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17 pages, 3704 KiB

Open AccessArticle

Spatiotemporal Differentiation of Alpine Butterfly Parnassius glacialis (Papilionidae: Parnassiinae) in China: Evidence from Mitochondrial DNA and Nuclear Single Nucleotide Polymorphisms

by Ruisong Tao, Chang Xu, Yunliang Wang, Xiaoyan Sun, Chunxiang Li, Junye Ma, Jiasheng Hao and Qun Yang

Genes 2020, 11(2), 188; https://doi.org/10.3390/genes11020188 - 11 Feb 2020

Cited by 11 | Viewed by 3603

Abstract

The Apollo butterfly, Parnassius glacialis, is one of the most charming members of its genus and includes two subspecies locally distributed in montane areas of south-central China and Japan. In this study, we investigated the genetic structure and demographic history of P. [...] Read more.

The Apollo butterfly, Parnassius glacialis, is one of the most charming members of its genus and includes two subspecies locally distributed in montane areas of south-central China and Japan. In this study, we investigated the genetic structure and demographic history of P. glacialis by analyzing partial sequences of four mitochondrial genes and nuclear single nucleotide polymorphisms (SNPs) via genotyping-by-sequencing (GBS) of samples from nearly the entire known distributional range in China. The mitochondrial DNA (mtDNA) data demonstrated that a total of 39 haplotypes were present, and the species was estimated to have diverged about 0.95 million years ago during the middle Pleistocene transition into two main clades that likely formed during the Kunlun-Huanghe tectonic movement. The two clades then dispersed independently in distinct geographic areas alongside the mountainous routes in central and southern China, most likely driven by the Pleistocene glacial-interglacial cycles. Nuclear SNP analysis was generally congruent with mtDNA results at the individual level. A minor incongruence of genetic structures that was detected between mtDNA and nuclear SNP data from the Laojunshan and Tiantangzhai populations was likely due to secondary contact and male-biased dispersal. Our work demonstrates that complicated dispersal-vicariance evolutionary processes likely led to the current geographic distribution of P. glacialis in China, particularly the uplift of the Qinghai-Tibet Plateau and related climatic oscillations during the Quaternary period. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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14 pages, 1203 KiB

Open AccessArticle

Ovarian Transcriptomic Analyses in the Urban Human Health Pest, the Western Black Widow Spider

by Lindsay S. Miles, Nadia A. Ayoub, Jessica E. Garb, Robert A. Haney and Brian C. Verrelli

Genes 2020, 11(1), 87; https://doi.org/10.3390/genes11010087 - 12 Jan 2020

Cited by 2 | Viewed by 3897

Abstract

Due to their abundance and ability to invade diverse environments, many arthropods have become pests of economic and health concern, especially in urban areas. Transcriptomic analyses of arthropod ovaries have provided insight into life history variation and fecundity, yet there are few studies [...] Read more.

Due to their abundance and ability to invade diverse environments, many arthropods have become pests of economic and health concern, especially in urban areas. Transcriptomic analyses of arthropod ovaries have provided insight into life history variation and fecundity, yet there are few studies in spiders despite their diversity within arthropods. Here, we generated a de novo ovarian transcriptome from 10 individuals of the western black widow spider (Latrodectus hesperus), a human health pest of high abundance in urban areas, to conduct comparative ovarian transcriptomic analyses. Biological processes enriched for metabolism—specifically purine, and thiamine metabolic pathways linked to oocyte development—were significantly abundant in L. hesperus. Functional and pathway annotations revealed overlap among diverse arachnid ovarian transcriptomes for highly-conserved genes and those linked to fecundity, such as oocyte maturation in vitellogenin and vitelline membrane outer layer proteins, hormones, and hormone receptors required for ovary development, and regulation of fertility-related genes. Comparative studies across arachnids are greatly needed to understand the evolutionary similarities of the spider ovary, and here, the identification of ovarian proteins in L. hesperus provides potential for understanding how increased fecundity is linked to the success of this urban pest. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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18 pages, 1952 KiB

Open AccessArticle

Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus

by Joshua B. Gross, Dennis A. Sun, Brian M. Carlson, Sivan Brodo-Abo and Meredith E. Protas

Genes 2020, 11(1), 42; https://doi.org/10.3390/genes11010042 - 29 Dec 2019

Cited by 8 | Viewed by 3985

Abstract

Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ [...] Read more.

Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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18 pages, 3633 KiB

Open AccessArticle

Comparative Transcriptome Analysis of Gonads for the Identification of Sex-Related Genes in Giant Freshwater Prawns (Macrobrachium Rosenbergii) Using RNA Sequencing

by Jianping Jiang, Xiang Yuan, Qingqing Qiu, Guanghua Huang, Qinyang Jiang, Penghui Fu, Yu Zhang, Yinhai Jia, Xiurong Yang and Hesheng Jiang

Genes 2019, 10(12), 1035; https://doi.org/10.3390/genes10121035 - 11 Dec 2019

Cited by 28 | Viewed by 4377

Abstract

The giant freshwater prawn (Macrobrachium rosenbergii) exhibits sex dimorphism between the male and female individuals. To date, the molecular mechanism governing gonadal development was unclear, and limited data were available on the gonad transcriptome of M. rosenbergii. Here, we conducted [...] Read more.

The giant freshwater prawn (Macrobrachium rosenbergii) exhibits sex dimorphism between the male and female individuals. To date, the molecular mechanism governing gonadal development was unclear, and limited data were available on the gonad transcriptome of M. rosenbergii. Here, we conducted comprehensive gonadal transcriptomic analysis of female (ZW), super female (WW), and male (ZZ) M. rosenbergii for gene discovery. A total of 70.33 gigabases (Gb) of sequences were generated. There were 115,338 unigenes assembled with a mean size of 1196 base pair (bp) and N50 of 2195 bp. Alignment against the National Center for Biotechnology Information (NCBI) non-redundant nucleotide/protein sequence database (NR and NT), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, SwissProt database, Protein family (Pfam), Gene ontology (GO), and the eukaryotic orthologous group (KOG) database, 36,282 unigenes were annotated at least in one database. Comparative transcriptome analysis observed that 10,641, 16,903, and 3393 genes were significantly differentially expressed in ZW vs. ZZ, WW vs. ZZ, and WW vs. ZW samples, respectively. Enrichment analysis of differentially expressed genes (DEGs) resulted in 268, 153, and 42 significantly enriched GO terms, respectively, and a total of 56 significantly enriched KEGG pathways. Additionally, 23 putative sex-related genes, including Gtsf1, IR, HSP21, MRPINK, Mrr, and other potentially promising candidate genes were identified. Moreover, 56,241 simple sequence repeats (SSRs) were identified. Our findings provide a valuable archive for further functional analyses of sex-related genes and future discoveries of underlying molecular mechanisms of gonadal development and sex determination. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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17 pages, 4916 KiB

Open AccessArticle

Identification and Description of the Key Molecular Components of the Egg Strings of the Salmon Louse (Lepeophtheirus salmonis)

by Andreas Borchel, Heidi Kongshaug and Frank Nilsen

Genes 2019, 10(12), 1004; https://doi.org/10.3390/genes10121004 - 3 Dec 2019

Cited by 6 | Viewed by 3899

Abstract

The salmon louse Lepeophtheirus salmonis is a parasite of Atlantic salmon and other salmonids. Every year, it causes high costs for the Norwegian aquaculture industry. While the morphology of the female genital tract has been described, knowledge of the molecular basis of reproduction [...] Read more.

The salmon louse Lepeophtheirus salmonis is a parasite of Atlantic salmon and other salmonids. Every year, it causes high costs for the Norwegian aquaculture industry. While the morphology of the female genital tract has been described, knowledge of the molecular basis of reproduction is very limited. We identified nine genes which are expressed exclusively in the female cement gland, the organ responsible for cement production, which is used to hold the eggs together and keep them attached to their mother in egg strings. Six of these genes encode proteins with signal peptides and probably form the main component of the cement. Two other genes are peroxidases, which are probably important in the cement formation. The last gene is not similar to any known protein, but contains a transmembrane domain. A knockdown of all these genes leads to missing or deformed egg strings, preventing reproduction of the lice. The correct assemblage of the cement in the cement gland is essential for successful reproduction of salmon lice. Similar proteins seem to be present in other copepod species, as well. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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18 pages, 38642 KiB

Open AccessArticle

Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications

by Lifang Xiao, Shengdi Zhang, Chengpeng Long, Qingyun Guo, Jiasheng Xu, Xiaohua Dai and Jianguo Wang

Genes 2019, 10(12), 992; https://doi.org/10.3390/genes10120992 - 1 Dec 2019

Cited by 10 | Viewed by 3259

Abstract

A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains [...] Read more.

