1
|
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.
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Tan B, Wei M, Niu G. The complete mitochondrial genome of Moricella rufonota Rohwer, 1916 (Hymenoptera: Tenthredinidae) and phylogenetic analysis. Mitochondrial DNA B Resour 2021; 6:2285-2287. [PMID: 34291162 PMCID: PMC8279154 DOI: 10.1080/23802359.2021.1920859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We sequenced the complete mitochondrial genome of Moricella rufonota Rohwer, 1916 (Tenthredinidae: Nematinae). The mitogenome is 15,731 bp in length with an A + T content of 81.9%, 37 typical animal mitochondrial genes, and a 386 bp control region. All the 13 protein-coding genes initiate with a typical ATN and end with TAA. The trnI(+)-trnQ(−)-trnM(+) cluster rearranged as trnM(+)-trnQ(−)-trnI(+) cluster, and the trnW(+)-trnC(−)-trnY(−) cluster rearranged as trnC(+)-trnW(+)-trnY(−) cluster. Phylogenetic analysis confirmed that the Nematinae is the basal lineage of Tenthredinidae, and Moricella rufonota is the basal lineage of Nematinae.
Collapse
Affiliation(s)
- Beibei Tan
- College of Life Sciences, Jiangxi Normal University, Nanchang, PR China
| | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, Nanchang, PR China
| | - Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang, PR China
| |
Collapse
|
4
|
Niu G, Jiang S, Doğan Ö, Korkmaz EM, Budak M, Wu D, Wei M. Mitochondrial Phylogenomics of Tenthredinidae (Hymenoptera: Tenthredinoidea) Supports the Monophyly of Megabelesesinae as a Subfamily. INSECTS 2021; 12:495. [PMID: 34073280 PMCID: PMC8227683 DOI: 10.3390/insects12060495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022]
Abstract
Tenthredinidae represents one of the external feeders of the most diverse superfamily, Tenthredinoidea, with diverse host plant utilization. In this study, four complete mitochondrial genomes (mitogenomes), those of Cladiucha punctata, Cladiucha magnoliae, Megabeleses magnoliae, and Megabeleses liriodendrovorax, are newly sequenced and comparatively analyzed with previously reported tenthredinid mitogenomes. The close investigation of mitogenomes and the phylogeny of Tenthredinidae leads us to the following conclusions: The subfamilial relationships and phylogenetic placements within Tenthredinidae are mostly found to be similar to the previously suggested phylogenies. However, the present phylogeny supports the monophyly of Megabelesesinae as a subfamily, with the sister-group placement of Cladiucha and Megabeleses outside of Allantinae. The occurrence of the same type of tRNA rearrangements (MQI and ANS1ERF) in the mitogenomes of Megabelesesinae species and the presence of apomorphic morphological characters also provide robust evidence for this new subfamily. The divergence and diversification times of the subfamilies appear to be directly related to colonization of the flowering plants following the Early Cretaceous. The origin time and diversification patterns of Megabelesesinae were also well matched with the divergence times of their host plants from Magnoliaceae.
Collapse
Affiliation(s)
- Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.N.); (D.W.)
| | - Sijia Jiang
- College of Forestry, Beijing Forestry University, Beijing 100083, China;
| | - Özgül Doğan
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey; (Ö.D.); (M.B.); (E.M.K.)
| | - Ertan Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey; (Ö.D.); (M.B.); (E.M.K.)
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas 58140, Turkey; (Ö.D.); (M.B.); (E.M.K.)
| | - Duo Wu
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.N.); (D.W.)
| | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, Nanchang 330022, China; (G.N.); (D.W.)
| |
Collapse
|
5
|
Comparative mitogenomics of Hymenoptera reveals evolutionary differences in structure and composition. Int J Biol Macromol 2020; 144:460-472. [DOI: 10.1016/j.ijbiomac.2019.12.135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/06/2019] [Accepted: 12/15/2019] [Indexed: 01/26/2023]
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Prous M, Liston A, Kramp K, Savina H, Vårdal H, Taeger A. The West Palaearctic genera of Nematinae (Hymenoptera, Tenthredinidae). Zookeys 2019; 875:63-127. [PMID: 31579113 PMCID: PMC6760214 DOI: 10.3897/zookeys.875.35748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/30/2019] [Indexed: 11/28/2022] Open
Abstract
Keys to adults and larvae of the genera of West Palaearctic nematine sawflies are presented. Species of some of the smaller genera are keyed, and their taxonomy, distribution, and host plants reviewed, with a geographic focus on north-western Europe, particularly Sweden. Dinematus Lacourt, 2006 is a new junior subjective synonym of Pristiphora Latreille, 1810, resulting in the new combination Pristiphora krausi (Lacourt, 2006) for the type species of Dinematus. Hemichroa monticola Ermolenko, 1960 is a new junior subjective synonym of Hemichroa australis (Serville, 1823). Lectotypes are designated for Tenthredo opaca Fabricius, 1775, Mesoneura opaca var. nigerrima Enslin, 1914, Mesoneura opaca var. obscuriventris Enslin, 1914, Nematus hypogastricus Hartig, 1837, Nematus alnivorus Hartig, 1840, Leptopus rufipes Förster, 1854, Nematus protensus Förster, 1854, and Platycampus luridiventris var. pleuritica Enslin, 1915. A phylogenetic analysis based on four genes (mitochondrial COI and nuclear NaK, POL2, and TPI) supports the current generic classification.
Collapse
Affiliation(s)
- Marko Prous
- Senckenberg Deutsches Entomologisches Institut, Eberswalder Str. 90, 15374 Müncheberg, GermanySenckenberg Deutsches Entomologisches InstitutMünchebergGermany
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014 Tartu, EstoniaUniversity of TartuTartuEstonia
| | - Andrew Liston
- Senckenberg Deutsches Entomologisches Institut, Eberswalder Str. 90, 15374 Müncheberg, GermanySenckenberg Deutsches Entomologisches InstitutMünchebergGermany
| | - Katja Kramp
- Senckenberg Deutsches Entomologisches Institut, Eberswalder Str. 90, 15374 Müncheberg, GermanySenckenberg Deutsches Entomologisches InstitutMünchebergGermany
| | - Henri Savina
- Parc Majorelle, 33 chemin du Ramelet-Moundi, bât. C, apt. 16, 31100 Toulouse, FranceUnaffiliatedToulouseFrance
| | - Hege Vårdal
- Swedish Museum of Natural History, Box 50007, SE-10405 Stockholm, SwedenSwedish Museum of Natural HistoryStockholmSweden
| | - Andreas Taeger
- Senckenberg Deutsches Entomologisches Institut, Eberswalder Str. 90, 15374 Müncheberg, GermanySenckenberg Deutsches Entomologisches InstitutMünchebergGermany
| |
Collapse
|