Comparison of full mitochondrial genomes for the rice weevil, Sitophilus oryzae and the maize weevil, Sitophilus zeamais (Coleoptera: Curculionidae)

Ojo, James Adebayo; Valero, M. Carmen; Sun, Weilin; Coates, Brad S.; Omoloye, A. A.; Pittendrigh, Barry R.

doi:10.1016/j.aggene.2016.09.007

Cited by 12 publications

(12 citation statements)

References 65 publications

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“…However, the origins of replication of plus and minus strands are not conserved across species, for neither their primary nucleotide sequence, nor their secondary structure. It is remarkable that a similar pattern of two non-coding regions was described in some orthocerous species of weevils ( Song et al, 2020 for Apion squamigerum -Brentidae, Ojo et al, 2016 ) for Sitophilus - Rhynchophorinae), as well as in some Curculionidae ( Ceutorhynchus obstrictus - Ceutorhynchinae, Lee et al, 2019 and Trigonopterus spp-Cryptorhynchinae herein) while it is allegedly missing in other closely related species ( Rhynchophorus ferrugineus - Rhynchophorinae, Zhang et al, 2017 , Eucryptorhynchus brandti and E. chinensis - Cryptorhynchinae, Liu et al, 2016 ). Interestingly, the Rhynchophorus mitogenome of Zhang et al (2017) shows strange duplications of tRNA-Ile, tRNA-Met and tRNA-Thr, while the Eucryptorhynchus mitogenomes of Zhang et al, 2017 are missing the tRNA-Ile.…”

Section: Discussionsupporting

confidence: 65%

“…Furthermore, the precise boundaries of protein coding genes (PCGs), tRNA, and rRNA were determined by aligning the individual genes with MUSCLE v3.8.1551 ( Edgar, 2004 ) as implemented in Seaview v4.7 ( Gouy, Guindon & Gascuel, 2010 ). We used the annotated gene sequences of other beetle mitogenomes available in Genbank as references to assess the 5′ and 3′ ends of PCGs and rRNAs: Tribolium castaneum , NC_003081 ( Friedrich & Muqim, 2003 ), Eucryptorhynchus brandti , NC_025945 ( Nan, Wei & He, 2016 ), Eucryptorrhynchus chinensis NC_026719 ( Liu et al, 2016 ), Anoplophora glabripennis , DQ768215 (unpublished), Sphenophorus sp., GU176342 ( Song et al, 2010 ), Naupactus xanthographus GU176345 ( Song et al, 2010 ), Rhynchophorus ferrugineus , KT428893 ( Zhang et al, 2017 ), Sitophilus oryzae , KX373615 ( Ojo et al, 2016 ). The annotation of each tRNA gene was validated as accurate if its secondary structure matched the canonical cloverleaf structure of tRNAs in metazoans.…”

Section: Methodsmentioning

confidence: 99%

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Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

Narakusumo

Riedel

Pons

2020

PeerJ

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Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.

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Section: Discussionsupporting

confidence: 65%

Section: Methodsmentioning

confidence: 99%

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

Narakusumo

Riedel

Pons

2020

PeerJ

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“…8.7 million years ago) and closer association between the maize and rice weevils were recently reinforced with comprehensive molecular data (Ojo et al 2016, Corrêa et al 2017). This finding is consistent with the ancestral karyotype shared by both species and also resemble that of the granary weevil and their fossil records (Plarre 2010, Corrêa et al 2017), but is significantly distinct from that of the tamarind weevil.…”

Section: Discussionmentioning

confidence: 94%

Comparative cytogenetics and derived phylogenic relationship among Sitophilus grain weevils (Coleoptera, Curculionidae, Dryophthorinae)

Silva

Braga

Corrêa

et al. 2018

CCG

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Cytogenetic characteristics and genome size are powerful tools for species characterization and identification of cryptic species, providing critical insights into phylogenetic and evolutionary relationships. Sitophilus Linnaeus, 1758 grain weevils can benefit from such tools as key pest species of stored products and also as sources of archeological information on human history and past urban environments. Moreover, the phylogenetic relationship among these weevil species remains controversial and is largely based on single DNA fragment analyses. Therefore, cytogenetic analyses and genome size determinations were performed for four Sitophilus grain weevil species, namely the granary weevil Sitophilus granarius (Linnaeus, 1758), the tamarind weevil S. linearis (Herbst, 1797), the rice weevil S. oryzae (Linnaeus, 1763), and the maize weevil S. zeamais Motschulsky, 1855. Both maize and rice weevils exhibited the same chromosome number (2n=22; 10 A + Xyp). In contrast, the granary and tamarind weevils exhibited higher chromosome number (2n=24; 11 A + Xyp and 11 A + neo-XY, respectively). The nuclear DNA content of these species was not proportionally related to either chromosome number or heterochromatin amount. Maize and rice weevils exhibited similar and larger genome sizes (0.730±0.003 pg and 0.786±0.003 pg, respectively), followed by the granary weevil (0.553±0.003 pg), and the tamarind weevil (0.440±0.001 pg). Parsimony phylogenetic analysis of the insect karyotypes indicate that S. zeamais and S. oryzae were phylogenetically closer than S. granarius and S. linearis, which were more closely related and share a more recent ancestral relationship.

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“…There is only one other mitochondrial sequence of S. zeamais (GenBank: NC_030764.1) from Nigeria (Ojo et al. 2016 ). Here, we report the characterization and phylogenetic studies of the complete mitogenome of S. zeamais , which obtained by Yu Bai from Guiyang University (E106.7748235166073°, N26.556384479324556°), Guiyang City, Guizhou Province, China, on 25 August 2019, to obtain more comprehensive biological insight into the population genetics of S. zeamais .…”

mentioning

confidence: 99%

Characterization of the complete mitochondrial genome of the maize weevil, Sitophilus zeamais (Insecta: Coleoptera: Curculionidae) from Guizhou province

Zhou

2020

Mitochondrial DNA Part B

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The complete mitochondrial genome of the maize weevil Sitophilus zeamais (GenBank accession number: MN905575) from Guizhou Province consists of a circular DNA molecule of 18,421 bp (with 75.69% A þ T content), which is longer by 316 bp than that of the mitogenome of S. zeamais from Nigeria. The mitogenome comprises 13 protein-coding, 22 tRNA, and two rDNA genes. The protein-coding genes have typical ATN (Met) initiation codons and are terminated by typical TAN stop codons.

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Comparison of full mitochondrial genomes for the rice weevil, Sitophilus oryzae and the maize weevil, Sitophilus zeamais (Coleoptera: Curculionidae)

Cited by 12 publications

References 65 publications

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

Comparative cytogenetics and derived phylogenic relationship among Sitophilus grain weevils (Coleoptera, Curculionidae, Dryophthorinae)

Characterization of the complete mitochondrial genome of the maize weevil, Sitophilus zeamais (Insecta: Coleoptera: Curculionidae) from Guizhou province

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