1
|
Yi J, Wu H, Liu J, Li J, Lu Y, Zhang Y, Cheng Y, Guo Y, Li D, An Y. Novel gene rearrangement in the mitochondrial genome of Anastatus fulloi (Hymenoptera Chalcidoidea) and phylogenetic implications for Chalcidoidea. Sci Rep 2022; 12:1351. [PMID: 35079090 PMCID: PMC8789778 DOI: 10.1038/s41598-022-05419-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
The genus Anastatus comprises a large group of parasitoids, including several biological control agents in agricultural and forest systems. The taxonomy and phylogeny of these species remain controversial. In this study, the mitogenome of A. fulloi Sheng and Wang was sequenced and characterized. The nearly full-length mitogenome of A. fulloi was 15,692 bp, compromising 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and a control region (CR). The total A + T contents were 83.83%, 82.18%, 87.58%, 87.27%, and 82.13% in the whole mitogenome, 13 PCGs, 22 tRNA genes, 2 rRNA genes, and CR, respectively. The mitogenome presented negative AT skews and positive GC skews, except for the CR. Most PCGs were encoded on the heavy strand, started with ATN codons, and ended with TAA codons. Among the 3736 amino acid-encoding codons, TTA (Leu1), CGA (Arg), TCA (Ser2), and TCT (Ser2) were predominant. Most tRNAs had cloverleaf secondary structures, except trnS1, with the absence of a dihydrouridine (DHU) arm. Compared with mitogenomes of the ancestral insect and another parasitoid within Eupelmidae, large-scale rearrangements were found in the mitogenome of A. fulloi, especially inversions and inverse transpositions of tRNA genes. The gene arrangements of parasitoid mitogenomes within Chalcidoidea were variable. A novel gene arrangement was presented in the mitogenome of A. fulloi. Phylogenetic analyses based on the 13 protein-coding genes of 20 parasitoids indicated that the phylogenetic relationship of 6 superfamilies could be presented as Mymaridae + (Eupelmidae + (Encyrtidae + (Trichogrammatidae + (Pteromalidae + Eulophidae)))). This study presents the first mitogenome of the Anastatus genus and offers insights into the identification, taxonomy, and phylogeny of these parasitoids.
Collapse
Affiliation(s)
- Jiequn Yi
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Han Wu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Jianbai Liu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Jihu Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yinglin Lu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yifei Zhang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yinjie Cheng
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Yi Guo
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection/Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dunsong Li
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection/Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yuxing An
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, 510316, China.
| |
Collapse
|
2
|
Zhao H, Chen Y, Wang Z, Chen H, Qin Y. Two Complete Mitogenomes of Chalcididae (Hymenoptera: Chalcidoidea): Genome Description and Phylogenetic Implications. INSECTS 2021; 12:insects12121049. [PMID: 34940137 PMCID: PMC8707279 DOI: 10.3390/insects12121049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/12/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The Chalcididae are a moderate-sized family of the superfamily Chalcidoidea in Hymenoptera, comprising 1548 species in 87 genera worldwide. Some species are potential natural enemies of pests in agriculture and forestry. Currently, there are still some controversies about the monophyly of Chalcididae and the phylogenetic relationships between Chalcididae and other families in Chalcidoidea. Based on the fact that no mitogenomic phylogenetic analyses of all of the published mitogenomes of Chalcidoidea have been conducted and no complete mitogenome of Chalcididae species has been reported, two newly completed mitochondrial genomes of Chalcididae species (Brachymeria lasus and Haltichella nipponensis) were sequenced and analyzed. The results show that the two chalcidid mitogenomes have quite similar structures and features. In phylogenetic analyses based on 13 PCGs of mitogenomes, the basal position and monophyly of Chalcididae within Chalcidoidea were supported by all trees derived from maximum likelihood (ML) and Bayesian inference (BI) methods. Abstract The complete mitochondrial genomes of two species of Chalcididae were newly sequenced: Brachymeria lasus and Haltichella nipponensis. Both circular mitogenomes are 15,147 and 15,334 bp in total length, respectively, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A+T-rich region. The nucleotide composition indicated a strong A/T bias. All PCGs of B. lasus and H. nipponensis began with the start codon ATD, except for B. lasus, which had an abnormal initiation codon TTG in ND1. Most PCGs of the two mitogenomes are terminated by a codon of TAR, and the remaining PCGs by the incomplete stop codon T or TA (ATP6, COX3, and ND4 in both species, with an extra CYTB in B. lasus). Except for trnS1 and trnF, all tRNAs can be folded into a typical clover structure. Both mitogenomes had similar control regions, and two repeat units of 135 bp were found in H. nipponensis. Phylogenetic analyses based on two datasets (PCG123 and PCG12) covering Chalcididae and nine families of Chalcidoidea were conducted using two methods (maximum likelihood and Bayesian inference); all the results support Mymaridae as the sister group of the remaining Chalcidoidea, with Chalcididae as the next successive group. Only analyses of PCG123 generated similar topologies of Mymaridae + (Chalcididae + (Agaonidae + remaining Chalcidoidea)) and provided one relative stable clade as Eulophidae + (Torymidae + (Aphelinidae + Trichogrammatidae)). Our mitogenomic phylogenetic results share one important similarity with earlier molecular phylogenetic efforts: strong support for the monophyly of many families, but a largely unresolved or unstable “backbone” of relationships among families.
