A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchers
The rapid uptake of transcriptomic approaches in freshwater ecology has seen a wealth of data produced concerning the ways in which organisms interact with their environment on a molecular level. Typically, such studies focus either at the community level and so don’t require species identifications...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
NTNU University Museum Norwegian University of Science and Technology
2015-12-01
|
| Series: | CHIRONOMUS Journal of Chironomidae Research |
| Subjects: | |
| Online Access: | https://www.ntnu.no/ojs/index.php/chironomus/article/view/1877 |
| _version_ | 1818759134749655040 |
|---|---|
| author | Matt N Krosch Litticia M Bryant |
| author_facet | Matt N Krosch Litticia M Bryant |
| author_sort | Matt N Krosch |
| collection | DOAJ |
| description | The rapid uptake of transcriptomic approaches in freshwater ecology has seen a wealth of data produced concerning the ways in which organisms interact with their environment on a molecular level. Typically, such studies focus either at the community level and so don’t require species identifications, or on laboratory strains of known species identity or natural populations of large, easily identifiable taxa. For chironomids, impediments still exist for applying these technologies to natural populations because they are small-bodied and often require time-consuming secondary sorting of stream material and morphological voucher preparation to confirm species diagnosis. These procedures limit the ability to maintain RNA quantity and quality in such organisms because RNA degrades rapidly and gene expression can be altered rapidly in organisms; thereby limiting the inclusion of such taxa in transcriptomic studies. Here, we demonstrate that these limitations can be overcome and outline an optimised protocol for collecting, sorting and preserving chironomid larvae that enables retention of both morphological vouchers and RNA for subsequent transcriptomics purposes. By ensuring that sorting and voucher preparation are completed within <4 hours after collection and that samples are kept cold at all times, we successfully retained both RNA and morphological vouchers from all specimens. Although not prescriptive in specific methodology, we anticipate that this paper will assist in promoting transcriptomic investigations of the sublethal impact on chironomid gene expression of changes to aquatic environments. |
| first_indexed | 2024-12-18T06:37:54Z |
| format | Article |
| id | doaj.art-84069a9016a44fbb8bca447e2eae217e |
| institution | Directory Open Access Journal |
| issn | 0172-1941 2387-5372 |
| language | English |
| last_indexed | 2024-12-18T06:37:54Z |
| publishDate | 2015-12-01 |
| publisher | NTNU University Museum Norwegian University of Science and Technology |
| record_format | Article |
| series | CHIRONOMUS Journal of Chironomidae Research |
| spelling | doaj.art-84069a9016a44fbb8bca447e2eae217e2022-12-21T21:17:44ZengNTNU University Museum Norwegian University of Science and TechnologyCHIRONOMUS Journal of Chironomidae Research0172-19412387-53722015-12-012810.5324/cjcr.v0i28.18771711A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchersMatt N Krosch0Litticia M Bryant11. Queensland University of Technology, Brisbane, Australia 2. University of Queensland, St Lucia, Australia1. Queensland University of Technology, Brisbane, AustraliaThe rapid uptake of transcriptomic approaches in freshwater ecology has seen a wealth of data produced concerning the ways in which organisms interact with their environment on a molecular level. Typically, such studies focus either at the community level and so don’t require species identifications, or on laboratory strains of known species identity or natural populations of large, easily identifiable taxa. For chironomids, impediments still exist for applying these technologies to natural populations because they are small-bodied and often require time-consuming secondary sorting of stream material and morphological voucher preparation to confirm species diagnosis. These procedures limit the ability to maintain RNA quantity and quality in such organisms because RNA degrades rapidly and gene expression can be altered rapidly in organisms; thereby limiting the inclusion of such taxa in transcriptomic studies. Here, we demonstrate that these limitations can be overcome and outline an optimised protocol for collecting, sorting and preserving chironomid larvae that enables retention of both morphological vouchers and RNA for subsequent transcriptomics purposes. By ensuring that sorting and voucher preparation are completed within <4 hours after collection and that samples are kept cold at all times, we successfully retained both RNA and morphological vouchers from all specimens. Although not prescriptive in specific methodology, we anticipate that this paper will assist in promoting transcriptomic investigations of the sublethal impact on chironomid gene expression of changes to aquatic environments.https://www.ntnu.no/ojs/index.php/chironomus/article/view/1877chironomidsRNAseqtranscriptomeRNA extraction |
| spellingShingle | Matt N Krosch Litticia M Bryant A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchers CHIRONOMUS Journal of Chironomidae Research chironomids RNAseq transcriptome RNA extraction |
| title | A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchers |
| title_full | A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchers |
| title_fullStr | A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchers |
| title_full_unstemmed | A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchers |
| title_short | A note on sampling chironomids for RNA-based studies of natural populations that retains critical morphological vouchers |
| title_sort | note on sampling chironomids for rna based studies of natural populations that retains critical morphological vouchers |
| topic | chironomids RNAseq transcriptome RNA extraction |
| url | https://www.ntnu.no/ojs/index.php/chironomus/article/view/1877 |
| work_keys_str_mv | AT mattnkrosch anoteonsamplingchironomidsforrnabasedstudiesofnaturalpopulationsthatretainscriticalmorphologicalvouchers AT litticiambryant anoteonsamplingchironomidsforrnabasedstudiesofnaturalpopulationsthatretainscriticalmorphologicalvouchers AT mattnkrosch noteonsamplingchironomidsforrnabasedstudiesofnaturalpopulationsthatretainscriticalmorphologicalvouchers AT litticiambryant noteonsamplingchironomidsforrnabasedstudiesofnaturalpopulationsthatretainscriticalmorphologicalvouchers |