A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and −0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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18 pages, 2559 KiB

Open AccessArticle

Transcriptome Analysis and Identification of Insecticide Tolerance-Related Genes after Exposure to Insecticide in Sitobion avenae

by Ning Wei, Yongzhi Zhong, Lulu Lin, Minghui Xie, Guangling Zhang, Weihua Su, Chuanren Li and Haoliang Chen

Genes 2019, 10(12), 951; https://doi.org/10.3390/genes10120951 - 20 Nov 2019

Cited by 22 | Viewed by 3882

Abstract

Aphids cause serious losses to the production of wheat. The grain aphid, Sitobion avenae, which is the dominant species of aphid in all wheat regions of China, is resistant to a variety of insecticides, including imidacloprid and chlorpyrifos. However, the resistance and mechanism [...] Read more.

Aphids cause serious losses to the production of wheat. The grain aphid, Sitobion avenae, which is the dominant species of aphid in all wheat regions of China, is resistant to a variety of insecticides, including imidacloprid and chlorpyrifos. However, the resistance and mechanism of insecticide tolerance of S. avenae are still unclear. Therefore, this study employed transcriptome analysis to compare the expression patterns of stress response genes under imidacloprid and chlorpyrifos treatment for 15 min, 3 h, and 36 h of exposure. S. avenae adult transcriptome was assembled and characterized first, after which samples treated with insecticides for different lengths of time were compared with control samples, which revealed 60–2267 differentially expressed unigenes (DEUs). Among these DEUs, 31–790 unigenes were classified into 66–786 categories of gene ontology (GO) functional groups, and 24–760 DEUs could be mapped into 54–268 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Finally, 11 insecticide-tolerance-related unigenes were chosen to confirm the relative expression by quantitative real-time polymerase chain reaction (qRT-PCR) in each treatment. Most of the results between qRT-PCR and RNA sequencing (RNA-Seq) are well-established. The results presented herein will facilitate molecular research investigating insecticide resistance in S. avenae, as well as in other wheat aphids. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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13 pages, 1314 KiB

Open AccessArticle

The Complete Mitogenome of Pyrrhocoris tibialis (Hemiptera: Pyrrhocoridae) and Phylogenetic Implications

by Qi-Lin Zhang, Run-Qiu Feng, Min Li, Zhong-Long Guo, Li-Jun Zhang, Fang-Zhen Luo, Ya Cao and Ming-Long Yuan

Genes 2019, 10(10), 820; https://doi.org/10.3390/genes10100820 - 18 Oct 2019

Cited by 12 | Viewed by 2972

Abstract

We determined the complete mitogenome of Pyrrhocoris tibialis (Hemiptera: Heteroptera: Pyrrhocoridae) to better understand the diversity and phylogeny within Pentatomomorpha, which is the second largest infra-order of Heteroptera. Gene content, gene arrangement, nucleotide composition, codon usage, ribosomal RNA (rRNA) structures, and sequences of [...] Read more.

We determined the complete mitogenome of Pyrrhocoris tibialis (Hemiptera: Heteroptera: Pyrrhocoridae) to better understand the diversity and phylogeny within Pentatomomorpha, which is the second largest infra-order of Heteroptera. Gene content, gene arrangement, nucleotide composition, codon usage, ribosomal RNA (rRNA) structures, and sequences of the mitochondrial transcription termination factor were well conserved in Pyrrhocoroidea. Different protein-coding genes have been subject to different evolutionary rates correlated with the G + C content. The size of control regions (CRs) was highly variable among mitogenomes of three sequenced Pyrrhocoroidea species, with the P. tibialis CR being the largest. All the transfer RNA genes found in Pyrrhocoroidea had the typical clover leaf secondary structure, except for trnS1 (AGN), which lacked the dihydrouridine arm and possessed an unusual anticodon stem (9 bp vs. the normal 5 bp). A total of three different phylogenetic relationships among the five super-families of Pentatomomorpha were obtained using three analytical methods (MrBayes and RAxML under site-homogeneous models and PhyloBayes under a site-heterogeneous CAT + GTR model) and two mitogenomic datasets (nucleotides and amino acids). The tree topology test using seven methods statistically supported a phylogeny of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))) as the best topology, as recognized by both RAxML and MrBayes based on the two datasets. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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14 pages, 2845 KiB

Open AccessArticle

Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses

by Xiaolei Yu, Wei Tan, Huanyu Zhang, Weiling Jiang, Han Gao, Wenxiu Wang, Yuxia Liu, Yu Wang and Xiaoxuan Tian

Genes 2019, 10(9), 724; https://doi.org/10.3390/genes10090724 - 18 Sep 2019

Cited by 17 | Viewed by 4527

Abstract

In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The [...] Read more.

