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The complete mitochondrial genome and novel gene arrangement in Nesodiprion zhejiangensis Zhou & Xiao (Hymenoptera: Diprionidae). Funct Integr Genomics 2023; 23:41. [PMID: 36650401 DOI: 10.1007/s10142-022-00959-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/29/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023]
Abstract
The complete mitochondrial genome (mitogenome) of the sawfly, Nesodiprion zhejiangensis Zhou & Xiao, was sequenced, assembled, and deposited in GenBank (Accession Number: OM501121). The 15,660 bp N. zhejiangensis mitogenome encodes for 2 ribosomal RNAs (rrnL and rrnS), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and an AT-rich region of 450 bp in length. The nucleotide composition is biased toward adenine and thymine (A + T = 81.8%). Each PCG is initiated by an ATN codon, except for cox2, which starts with a TTG. Of 13 PCGs, 9 have a TAA termination codon, while the remainder terminate with a TAG or a single T. All tRNAs have the classic cloverleaf structure, except for the dihydrouridine (DHU) arm of tRNAval, which forms a simple loop. There are 49 helices belonging to 6 domains in rrnL and 30 helices belonging to 4 domains in rrnS. In comparison to the ancestral architecture, N. zhejiangensis has the most rearranged mitogenome in Symphyta, in which rearrangement events of local inversion and transposition are identified in three gene clusters. Specifically, the main hotspot of gene rearrangement occurred between rrnS and trnY, and rearranged from rrnS-(AT-rich region)-I-Q-M-nd2-W-C-Y to rrnS-Q-W-C-nd2-I-M-(AT-rich region)-Y, involving a local inversion event of a large gene cluster and transposition events of some tRNAs. Transposition of trnA and trnR (rearranged from A-R to R-A) was observed at the nd3-nd5 gene junction while shuffling of trnP and trnT (rearranged from T-P to P-T) occurred at the nd4l-nd6 gene junction. While illegitimate inter-mtDNA recombination might explain the opposite orientations of transcription between rrnS and trnY, transposition events of tRNA in some gene blocks can be accounted for by the tandem duplication/random loss (TDRL) model. Our phylogenetic analysis suggests that N. zhejiangensis is closely related to congeneric species N. biremis and N. japonicus, which together form a sister lineage with the European pine sawfly, Neodiprion sertifer.
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Niu G, Budak M, Korkmaz EM, Doğan Ö, Nel A, Wan S, Cai C, Jouault C, Li M, Wei M. Phylogenomic Analyses of the Tenthredinoidea Support the Familial Rank of Athaliidae (Insecta, Tenthredinoidea). INSECTS 2022; 13:858. [PMID: 36292806 PMCID: PMC9604231 DOI: 10.3390/insects13100858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
The systematic status of the genus Athalia and related genera is a perennial controversy in sawfly taxonomy. Several authors have hypothesized that the placement of Athalia within the Tenthredinidae is artificial, but no studies have focused on this topic. If the hypothesis that Athalia does not belong to Tenthredinidae can be supported, the taxonomic framework of Tenthredinoidea needs revision. We present a comprehensive phylogenomic study of Tenthredinoidae, focusing on the positions of Athalia and related genera by sampling 80 representatives mainly of the Tenthredinoidea, including Heptamelinae and Blasticotomidae. Our phylogenetic reconstructions based on nuclear genes and mitochondrial (mt) sequences support Athalia and related genera as a distinct clade sister to Tenthredinidae + (Cimbicidae + Diprionidae). A comparison of symphytan mitochondrial genomes reveals an innovative gene rearrangement pattern in Athaliidae, in which Dentathalia demonstrates a more ancestral pattern than Athalia and Hypsathalia. The lineage specificity of mt rRNA secondary structures also provides sufficient support to consider Athaliidae as a separate family. In summary, the phylogeny and genomic structural changes unanimously support the taxonomic treatment of Athaliidae as a family and the re-establishment of Dentathalia as a valid genus.
