Open access genomic resources for terrestrial arthropods

González, Vanessa L.; Devine, Amanda; Trizna, Michael; Mulcahy, Daniel G.; Barker, Katharine; Coddington, Jonathan A.

doi:10.1016/j.cois.2017.12.003

Cited by 18 publications

(9 citation statements)

References 16 publications

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“…Because of the very small size (2–3 mm) of the Prokelisia specimens, entire specimens were digested to provide sufficient DNA quantity (>50 ng/µL) and quality (≥10,000 bp length) to perform this SA-HRMA and subsequent sequencing experiments, including Sanger and next-generation sequencing (NGS). However, it should be noted that arthropods often contain gut endosymbionts that can contaminate massive parallel sequencing experiments 20 . Therefore, investigators wishing to use NGS or RNA-seq techniques on these species should consider isolating nucleic acids from body parts, such as the legs or the head.…”

Section: Resultsmentioning

confidence: 99%

Genetic species identification of ecologically important planthoppers (Prokelisia spp.) of coastal Spartina saltmarshes using High Resolution Melting Analysis (HRMA)

Espinoza

Bremer

2019

Sci Rep

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Phloem-feeding planthoppers of the genus Prokelisia rank among the most abundant and ecologically important browsers of coastal saltmarsh grasses of eastern North America and the Caribbean. Along the Spartina marshes of the northern Gulf of Mexico, the sympatric species P. marginata and P. dolus are the most abundant, but are difficult to distinguish from each other based solely on morphology. This study seeks to design a molecular assay based on High Resolution Melting Analysis (HRMA) as a fast, cost-effective alternative to differentiate these species. A 450 base pairs (bp) segment of cytochrome c oxidase subunit I (COI) was amplified and sequenced for representative samples of both species, and a short amplicon (SA) HRMA was designed based on the presence of fixed nucleotide differences between species found along a 60 bp segment of COI. The unambiguous identification of individual specimens of P. marginata or P. dolus was possible due to easily discernable differences in the melting temperatures of the two species along this mini barcode. This assay may prove useful for future genetic studies involving these species by preventing the overestimation of genetic diversity via inclusion of conspecifics, and in ecological studies by improving data on the effects of individual species of Prokelisia.

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Section: Resultsmentioning

confidence: 99%

Genetic species identification of ecologically important planthoppers (Prokelisia spp.) of coastal Spartina saltmarshes using High Resolution Melting Analysis (HRMA)

Espinoza

Bremer

2019

Sci Rep

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“…An initial analysis of the data revealed contamination with sequences from thrips, likely due to infestation of the plants by these animals. Hence, we removed reads matching to the genome of the thrips Frankliniella occidentalis (González et al 2018) as well as uncorrectable and unpaired reads and reads corresponding to organelle sequences. After this filtering step, 42 Mio.…”

Section: Overview Of the Rna-seq Analysis And Transcriptome Assemblymentioning

confidence: 99%

Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

Gramzow

Klupsch

Fernandez-Pozo

et al. 2021

Preprint

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BackgroundFruits are the seed-bearing structures of flowering plants and are highly diverse in terms of morphology, texture and maturation. Dehiscent fruits split open upon maturation to discharge their seeds while indehiscent fruits are dispersed as a whole. Indehiscent fruits evolved from dehiscent fruits several times independently in the crucifer family (Brassicaceae). The fruits of Lepidium appelianum, for example, are indehiscent while the fruits of the closely related L. campestre are dehiscent. Here, we investigate the molecular and genetic mechanisms underlying the evolutionary transition from dehiscent to indehiscent fruits using these two Lepidium species as model system.ResultsWe have sequenced the transcriptomes and small RNAs of floral buds, flowers and fruits of L. appelianum and L. campestre and analyzed differentially expressed genes (DEGs) and differently differentially expressed genes (DDEGs). DEGs are genes that show significantly different transcript levels in the same structures (buds, flowers and fruits) in different species, or in different structures in the same species. DDEGs are genes for which the change in expression level between two structures is significantly different in one species than in the other. Comparing the two species, the highest number of DEGs was found in flowers, followed by fruits and floral buds while the highest number of DDEGs was found in fruits versus flowers followed by flowers versus floral buds. Several gene ontology terms related to cell wall synthesis and degradation were overrepresented in different sets of DEGs highlighting the importance of these processes for fruit opening. Furthermore, the fruit valve identity genes FRUITFUL and YABBY3 were among the DEGs identified. Finally, the microRNA miR166 as well as the TCP transcription factors BRANCHED1 (BRC1) and TCP FAMILY TRANSCRIPTION FACTOR 4 (TCP4) were found to be DDEGs.ConclusionsOur study reveals differences in gene expression between dehiscent and indehiscent fruits and uncovers miR166, BRC1 and TCP4 as possible causes for the evolutionary transition from dehiscent to indehiscent fruits in Lepidium.

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“…Curation of reference libraries is also facilitated by high-resolution images of specimens, either as ‘e-vouchers’ 31 that can be digitally distributed, or better yet, images are taken in addition to voucher specimens. It is also apparent that cryopreserving genomic DNA extracts derived from the construction of reference libraries will become increasingly important 32,33 . DNA vouchering provides another opportunity for taxonomic ‘quality control’, in those taxa where the primary barcode region fails to differentiate closely-related taxa, as additional sequence information can be gathered (e.g.…”

Section: Background and Summarymentioning

confidence: 99%

A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

et al. 2019

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The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet’s land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.

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Open access genomic resources for terrestrial arthropods

Cited by 18 publications

References 16 publications

Genetic species identification of ecologically important planthoppers (Prokelisia spp.) of coastal Spartina saltmarshes using High Resolution Melting Analysis (HRMA)

Genetic species identification of ecologically important planthoppers (Prokelisia spp.) of coastal Spartina saltmarshes using High Resolution Melting Analysis (HRMA)

Comparative transcriptomics identifies the transcription factors BRANCHED1 and TCP4, as well as the microRNA miR166 as candidate genes involved in the evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae)

A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

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