The complete mitochondrial genome of the red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae)

Population genomics and phylogeography of the boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), in the United States, northern Mexico, and Argentina

The boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), is an important pest of commercial cotton across the Americas. In the United States, eradication of this species is complicated by re-infestations of areas where eradication has been previously successful and by the existence of morphologically similar variants that can confound identification efforts. To date, no study has applied a high-throughput sequencing approach to better understand the population genetic structure of the boll weevil. Furthermore, only a single study has investigated genetic relationships between populations in North and South America. We used double digest restriction site-associated DNA sequencing (ddRADseq) to resolve the population genomic structure of the boll weevil in the southern United States, northern Mexico, and Argentina. Additionally, we assembled the first complete mitochondrial genome for this species and generated a preliminary whole genome assembly, both of which were used to improve the identification of informative loci. Downstream analyses revealed two main lineages-one consisting of populations found geographically west of the Sierra Madre Occidental mountain range and the second consisting of populations found to the east-were revealed, and both were sub-structured. Population geographic structure was consistent with the isolation by distance model, indicating that geogrpahic distance is likely a primary mechanism driving divergence in this species. Boll weevil populations from Argentina were found to be more closely related to the eastern lineage, suggesting a recent colonization of South America by the eastern lineage, but additional sampling across Mexico, Central America and South America is needed to further clarify their origin. Finally, we uncovered an instance of population turnover or replacement, highlighting the temporal instability of population structure.

Variants in the Mitochondrial Genome Sequence of Rhyzopertha dominica (Fabricius) (Coleoptera: Bostrycidae)

Simple Summary

The lesser grain borer damages grains in storage worldwide. The major control method for this beetle is phosphine fumigation, but the increase in resistant populations has led to a loss in phosphine efficacy. Insect mitochondria are the major source of energy, and some phosphine-resistant insects have reduced energy production. Therefore, we want to understand whether changes in the mitochondrial genome may promote phosphine resistance in insects, but we need an accurate mitogenome sequence and annotation. We extracted and sequenced genomic DNA from a laboratory colony of the lesser grain borer and assembled and annotated the mitochondrial genome. The mitochondrial genome sequence was similar in structure to other insect mitochondria and encoded typical mitochondrial genes. We compared our predicted mitochondrial genome sequence to that of another lesser grain borer strain from Jingziguan (China). While there was mostly agreement among the two sequences, the data will be used to determine if key differences may suggest mutations in the two populations related to phosphine control pressure. However, differences also could be the result in different genome sequences and interpretations. The data will be useful as a research tool to examine the expression of mitochondrial genes in phosphine susceptible and -resistant insect populations.

Abstract

The lesser grain borer, Rhyzopertha dominica, is a coleopteran pest of stored grains and is mainly controlled by phosphine fumigation, but the increase in phosphine-resistant populations threatens efficacy. Some phosphine-resistant insects have reduced respiration, and thus studying the mitochondrial genome may provide additional information regarding resistance. Genomic DNA from an inbred laboratory strain of R. dominica was extracted and sequenced with both short (Illumina) and long (Pacific Biosciences) read technologies for whole genome sequence assembly and annotation. Short read sequences were assembled and annotated by open software to identify mitochondrial sequences, and the assembled sequence was manually annotated and verified by long read sequences. The mitochondrial genome sequence for R. dominica had a total length of 15,724 bp and encoded 22 trna genes, 2 rRNA genes, 13 protein coding genes (7 nad subunits, 3 cox, 2 atp, and 1 cytB), flanked by a long control region. We compared our predicted mitochondrial genome to that of another from a R. dominica strain from Jingziguan (China). While there was mostly agreement between the two assemblies, key differences will be further examined to determine if mutations in populations are related to insecticide control pressure, mainly that of phosphine. Differences in sequence data, assembly, and annotation also may result in different genome interpretations.

The complete mitochondrial genome of a walnut weevil, Alcidodes juglans Chao (Coleoptera: Curculionidae)

The walnut weevil, Alcidodes juglans Chao (Coleoptera: Curculionidae), is an important agricultural pest and distributed widely in China. The complete mitochondrial genome of A. juglans is 15,638 bp long, and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 21 transfer RNA (tRNA) genes and a putative control region (GenBank accession No. MH819192). The trnI gene has not been observed in the A. juglans mitogenome. The nucleotide composition is significantly biased (A, G, C, and T was 38.35%, 10.02%, 14.96%, and 36.67%, respectively) with A + T contents of 75.02%. All of the 21 tRNAs have the typical cloverleaf structure, with an exception for trnS₁ (AGN). All PCGs are initiated by ATN codons, except for cox1 with AAT instead. Ten PCGs use a common stop codon of TAA or TAG, whereas the remaining three were terminated with a single T. The phylogenetic relationships based on neighbour-joining method showed that A. juglans is closely related to Naupactus xanthographus, which is in accordance with the traditional morphological classification.

