has been studied in various regions, little is known about distribution in Bangladesh, which is covered by the Bengal delta, the largest delta on Earth. We conducted an extensive survey throughout the country and determined the nucleotide sequence of mitochondrial cytochrome c oxidase subunit 1 (COI) from 110 individuals. We then examined phylogenetic relationships. The results identified four cryptic species that expressed distinct interspecific variation but low intraspecific variation. Asia I was the most abundant, both Asia II 1 and Asia II 5 were moderately abundant, and Asia II 10 was found only in the central region. COI sequences of each cryptic species were distinctive and differentiated into many haplotypes. Our study provides important information to better understand the genetic diversity and geographic distribution of cryptic species in Bangladesh and nearby countries.
Collapse
Affiliation(s)
- M F Khatun
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Department of Entomology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Dhaka, Bangladesh
| | - S M H Jahan
- Department of Entomology, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Republic of Korea
| | - Kyeong-Yeoll Lee
- Division of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea; Institute of Plant Medicine, Kyungpook National University, Daegu, Republic of Korea; Institute of Agricultural Science and Technology, Kyungpook National University, Daegu, Republic of Korea.
| |
Collapse
|