Mining insect genomes for functionally affiliated genes

Perry, Caitlyn; Scanlan, Jack L.; Robin, Charles

doi:10.1016/j.cois.2018.12.006

Cited by 6 publications

(5 citation statements)

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“…More and more insect genomes were reported especially in 2018 to now. However, a major challenge now confronting insect science is how best to use genomic data to improve our understanding of insect biology and mine insect genomes for functionally a liated genes [35].…”

Section: Discussionmentioning

confidence: 99%

Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

Peng

Zhende

et al. 2021

Preprint

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The white-striped longhorn beetle Batocera horsfieldi (Coleoptera: Cerambycidae) is a polyphagous wood-boring pest that causes substantial damage to the lumber, fruit and nut industry. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for it. The genome size of B. horsfieldi was estimated as approximate 520 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.26% and 51.03%, respectively. The assembled genome was 528.56Mb with GC content of 35.40%. A total of 121750 microsatellite motifs were identified. The most frequent repeat motif was mononucleotide with a frequency of 85.84%, followed by 8.08% of dinonucleotide, 5.04% of trinonucleotide, 0.73% of tetranonucleotide, 0.20% of pentanonucleotide and 0.12% of hexanonucleotide motifs. The AT/AT, TA/TAand GA/TC repeats were the most abundant motifs of dinucleotide motifs, and AAT/ATT, TAA/TTA and ATA/TAT were the most abundant motifs of trinucleotide motifs, respectively. ninety six pairs of SSR primers were randomly selected for PCR amplification and agarose gel electrophoresis detection, among which 56 pairs of primers can be effectively amplified to obtain the target fragment. In summary, various candidate microsatellite markers were identified and characterized in this study using genome survey analysis.

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Section: Discussionmentioning

confidence: 99%

Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

Peng

Zhende

et al. 2021

Preprint

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“…We have found that a few EcKLs belonging to stable clades in Drosophila are also highly conserved across insects as a whole (Scanlan and Robin, unpublished); these are good candidates for genes with essential E-class functions. It is important to note, however, that not all genes with E-class functions are necessarily stable over evolutionary time: Cyp4g1 and Cyp4g15 orthologs in insects encode enzymes responsible for alkane and alkene biosynthesis, yet this physiologically essential function is maintained despite seemingly random duplications and losses in many lineages (Feyereisen, 2020); similarly, orthologs of the Halloween genes spook ( Cyp307a1 ) and spookier ( Cyp307a2 ) encode genes essential for the biosynthesis of ecdysteroids, yet also have experienced elevated rates of duplication and loss in insects and other arthropods (Perry et al, 2019; Rewitz et al, 2007; Sezutsu et al, 2013; Sztal et al, 2007).…”

Section: Discussionmentioning

confidence: 99%

Identifying candidate detoxification genes in the ecdysteroid kinase-like (EcKL) and cytochrome P450 gene families inDrosophila melanogasterby integrating evolutionary and transcriptomic data

Scanlan

Battlay

et al. 2020

Preprint

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1 and cytochrome P450 gene families in Drosophila melanogaster by integrating 2 evolutionary and transcriptomic data 3 4Abstract: The capacity to detoxify toxic compounds is essential for adaptation to the 22 ecological niches of many organisms, especially insects. However, detoxification in 23 insects is often viewed through the lens of mammalian detoxification research, even 24 though the organ and enzyme systems involved have diverged for over half a billion 25 years. Phosphorylation is a non-canonical phase II detoxification reaction that, 26 among animals, occurs near exclusively in insects, but the enzymes responsible 27 have never been cloned or otherwise identified. We propose the hypothesis that 28 members of the arthropod-specific ecdysteroid kinase-like (EcKL) gene family 29 encode detoxicative kinases. To test this hypothesis, we annotated the EcKL gene 30 family in 12 species of Drosophila and explored their evolution within the genus. 31 Many ancestral EcKL clades are evolutionarily unstable and have experienced 32 repeated gene gain and loss events, while others are conserved as single copy 33 orthologs. Leveraging multiple published gene expression datasets from D. 34 melanogaster, and using the cytochrome P450s-a canonical detoxification family-35 as a test case, we demonstrate relationships between xenobiotic induction, 36 detoxification tissue-enriched expression and evolutionary instability in the EcKLs 37 and the P450s. We also found previously unreported genomic and transcriptomic 38 variation in a number of EcKLs and P450s associated with toxic stress phenotypes 39 using a targeted phenome-wide association study (PheWAS) approach. Lastly, we 40 devised a systematic method for identifying candidate detoxification genes in large 41 gene families that is concordant with experimentally determined functions of P450 42 genes in D. melanogaster. Applying this method to the EcKLs suggested a 43 significant proportion of these genes play roles in detoxification, and that the EcKLs 44 may constitute a detoxification gene family in insects. Additionally, we estimate that 45 between 11-16 uncharacterised D. melanogaster P450s are strong detoxification 46 candidates. 47 48 Highlights 49 50• The poorly characterised ecdysteroid kinase-like (EcKL) gene family is 51 hypothesised to encode enzymes responsible for detoxification by 52 phosphorylation in insects. 53• An integrative 'detoxification score' method accurately categorises the known 54 functions of a canonical detoxification family, the cytochrome P450s, and 55 suggests many EcKLs are also involved in detoxification. 56• A targeted phenome-wide association study finds novel associations between 57 EcKL/P450 variation and a number of toxic stress phenotypes, such as two 58 unlinked EcKL paralogs that are both associated with developmental 59 methylmercury resistance. 60 61 1983 131 132The identification of detoxification genes and enzymes is an important part of 133 bridging the gap between toxicology, chemical ecology and functional genomics in ...

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“…It is important to note, however, that not all genes with E-class functions are necessarily stable over evolutionary time: Cyp4g1 and Cyp4g15 orthologs in insects encode enzymes responsible for alkane and alkene biosynthesis, yet this physiologically essential function is maintained despite seemingly random duplications and losses in many lineages (Feyereisen, 2020); similarly, orthologs of the Halloween genes spook (Cyp307a1) and spookier (Cyp307a2) encode genes essential for the biosynthesis of ecdysteroids, yet also have experienced elevated rates of duplication and loss in insects and other arthropods (Perry et al, 2019;Rewitz et al, 2007;Sezutsu et al, 2013;Sztal et al, 2007).…”

Section: Eckl Evolution In Drosophilamentioning

confidence: 99%

Genomic and transcriptomic analyses in Drosophila suggest that the ecdysteroid kinase-like (EcKL) gene family encodes the ‘detoxification-by-phosphorylation’ enzymes of insects

Scanlan

Gledhill-Smith

Battlay

et al. 2020

Insect Biochemistry and Molecular Biology

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Mining insect genomes for functionally affiliated genes

Cited by 6 publications

References 95 publications

Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

Genome survey sequencing and identification of genomic SSR markers for Batocera horsfieldi (Coleoptera: Cerambycidae)

Identifying candidate detoxification genes in the ecdysteroid kinase-like (EcKL) and cytochrome P450 gene families inDrosophila melanogasterby integrating evolutionary and transcriptomic data

Genomic and transcriptomic analyses in Drosophila suggest that the ecdysteroid kinase-like (EcKL) gene family encodes the ‘detoxification-by-phosphorylation’ enzymes of insects

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