Complete mitochondrial genome sequence of fruit-piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea)

The complete mitochondrial genome of the fruit piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea) was sequenced and characterized (Genbank Accession No: KY196412). The complete mitogenome is a circular molecule of 15,575 bp length, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rrnS and rrnL), 22 transfer RNA (tRNA) genes and an A + T-rich region (D-loop). The nucleotide composition of the genome is highly A + T biased, accounting for 80.67% of nucleotides. All tRNAs have putative secondary structures that are characteristic of mitochondrial tRNA. Most of the PCGs were initiated by typical ATN codons. Five genes were initiated by unusual codons. Cox1 gene was initiated by an unusual CGA codon and terminated by the typical stop codon GAA. Six genes ended with a single T. The A + T-rich region of 336 bp consisted of repetitive sequences, including two ATAGA motifs, a 19 bp poly-T stretch and three microsatellite-like regions ((TA)4, (TA)6 and two (TA)7). Moreover, three large tandem (one 40 bp and two 25 bp) repeated elements were identified in A + T-rich region. Phylogenetic analysis using PCGs revealed that Superfamily Noctuoidea is a monophyletic group.

The complete mitochondrial genome of the cigarette beetle, Lasioderma serricorne (Coleoptera: Anobiidae)

The cigarette beetle, Lasioderma serricorne (Fabricius), is an important pest of stored commodities and distributed widely in the world. Here, we report the complete mitochondrial genome of L. serricorne which was 15,958 bp and composed of 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and a control region. The gene order and orientation of L. serricorne were identical to those of other Coleopteran mitogenomes. ATG, ATA, ATT, ATC, TTG were initiation codons and TAA, TAG, T were termination codons. All 22 tRNA genes were predicted with a typical cloverleaf structure except for trnS1 (AGN). Phylogenetic analysis performed using 13 PCGs with 14 other beetles showed that L. serricorne is closely related to Stegobium paniceum, which agree with the conventional taxonomy.

The complete mitochondrial genome of Stegobium paniceum (Coleoptera: Anobiidae)

The complete mitochondrial genome of Stegobium paniceum (Coleoptera: Anobiidae) is a circular DNA molecule of 15,271 bp (GenBank accession number XK819317), and its nucleotide composition is biased towards A + T nucleotides (78.32%). This genome comprises 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and an A + T-rich region. The gene order of S. paniceum was similar to those found in other known Coleoptera species. Sixteen reading frame overlaps and six intergenic regions were found in the mitochondrial genome of S. paniceum. All 22 tRNA genes have the typical cloverleaf secondary structure, with an exception for trnS₁ (AGN). The phylogenetic relationships based on neighbour-joining method revealed that S. paniceum is closely related to Apatides fortis, which is consistent with the traditional morphological classification.

Identification of the complete mitochondrial genome of the pacific white shrimp Litopenaeus vannamei (Decapoda: Penaeidae)

The complete mitochondrial genome (mitogenome) of Litopenaeus vannamei was determined to be 15 989 bp in size, it contains 22 tRNA genes, 13 protein-coding genes (PCGs), two rRNA genes and a D-loop region. The nucleotide composition was biased toward A + T nucleotides (67.8%) and the AT skew of this mitogenome was slightly negative (-0.025). All tRNA genes displayed a typical clover-leaf structure, except for trnS1 (AGN). Thirteen PCGs were initiated by ATN codons, except for cox1 gene which was initiated by ACG. Four of the 13 PCGs had the incomplete termination codon by T. The rrnL was 1371 bp and the rrnS was 853 bp, and the AT content of the combined rRNA genes was 70.9%. The D-loop region of the mitogenome was 985 bp in length and the A + T content was 82.7%, and no tandem repeat was found in this region. Phylogenetic analysis showed that the placement of L. vannamei was within the Penaeidae.

Characterization of the complete mitochondrial genome of the red crayfish, Procambarus clarkii (Decapoda: Cambaridae)

Here we present the complete mitochondrial (mt) genome of Procambarus clarkii (Decapoda: Cambaridae) and provide its annotation. The complete mt genome was determined to be 15 929 bp and contains 22 tRNA genes, 13 protein-coding genes (PCGs), two rRNA genes, and a D-loop region. The nucleotide composition was biased toward A + T nucleotides (72.91%) and the AT skew of this mt genome was slightly negative. All the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of trnS1 (AGN). About 13 PCGs were initiated by ATN codons, except for cox1 and nad2 genes which were initiated by ACG and GTG, respectively. Six of the 13 PCGs harbor the incomplete termination codon by T or TA. The D-loop region of the mt genome was 1188 bp in length and the A + T content was 81.08%. Phylogenetic analysis showed that the placement of P. clarkii was within the Cambaridae. This mt genome sequence will provide a better understanding for crayfish evolution in the future.