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Affiliation(s)
- Gengyun Niu
- Laboratory of Insect Systematics and Evolutionary Biology, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Ertan Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - Özgül Doğan
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey
| | - André Nel
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Siying Wan
- Laboratory of Insect Systematics and Evolutionary Biology, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Chenyang Cai
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Corentin Jouault
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
- Univ. Rennes, CNRS, Géosciences Rennes, UMR 6118, F-35000 Rennes, France
- CNRS, Institut des Sciences de l’Évolution de Montpellier, UMR 5554, 34090 Montpellier, France
| | - Min Li
- Laboratory of Insect Systematics and Evolutionary Biology, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
| | - Meicai Wei
- Laboratory of Insect Systematics and Evolutionary Biology, College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China
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Guzmán LB, Vogler RE, Beltramino AA. The mitochondrial genome of the semi-slug Omalonyx unguis (Gastropoda: Succineidae) and the phylogenetic relationships within Stylommatophora. PLoS One 2021; 16:e0253724. [PMID: 34170937 PMCID: PMC8232460 DOI: 10.1371/journal.pone.0253724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/10/2021] [Indexed: 11/23/2022] Open
Abstract
Here we report the first complete mitochondrial genome of the semi-slug Omalonyx unguis (d’Orbigny, 1836) (Gastropoda: Succineidae). Sequencing was performed on a specimen from Argentina. Assembly was performed using Sanger data and Illumina next generation sequencing (NGS). The mitogenome was 13,984 bp in length and encoded the 37 typical Metazoan genes. A potential origin for mitochondrial DNA replication was found in a non-coding intergenic spacer (49 bp) located between cox3 and tRNA-Ile genes, and its secondary structure was characterized. Secondary structure models of the tRNA genes of O. unguis largely agreed with those proposed for other mollusks. Secondary structure models for the two rRNA genes were also obtained. To our knowledge, the 12S-rRNA model derived here is the first complete one available for mollusks. Phylogenetic analyses based on the mitogenomes of O. unguis and 37 other species of Stylommatophora were performed using amino acid sequences from the 13 protein-coding genes. Our results located Succineoidea as a sister group of Helicoidea + Urocoptoidea, similar to previous studies based on mitochondrial genomes. The gene arrangement of O. unguis was identical to that reported for another species of Succineoidea. The unique rearrangements observed for this group within Stylommatophora, may constitute synapomorphies for the superfamily.
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Affiliation(s)
- Leila Belén Guzmán
- Grupo de Investigación en Genética de Moluscos (GIGeMol), Instituto de Biología Subtropical (IBS), CONICET–UNaM, Posadas, Misiones, Argentina
- * E-mail: (LBG); (AAB)
| | - Roberto Eugenio Vogler
- Grupo de Investigación en Genética de Moluscos (GIGeMol), Instituto de Biología Subtropical (IBS), CONICET–UNaM, Posadas, Misiones, Argentina
| | - Ariel Aníbal Beltramino
- Grupo de Investigación en Genética de Moluscos (GIGeMol), Instituto de Biología Subtropical (IBS), CONICET–UNaM, Posadas, Misiones, Argentina
- * E-mail: (LBG); (AAB)
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Yan Y, Niu G, Zhang Y, Ren Q, Du S, Lan B, Wei M. Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China. PeerJ 2019; 7:e7853. [PMID: 31608181 PMCID: PMC6786251 DOI: 10.7717/peerj.7853] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/08/2019] [Indexed: 11/25/2022] Open
Abstract
Labriocimbex sinicus Yan & Wei gen. et sp. nov. of Cimbicidae is described. The new genus is similar to Praia Andre and Trichiosoma Leach. A key to extant Holarctic genera of Cimbicinae is provided. To identify the phylogenetic placement of Cimbicidae, the mitochondrial genome of L. sinicus was annotated and characterized using high-throughput sequencing data. The complete mitochondrial genome of L. sinicus was obtained with a length of 15,405 bp (GenBank: MH136623; SRA: SRR8270383) and a typical set of 37 genes (22 tRNAs, 13 PCGs, and two rRNAs). The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. Remarkably, the secondary structures of the rrnS and rrnL of L. sinicus were much different from those of Corynis lateralis. Phylogenetic analyses verified the monophyly and positions of the three Cimbicidae species within the superfamily Tenthredinoidea and demonstrated a relationship as (Tenthredinidae + Cimbicidae) + (Argidae + Pergidae) with strong nodal supports. Furthermore, we found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters. Phylogenetic tree based on two methods shows that L. sinicus is the sister group of Praia with high support values. We suggest that Labriocimbex belongs to the tribe Trichiosomini of Cimbicinae based on adult morphology and molecular data. Besides, we suggest to promote the subgenus Asitrichiosoma to be a valid genus.
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Affiliation(s)
- Yuchen Yan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees; Lab of Insect Systematics and Evolutionary Biology, Central South University of Forestry and Technology, Changsha, China
| | - Gengyun Niu
- Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Yaoyao Zhang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Qianying Ren
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees; Lab of Insect Systematics and Evolutionary Biology, Central South University of Forestry and Technology, Changsha, China
| | - Shiyu Du
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees; Lab of Insect Systematics and Evolutionary Biology, Central South University of Forestry and Technology, Changsha, China
| | - Bocheng Lan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees; Lab of Insect Systematics and Evolutionary Biology, Central South University of Forestry and Technology, Changsha, China
| | - Meicai Wei
- Jiangxi Normal University, Nanchang, Jiangxi, China
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Niu G, Zhang Y, Li Z, Wei M. Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae). PeerJ 2019; 7:e6866. [PMID: 31106070 PMCID: PMC6500721 DOI: 10.7717/peerj.6866] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/28/2019] [Indexed: 11/20/2022] Open
Abstract
A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.
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Affiliation(s)
- Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Yaoyao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Zhenyi Li
- Bangor College, Central South University of Forestry and Technology, Ministry of Education, Changsha, Hunan, China
| | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi, China
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