Collapse
Affiliation(s)
- Huifeng Zhao
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang 065000, China; (H.Z.); (Y.C.); (H.C.)
| | - Ye Chen
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang 065000, China; (H.Z.); (Y.C.); (H.C.)
| | - Zitong Wang
- School of Forestry, Northeast Forestry University, Harbin 150040, China;
| | - Haifeng Chen
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang 065000, China; (H.Z.); (Y.C.); (H.C.)
| | - Yaoguang Qin
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang 065000, China; (H.Z.); (Y.C.); (H.C.)
- Correspondence:
| |
Collapse
|
3
|
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.
Collapse
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)
| |
Collapse
|
4
|
Novel gene rearrangement in the mitochondrial genome of Pachyneuron aphidis (Hymenoptera: Pteromalidae). Int J Biol Macromol 2020; 149:1207-1212. [PMID: 32018006 DOI: 10.1016/j.ijbiomac.2020.01.308] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/04/2020] [Accepted: 01/31/2020] [Indexed: 11/21/2022]
Abstract
Species in Hymenoptera usually show exceptionally high rates of mitochondrial molecular evolution and dramatic gene rearrangements, which has been attributed to their parasitic lifestyle. However, mitochondrial genome (mitogenome) of chalcidoid wasps is still poorly understood and the evolution of gene rearrangements is still unclear. In this study, the nearly complete mitogenome of Pachyneuron aphidis, a chalcidoid wasp mainly hyperparasitizes the Aphidius gifuensis, was sequenced using a next-generation sequencing strategy. This genome is 15,137 bp in length, including 13 PCGs, 22 tRNAs, two rRNAs and a partial control region. Alignment with other Chalcidoidea mitogenomes revealed a novel inversion in the srRNA-trnV gene cluster in P. aphidis, which is the first of its kind to be reported in Chalcidoidea. Breakpoint distances analysis showed the high value of chalcidoid wasps compare to the ancestral arrangement pattern, which reflected as extensive gene rearrangements. Despite the high frequency of gene rearrangements in these insects, analyses of gene rearrangement and phylogenetic trees showed that species from the same family and the genus tent to have similar gene orders, and the conserved gene blocks (ND3-trnG, srRNA-trnV and COIII-ATP6-ATP8-trnD-trnK-COII-trnL2-COI) can usually be identified, especially at the family level of chalcidoid wasps.
Collapse
|
5
|
Samacá-Sáenz E, Meza-Lázaro RN, Branstetter MG, Zaldívar-Riverón A. Phylogenomics and mitochondrial genome evolution of the gall-associated doryctine wasp genera (Hymenoptera: Braconidae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1685608] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ernesto Samacá-Sáenz
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. circuito exterior s/n, Cd. Universitaria, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Circuito de Posgrados, Universidad Nacional Autónoma de México, Coyoacán, C. P. 04510, Ciudad de México, México
| | - Rubi N. Meza-Lázaro
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. circuito exterior s/n, Cd. Universitaria, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Michael G. Branstetter
- USDA-ARS Pollinating Insects Research Unit, Utah State University, 5310 Old Main Hill, Logan, UT 84322-5310, USA
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. circuito exterior s/n, Cd. Universitaria, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| |
Collapse
|
6
|
Xiong M, Zhou QS, Zhang YZ. The complete mitochondrial genome of Encyrtus infelix (Hymenoptera: Encyrtidae). MITOCHONDRIAL DNA PART B-RESOURCES 2018. [DOI: 10.1080/23802359.2018.1537727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Mei Xiong
- College of Life Sciences, Hebei University, Baoding, Hebei Province, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qing-Song Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yan-Zhou Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|