Sex- and tissue-specific transcriptome analyses and expression profiling of olfactory-related genes in Ceracris nigricornis Walker (Orthoptera: Acrididae)

Yuan, Hao; Chang, Huihui; Zhao, Lina; Yang, Chao; Huang, Yuan

doi:10.1186/s12864-019-6208-x

Cited by 13 publications

(11 citation statements)

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“…In general the number of olfactory gene family candidate transcripts were consistent with that of other species ( Liu et al, 2012 ; Pitts et al, 2011 ; Riveron, Boto & Alcorta, 2013 ), except for CSP and IR. We also found that the expression difference of olfactory genes between the sexes is consistent to that of other insects ( Leitch et al, 2015 ; Li et al, 2018 ; Yuan et al, 2019 ; Zhao et al, 2018 ). In addition, some olfactory genes are highly expressed in other organs (head, leg or wing) rather than antennae.…”

Section: Discussionsupporting

confidence: 85%

Identification of olfactory genes of a forensically important blow fly, Aldrichina grahami (Diptera: Calliphoridae)

Han

Liu

Meng

et al. 2020

PeerJ

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Background The time-length between the first colonization of necrophagous insect on the corpse and the beginning of investigation represents the most important forensic concept of minimum post-mortem inference (PMImin). Before colonization, the time spent by an insect to detect and locate a corpse could significantly influence the PMImin estimation. The olfactory system plays an important role in insect food foraging behavior. Proteins like odorant binding proteins (OBPs), chemosensory proteins (CSPs), odorant receptors (ORs), ionotropic receptors (IRs) and sensory neuron membrane proteins (SNMPs) represent the most important parts of this system. Exploration of the above genes and their necrophagous products should facilitate not only the understanding of their roles in forging but also their influence on the period before PMImin. Transcriptome sequencing has been wildly utilized to reveal the expression of particular genes under different temporal and spatial condition in a high throughput way. In this study, transcriptomic study was implemented on antennae of adult Aldrichina grahami (Aldrich) (Diptera: Calliphoridae), a necrophagous insect with forensic significance, to reveal the composition and expression feature of OBPs, CSPs, ORs, IRs and SNMPs genes at transcriptome level. Method Antennae transcriptome sequencing of A. grahami was performed using next-generation deep sequencing on the platform of BGISEQ-500. The raw data were deposited into NCBI (PRJNA513084). All the transcripts were functionally annotated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Differentially expressed genes (DEGs) were analyzed between female and male antennae. The transcripts of OBPs, CSPs, ORs, IRs and SNMPs were identified based on sequence feature. Phylogenetic development of olfactory genes of A. grahami with other species was analyzed using MEGA 5.0. RT-qPCR was utilized to verify gene expression generated from the transcriptome sequencing. Results In total, 14,193 genes were annotated in the antennae transcriptome based on the GO and the KEGG databases. We found that 740 DEGs were differently expressed between female and male antennae. Among those, 195 transcripts were annotated as candidate olfactory genes then checked by sequence feature. Of these, 27 OBPs, one CSPs, 49 ORs, six IRs and two SNMPs were finally identified in antennae of A. grahami. Phylogenetic development suggested that some olfactory genes may play a role in food forging, perception of pheromone and decomposing odors. Conclusion Overall, our results suggest the existence of gender and spatial expression differences in olfactory genes from antennae of A. grahami. Such differences are likely to greatly influence insect behavior around a corpse. In addition, candidate olfactory genes with predicted function provide valuable information for further studies of the molecular mechanisms of olfactory detection of forensically important fly species and thus deepen our understanding of the period before PMImin.

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Section: Discussionsupporting

confidence: 85%

Identification of olfactory genes of a forensically important blow fly, Aldrichina grahami (Diptera: Calliphoridae)

Han

Liu

Meng

et al. 2020

PeerJ

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show abstract

“…In general the number of olfactory gene family candidate transcripts were consistent with that of other species (Liu et al 2012;Pitts et al 2011;Riveron et al 2013), except for CSP and IR. We also found that the expression difference of olfactory genes between the sexes is consistent to that of other insects (Leitch et al 2015;Yuan et al 2019;Zhao et al 2018). In addition, some olfactory genes are highly expressed in other PeerJ reviewing PDF | (2019:12:44386:2:1:NEW 24 Jun 2020)…”

Section: Discussionsupporting

confidence: 82%

Peer Review #1 of "Identification of olfactory genes of a forensically important blow fly, Aldrichina grahami (Diptera: Calliphoridae) (v0.1)"

