Characterizing the Embryonic Transcriptome of the Snail Ilyanassa

Lambert, J. David; Chan, Xin Yi; Spiecker, Barbara; Sweet, Hyla C.

doi:10.1093/icb/icq121

Cited by 31 publications

(27 citation statements)

References 34 publications

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“…Carver Biotechnology Center, University of Illinois, Urbana-Champaign, following the procedures described by Lambert et al [51]. Firstly, messenger RNA was isolated from 20 μ g of total RNA using Oligotex kit (Qiagen, Valencia, CA), followed by the cDNA library construction with titanium adaptors (454 Life Sciences, Branford, CT).…”

Section: Methodsmentioning

confidence: 99%

Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies

Tian

Paudel

Vendrame

et al. 2017

International Journal of Genomics

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Jatropha (Jatropha curcas L.) is an economically important species with a great potential for biodiesel production. To enrich the jatropha genomic databases and resources for microgravity studies, we sequenced and annotated the transcriptome of jatropha and developed SSR and SNP markers from the transcriptome sequences. In total 1,714,433 raw reads with an average length of 441.2 nucleotides were generated. De novo assembling and clustering resulted in 115,611 uniquely assembled sequences (UASs) including 21,418 full-length cDNAs and 23,264 new jatropha transcript sequences. The whole set of UASs were fully annotated, out of which 59,903 (51.81%) were assigned with gene ontology (GO) term, 12,584 (10.88%) had orthologs in Eukaryotic Orthologous Groups (KOG), and 8,822 (7.63%) were mapped to 317 pathways in six different categories in Kyoto Encyclopedia of Genes and Genome (KEGG) database, and it contained 3,588 putative transcription factors. From the UASs, 9,798 SSRs were discovered with AG/CT as the most frequent (45.8%) SSR motif type. Further 38,693 SNPs were detected and 7,584 remained after filtering. This UAS set has enriched the current jatropha genomic databases and provided a large number of genetic markers, which can facilitate jatropha genetic improvement and many other genetic and biological studies.

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Section: Methodsmentioning

confidence: 99%

Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies

Tian

Paudel

Vendrame

et al. 2017

International Journal of Genomics

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“…Carver Biotechnology Center High-Throughput Sequencing and Genotyping Unit of the W. M. Keck Center for Comparative and Functional Genomics (University of Illinois, Urbana, IL). Construction of a normalized cDNA library and 454 pyrosequencing were carried out at the Keck Center as described by Lambert et al (2010). Assembly also was performed at the Keck Center using SeqMan Pro sequence assembly software (DNASTAR Inc., Madison, WI, USA).…”

Section: Methodsmentioning

confidence: 99%

Sequencing and characterizing odorant receptors of the cerambycid beetle Megacyllene caryae

Mitchell

Hughes

Luetje

et al. 2012

Insect Biochemistry and Molecular Biology

115

180

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Odorant receptors (Ors) are a unique family of ligand-gated ion channels and the primary mechanism by which insects detect volatile chemicals. Here, we describe 57 putative Ors sequenced from an antennal transcriptome of the cerambycid beetle Megacyllene caryae (Gahan). The male beetles produce a pheromone blend of nine components, and we functionally characterized Ors tuned to three of these chemicals: receptor McOr3 is sensitive to (S)-2-methyl-1-butanol; McOr20 is sensitive to (2S,3R)-2,3-hexanediol; and McOr5 is sensitive to 2-phenylethanol. McOr3 and McOr20 are also sensitive to structurally-related chemicals that are pheromones of other cerambycid beetles, suggesting that orthologous receptors may be present across many cerambycid species. These Ors are the first to be functionally characterized from any species of beetle and lay the groundwork for understanding the evolution of pheromones within the Cerambycidae.

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“…For each library, messenger RNA was isolated from 10 μg of pooled total RNA with the Oligotex kit (Qiagen, Valencia, CA). The messenger RNA was then converted to a primary cDNA library with adaptors compatible with the 454 system using Multiplex Identifier (MID) tags to distinguish the two population pools [28]. The libraries were diluted to 1 × 10 6 molecules/μL, pooled, and sequenced on a full plate using the 454 Genome Sequencer FLX + system according to the manufacturer’s instructions (454 Life Sciences, Branford, CT).…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica

Eierman

Hare

2014

BMC Genomics

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BackgroundThe eastern oyster, Crassostrea virginica, is a euryhaline species that can thrive across a wide range of salinities (5-35). As with all estuarine species, individual oysters must be able to regulate their osmotic balance in response to constant temporal variation in salinity. At the population level, recurrent viability selection may be an additional mechanism shaping adaptive osmoregulatory phenotypes at the margins of oyster salinity tolerance. To identify candidate genes for osmoregulation, we sequenced, assembled, and annotated the transcriptome of wild juvenile eastern oysters from ‘high’ and ‘low’ salinity regimes. Annotations and candidates were mostly based on the Pacific oyster (Crassostrea gigas) genome sequence so osmoregulatory relevance in C. virginica was explored by testing functional enrichment of genes showing spatially discrete patterns of expression and by quantifying coding sequence divergence.ResultsThe assembly of sequence reads and permissive clustering of potentially oversplit alleles resulted in 98,729 reftigs (contigs and singletons). Of these, 50,736 were annotated with 9,307 belonging to a set of candidate osmoregulatory genes identified from the C. gigas genome. A total of 218,777 SNPs (0.0185 SNPs/bp) were identified in annotated reftigs of C. virginica. Amino acid divergence between translations of C. virginica annotated reftigs and C. gigas coding sequence averaged 23.2 % with an average dN/dS ratio of 0.074, suggesting purifying selection on protein sequences. The high and low salinity source oysters each expressed a subset of genes unique to that group, and the functions for these annotated genes were consistent with known molecular mechanisms for osmotic regulation in molluscs.ConclusionsMost of the osmoregulatory gene candidates experimentally identified in C. gigas are present in this C. virginica transcriptome. In general these congeners show coding sequence divergence too high to make the C. gigas genome a useful reference for C. virginica bioinformatics. However, strong purifying selection is characteristic of the osmoregulatory candidates so functional annotations are likely to correspond. An initial examination of C. virginica presence/absence expression patterns across the salinity gradient in a single estuary suggests that many of these candidates have expression patterns that co-vary with salinity, consistent with osmoregulatory function in C. virginica.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-503) contains supplementary material, which is available to authorized users.

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Characterizing the Embryonic Transcriptome of the Snail Ilyanassa

Cited by 31 publications

References 34 publications

Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies

Enriching Genomic Resources and Marker Development from Transcript Sequences ofJatropha curcasfor Microgravity Studies

Sequencing and characterizing odorant receptors of the cerambycid beetle Megacyllene caryae

Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica

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