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Background: Amino acid substitution models play an important role in inferring phylogenies from proteins. Although different amino acid substitution models have been proposed, only a few were estimated from mitochondrial protein sequences for specific taxa such as the mtArt model for Arthropoda. The increasing of mitochondrial genome data from broad Orthoptera taxa provides an opportunity to estimate the Orthopteraspecific mitochondrial amino acid empirical model. Results: We sequenced complete mitochondrial genomes of 54 Orthoptera species, and estimated an amino acid substitution model (named mtOrt) by maximum likelihood method based on the 283 complete mitochondrial genomes available currently. The results indicated that there are obvious differences between mtOrt and the existing models, and the new model can better fit the Orthoptera mitochondrial protein datasets. Moreover, topologies of trees constructed using mtOrt and existing models are frequently different. MtOrt does indeed have an impact on likelihood improvement as well as tree topologies. The comparisons between the topologies of trees constructed using mtOrt and existing models show that the new model outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein data. Conclusions: The new mitochondrial amino acid substitution model of Orthoptera shows obvious differences from the existing models, and outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein sequences.

BackgroundThe sophisticated insect olfactory system plays an important role in recognizing external odors and enabling insects to adapt to environment. Foraging, host seeking, mating, ovipositing and other forms of chemical communication are based on olfaction, which requires the participation of multiple olfactory genes. The exclusive evolutionary trend of the olfactory system in Orthoptera insects is an excellent model for studying olfactory evolution, but limited olfaction research is available for these species. The olfactory-related genes of Ceracris nigricornis Walker (Orthoptera: Acrididae), a severe pest of bamboos, have not yet been reported.ResultsWe sequenced and analyzed the transcriptomes from different tissues of C. nigricornis and obtained 223.76 Gb clean data that were assembled into 43,603 unigenes with an N50 length of 2235 bp. Among the transcripts, 66.79% of unigenes were annotated. Based on annotation and tBLASTn results, 112 candidate olfactory-related genes were identified for the first time, including 20 odorant-binding proteins (OBPs), 10 chemosensory-binding proteins (CSPs), 71 odorant receptors (ORs), eight ionotropic receptors (IRs) and three sensory neuron membrane proteins (SNMPs). The fragments per kilobase per million mapped fragments (FPKM) values showed that most olfactory-related differentially expressed genes (DEGs) were enriched in the antennae, and these results were confirmed by detecting the expression of olfactory-related genes with quantitative real-time PCR (qRT-PCR). Among these antennae-enriched genes, some were sex-biased, indicating their different roles in the olfactory system of C. nigricornis.ConclusionsThis study provides the first comprehensive list and expression profiles of olfactory-related genes in C. nigricornis and a foundation for functional studies of these olfactory-related genes at the molecular level.

This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Background Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly in the host, continuously enlarging the host genome. However, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of TE invasion by imposing small-RNA-mediated silencing. Here we compare the TE activity of two grasshopper species with different genome sizes in Acrididae (Locusta migratoria manilensis♀1C = 6.60 pg, Angaracris rhodopa♀1C = 16.36 pg) to ascertain the influence of piRNAs. Results We discovered that repetitive sequences accounted for 74.56% of the genome in A. rhodopa, more than 56.83% in L. migratoria, and the large-genome grasshopper contained a higher TEs proportions. The comparative analysis revealed that 41 TEs (copy number > 500) were shared in both species. The two species exhibited distinct “landscapes” of TE divergence. The TEs outbreaks in the small-genome grasshopper occurred at more ancient times, while the large-genome grasshopper maintains active transposition events in the recent past. Evolutionary history studies on TEs suggest that TEs may be subject to different dynamics and resistances in these two species. We found that TE transcript abundance was higher in the large-genome grasshopper and the TE-derived piRNAs abundance was lower than in the small-genome grasshopper. In addition, we found that the piRNA methylase HENMT, which is underexpressed in the large-genome grasshopper, impedes the piRNA silencing to a lower level. Conclusions Our study revealed that the abundance of piRNAs is lower in the gigantic genome grasshopper than in the small genome grasshopper. In addition, the key gene HENMT in the piRNA biogenesis pathway (Ping-Pong cycle) in the gigantic genome grasshopper is underexpressed. We hypothesize that low-level piRNA silencing unbalances the original positive correlation between TEs and piRNAs, and triggers TEs to proliferate out of control, which may be one of the reasons for the gigantism of grasshopper genomes.

This paper provides the first description of a female of Shoveliteratura triangula Shi, Bian & Change, 2011, as well as the complete mitogenome sequence using next-generation sequencing (NGS) technology. The length of the entire mitogenome was 16,152 bp and contained the typical gene arrangement, base composition, and codon usage found in other related species. The overall base composition exhibited a clear anti-G (10.8%) and AT bias (70.5%). The third codon positions in all protein-coding genes (PCGs) displayed high AT-content values (81.4%) in contrast to lower values of 64.2%/64.5% in the first/second positions. Two tandem repeats, 2.49 repeats of 112 bp and 3.65 repeats of 201 bp, contributed 1013 bp to the length of the S. triangula control region (CR). A T-stretch as a recognition sequence of the replication origin and more than one distinct tandem repeat in the CR were common in the Tettigoniidae mitogenomes. Both the maximum likelihood (ML) and Bayesian inference (BI) analyses supported each subfamily of the Tettigoniidae as a monophyletic group. The relationships of the subfamilies were as follows: (Lipotactinae (Hexacentrinae (Conocephalinae (Meconematinae (Bradyporinae, Tettigoniinae))))). The newly sequenced species S. triangula was most closely related to Pseudokuzicus pieli.

In this study, the whole mitochondrial genomes (mitogenomes) from four species were sequenced. The complete mitochondrial genomes of Sinopodisma pieli, S. houshana, S. qinlingensis, and S. wulingshanensis are 15,857 bp, 15,818 bp, 15,843 bp, and 15,872 bp in size, respectively. The 13 protein-coding genes (PCGs) begin with typical ATN codons, except for COXI in S. qinlingensis, which begins with ACC. The highest A+T content in all the sequenced orthopteran mitogenomes is 76.8% (S. qinlingensis), followed by 76.5% (S. wulingshanensis), 76.4% (S. pieli) and 76.4% (S. houshana) (measured on the major strand). The long polythymine stretches (T-stretch) in the A+T-rich region of the four species are not adjacent to the trnI locus but are inside the stem-loop sequences on the major strand. Moreover, several repeated elements are found in the A+T-rich region of the four species. Phylogenetic analysis based on 53 mitochondrial genomes using Bayesian Inference (BI) and Maximum Likelihood (ML) revealed that Melanoplinae (Podismini) was a monophyletic group; however, the monophyly of Sinopodisma was not supported. These data will provide important information for a better understanding of the phylogenetic relationship of Melanoplinae.

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...