2020

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Background：The time-length between the first colonization of necrophagous insect on the corpse and the beginning of investigation represents the most important forensic concept of minimum post-mortem inference (PMImin). Before colonization, the time spent by an insect to detect and locate a corpse could significantly influence the PMImin estimation. The olfactory system plays an important role in insect food foraging behavior. Proteins like odorant binding proteins, chemosensory proteins, odorant receptors (ORs), ionotropic receptors and sensory neuron membrane proteins represent the most important parts of this system. Exploration of the above genes and their necrophagous products should facilitate not only the understanding of their roles in forging but also their influence on the period before PMImin. Transcriptome sequencing has been wildly utilized to reveal the expression of particular genes under different temporal and spatial condition in a high throughput way. In this study, transcriptomic study was implemented on antennae of adult Aldrichina grahami (Aldrich) (Diptera: Calliphoridae), a necrophagous insect with forensic significance, to reveal the composition and expression feature of OBPs, CSPs, ORs, IRs and SNMPs genes at transcriptome level. Method: Antennae transcriptome sequencing of A. grahami was performed using next-generation deep sequencing on the platform of BGISEQ-500. The raw data were deposited into NCBI (PRJNA513084). All the transcripts were functionally annotated using GO and KEGG database. Differentially expressed genes (DEGs) were analyzed between female and male antennae. The transcripts of OBPs, CSPs, ORs, IRs and SNMPs were identified based on sequence feature. Phylogenetic development of olfactory genes of A. grahami with other species was analyzed using MEGA 5.0. RT-qPCR was utilized to verify gene expression generated from the transcriptome sequencing. Results: In total, 14,193 genes were annotated in the antennae transcriptome based on the GO and the KEGG databases. We found that 740 DEGs were differently expressed between female and male antennae. Among those, 195 transcripts were annotated as candidate olfactory genes then checked by sequence feature. Of these, 27 OBPs, 1 CSPs, 49 ORs, 6 IRs and 2 SNMPs were finally identified in antennae of A. grahami. Phylogenetic development suggested that some olfactory genes may play a role in food forging, perception of pheromone and decomposing odors. Conclusion: Overall, our results suggest the existence of gender and spatial expression differences in olfactory genes from antennae of A. grahami. Such difference is likely to greatly influence insect behavior around a corpse. In addition, candidate olfactory genes with predicted function provide valuable information for further studies of the molecular mechanisms of olfactory detection of forensically important fly species and thus, deepen our understanding of the period before PMImin.

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“…The NR annotation revealed that the species with the largest distribution of unigenes in G. licenti and M. japonicus was Z. nevadensis rather than more closely related L. migratoria, which may be caused by the incomplete genome assembly of L. migratoria 17 . But compared with published RNA-seq of the Acrididae species, unigenes obtained by PacBio sequencing has a higher proportion of annotation on the genomes of L. migratoria 18,19,62 . The KEGG analysis showed that 209 and 211 KEGG pathways were successfully annotated in G. licenti and M. japonicus, respectively.…”

Section: Discussionmentioning

confidence: 94%

Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus

Yuan

Zhang

Zhao

et al. 2020

Sci Rep

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Acrididae are diverse in size, body shape, behavior, ecology and life history; widely distributed; easy to collect; and important to agriculture. they represent promising model candidates for functional genomics, but their extremely large genomes have hindered this research; establishing a reference transcriptome for a species is the primary means of obtaining genetic information. Here, two Acrididae species, Gomphocerus licenti and Mongolotettix japonicus, were selected for full-length (fL) pacBio transcriptome sequencing. for G. licenti and M. japonicus, respectively, 590,112 and 566,165 circular consensus sequences (CCS) were generated, which identified 458,131 and 428,979 full-length nonchimeric (fLnc) reads. After isoform-level clustering, next-generation sequencing (nGS) short sequences were used for error correction, and remove redundant sequences with cD-Hit, 17,970 and 16,766 unigenes were generated for G. licenti and M. japonicus. in addition, we obtained 17,495 and 16,373 coding sequences, 1,082 and 813 transcription factors, 11,840 and 10,814 simple sequence repeats, and 905 and 706 long noncoding RNAs by analyzing the transcriptomes of G. licenti and M. japonicus, respectively, and 15,803 and 14,846 unigenes were annotated in eight functional databases. This is the first study to sequence FL transcriptomes of G. licenti and M. japonicus, providing valuable genetic resources for further functional genomics research. One important goal of functional genomics is to establish relationships between genotypes and phenotypes based on genomic sequence information and various omics techniques 1. The rapid development of high-throughput sequencing technology has greatly facilitated the study of functional genomics, especially the completion of genome sequencing of a large number of species 2-5. However, genome assembly is difficult in species with large genomes, especially those with high heterozygosity and regions with high repeat content 6. Overall, genomic approaches to genotype-phenotype association in species with large genomes still face major challenges. Transcriptomics focuses on the transcribed portion of the genome by sequencing cDNA rather than genomic DNA, thus reducing the size of the sequencing target space, and can be viewed as an alternative to genomic approaches 7. Furthermore, a unique feature of transcriptomics is that it can quantify changes in expression level for each gene among different transcriptome samples. As a low-cost next-generation sequencing (NGS) technology, RNA sequencing (RNA-seq) has become a mainstream tool for studying transcriptomics 8. At present, RNAseq is widely used not only for gene expression profiling, genome annotation and noncoding RNA prediction and quantification but also to gain deep insight into the level of gene expression, the structure of genomic loci, and the sequence variation present at loci (e.g., SNPs) 7. RNA-seq has revolutionized the field of transcriptomics and improved our understanding of genome expression and regulation. Although RNA-seq has bee...

show abstract

Sex- and tissue-specific transcriptome analyses and expression profiling of olfactory-related genes in Ceracris nigricornis Walker (Orthoptera: Acrididae)

Cited by 13 publications

References 91 publications

Identification of olfactory genes of a forensically important blow fly, Aldrichina grahami (Diptera: Calliphoridae)

Identification of olfactory genes of a forensically important blow fly, Aldrichina grahami (Diptera: Calliphoridae)

Peer Review #1 of "Identification of olfactory genes of a forensically important blow fly, Aldrichina grahami (Diptera: Calliphoridae) (v0.1)"

Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus

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