In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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13 pages, 916 KiB

Open AccessArticle

Gradual Distance Dispersal Shapes the Genetic Structure in an Alpine Grasshopper

by Juan Carlos Illera, Miguel Arenas, Carlos A. López-Sánchez, José Ramón Obeso and Paola Laiolo

Genes 2019, 10(8), 590; https://doi.org/10.3390/genes10080590 - 5 Aug 2019

Cited by 4 | Viewed by 4260

Abstract

The location of the high mountains of southern Europe has been crucial in the phylogeography of most European species, but how extrinsic (topography of sky islands) and intrinsic features (dispersal dynamics) have interacted to shape the genetic structure in alpine restricted species is [...] Read more.

The location of the high mountains of southern Europe has been crucial in the phylogeography of most European species, but how extrinsic (topography of sky islands) and intrinsic features (dispersal dynamics) have interacted to shape the genetic structure in alpine restricted species is still poorly known. Here we investigated the mechanisms explaining the colonisation of Cantabrian sky islands in an endemic flightless grasshopper. We scrutinised the maternal genetic variability and haplotype structure, and we evaluated the fitting of two migration models to understand the extant genetic structure in these populations: Long-distance dispersal (LDD) and gradual distance dispersal (GDD). We found that GDD fits the real data better than the LDD model, with an onset of the expansion matching postglacial expansions after the retreat of the ice sheets. Our findings suggest a scenario with small carrying capacity, migration rates, and population growth rates, being compatible with a slow dispersal process. The gradual expansion process along the Cantabrian sky islands found here seems to be conditioned by the suitability of habitats and the presence of alpine corridors. Our findings shed light on our understanding about how organisms which have adapted to live in alpine habitats with limited dispersal abilities have faced new and suitable environmental conditions. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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13 pages, 3676 KiB

Open AccessArticle

Characterization and Phylogenetic Implications of the Complete Mitochondrial Genome of Syrphidae

by Hu Li

Genes 2019, 10(8), 563; https://doi.org/10.3390/genes10080563 - 25 Jul 2019

Cited by 11 | Viewed by 4199

Abstract

In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 [...] Read more.

In this study, the complete mitochondrial genomes (mitogenomes) of two hoverfly species of Korinchia angustiabdomena (Huo, Ren, and Zheng) and Volucella nigricans Coquillett (Diptera: Syrphidae) were determined and analyzed. The circular mitogenomes were 16,473 bp in K. angustiabdomena (GenBank No. MK870078) and 15,724 bp in V. nigricans (GenBank No. MK870079). Two newly sequenced mitogenomes both contained 37 genes, and the gene order was similar with other syrphine species. All the protein-coding genes (PCGs) were started with the standard ATN codons; and most of PCGs were terminated with a TAA stop codon, while ND1 in K. angustiabdomena ended with a TAG codon, and ND5 terminated with truncated T stop codons in both species. The phylogenetic relationship between K. angustiabdomena and V. nigricans with related lineages was reconstructed using Bayesian inference and Maximum-likelihood analyses. The monophyly of each family considered within Muscomorpha was confirmed by the clades in the phylogenetic tree, and superfamily of the Oestroidea (Calliphoridae, Sarcophagidae, and Oestridae) was unexpectedly found to be a paraphyletic group based on our selected data. This mitogenome information for K. angustiabdomena and V. nigricans could facilitate future studies of evolutionarily related insects. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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12 pages, 3045 KiB

Open AccessArticle

Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

by Haoliang Chen, Lulu Lin, Minghui Xie, Yongzhi Zhong, Guangling Zhang and Weihua Su

Genes 2019, 10(6), 481; https://doi.org/10.3390/genes10060481 - 25 Jun 2019

Cited by 8 | Viewed by 3018

Abstract

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed [...] Read more.

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga. Full article

(This article belongs to the Special Issue Arthropod Genetics and Genomics)

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