1
|
Pfingstl T, Hiruta SF, Shimano S. Mitochondrial metagenomics reveal the independent colonization of the world's coasts by intertidal oribatid mites (Acari, Oribatida, Ameronothroidea). Sci Rep 2024; 14:11634. [PMID: 38773202 PMCID: PMC11109099 DOI: 10.1038/s41598-024-59423-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/10/2024] [Indexed: 05/23/2024] Open
Abstract
Oribatid mites are an ancient group that already roamed terrestrial ecosystems in the early and middle Devonian. The superfamily of Ameronothroidea, a supposedly monophyletic lineage, represents the only group of oribatid mites that has successfully invaded the marine coastal environment. By using mitogenome data and nucleic ribosomal RNA genes (18S, 5.8S, 28S), we show that Ameronothroidea are a paraphyletic assemblage and that the land-to-sea transition happened three times independently. Common ancestors of the tropical Fortuyniidae and Selenoribatidae were the first to colonize the coasts and molecular calibration of our phylogeny dates this event to a period in the Triassic and Jurassic era (225-146 mya), whereas present-day distribution indicates that this event might have happened early in this period during the Triassic, when the supercontinent Pangaea still existed. The cold temperate northern hemispheric Ameronothridae colonized the marine littoral later in the late Jurassic-Early Cretaceous and had an ancient distribution on Laurasian coasts. The third and final land-to-sea transition happened in the same geological period, but approx. 30 my later when ancestors of Podacaridae invaded coastal marine environments of the Gondwanan landmasses.
Collapse
Affiliation(s)
- Tobias Pfingstl
- Department of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria.
| | - Shimpei F Hiruta
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki, 305-0005, Japan
| | - Satoshi Shimano
- Science Research Center, Hosei University, Fujimi 2-17-1 Chiyoda-ku, Tokyo, 102-8160, Japan.
| |
Collapse
|
2
|
Castañeda-Osorio R, Belokobylskij SA, Jasso-Martínez JM, Samacá-Sáenz E, Kula RR, Zaldívar-Riverón A. Mitogenome architecture supports the non-monophyly of the cosmopolitan parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) recovered by nuclear and mitochondrial phylogenomics. INVERTEBR SYST 2024; 38:IS24029. [PMID: 38740060 DOI: 10.1071/is24029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Mitochondrial DNA gene organisation is an important source of phylogenetic information for various metazoan taxa at different evolutionary timescales, though this has not been broadly tested for all insect groups nor within a phylogenetic context. The cosmopolitan subfamily Doryctinae is a highly diverse group of braconid wasps mainly represented by ectoparasitoids of xylophagous beetle larvae. Previous molecular studies based on Sanger and genome-wide (ultraconserved elements, UCE; and mitochondrial genomes) sequence data have recovered a non-monophyletic Doryctinae, though the relationships involved have always been weakly supported. We characterised doryctine mitogenomes and conducted separate phylogenetic analyses based on mitogenome and UCE sequence data of ~100 representative doryctine genera to assess the monophyly and higher-level classification of the subfamily. We identified rearrangements of mitochondrial transfer RNAs (tRNAs) that support a non-monophyletic Doryctinae consisting of two separate non-related clades with strong geographic structure ('New World' and 'Old World' clades). This geographic structure was also consistently supported by the phylogenetic analyses preformed with mitogenome and UCE sequence data. These results highlight the utility of the mitogenome gene rearrangements as a potential source of phylogenetic information at different evolutionary timescales.
Collapse
Affiliation(s)
- Rubén Castañeda-Osorio
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México; and Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1er Piso, Circuito de Posgrados, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sergey A Belokobylskij
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, Saint Petersburg, Russian Federation
| | - Jovana M Jasso-Martínez
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México; and Department of Entomology, Smithsonian Institution, National Museum of Natural History, 10th Street & Constitution Avenue NW, Washington, DC, USA
| | - Ernesto Samacá-Sáenz
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México
| | - Robert R Kula
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, c/o Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México
| |
Collapse
|
3
|
Najer T, Doña J, Buček A, Sweet AD, Sychra O, Johnson KP. Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution. PLoS Genet 2024; 20:e1011266. [PMID: 38701107 PMCID: PMC11095710 DOI: 10.1371/journal.pgen.1011266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 05/15/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
While mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, many species of parasitic lice (Insecta: Phthiraptera) are among the notable exceptions, having mitogenomes fragmented into multiple circular chromosomes. To better understand the process of mitogenome fragmentation, we conducted a large-scale genomic study of a major group of lice, Amblycera, with extensive taxon sampling. Analyses of the evolution of mitogenome structure across a phylogenomic tree of 90 samples from 53 genera revealed evidence for multiple independent origins of mitogenome fragmentation, some inferred to have occurred less than five million years ago. We leveraged these many independent origins of fragmentation to compare the rates of DNA substitution and gene rearrangement, specifically contrasting branches with fragmented and non-fragmented mitogenomes. We found that lineages with fragmented mitochondrial genomes had significantly higher rates of mitochondrial sequence evolution. In addition, lineages with fragmented mitochondrial genomes were more likely to have mitogenome gene rearrangements than those with single-chromosome mitochondrial genomes. By combining phylogenomics and mitochondrial genomics we provide a detailed portrait of mitogenome evolution across this group of insects with a remarkably unstable mitogenome structure, identifying processes of molecular evolution that are correlated with mitogenome fragmentation.
Collapse
Affiliation(s)
- Tomáš Najer
- Department of Veterinary Sciences, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
| | - Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
- Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Aleš Buček
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Okinawa Institute of Science & Technology Graduate University, Onna-son, Okinawa, Japan
| | - Andrew D. Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Oldřich Sychra
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, Illinois, United States of America
| |
Collapse
|
4
|
Sandberg TOM, Yahalomi D, Bracha N, Haddas-Sasson M, Pupko T, Atkinson SD, Bartholomew JL, Zhang JY, Huchon D. Evolution of myxozoan mitochondrial genomes: insights from myxobolids. BMC Genomics 2024; 25:388. [PMID: 38649808 PMCID: PMC11034133 DOI: 10.1186/s12864-024-10254-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both a lack of informative morphological characters and a shortage of molecular markers. Mitochondrial (mt) genomes are a common marker in phylogeny and biogeography. However, only five complete myxozoan mt genomes have been sequenced: four belonging to two closely related genera, Enteromyxum and Kudoa, and one from the genus Myxobolus. Interestingly, while cytochrome oxidase genes could be identified in Enteromyxum and Kudoa, no such genes were found in Myxobolus squamalis, and another member of the Myxobolidae (Henneguya salminicola) was found to have lost its entire mt genome. To evaluate the utility of mt genomes to reconstruct myxozoan relationships and to understand if the loss of cytochrome oxidase genes is a characteristic of myxobolids, we sequenced the mt genome of five myxozoans (Myxobolus wulii, M. honghuensis, M. shantungensis, Thelohanellus kitauei and, Sphaeromyxa zaharoni) using Illumina and Oxford Nanopore platforms. RESULTS Unlike Enteromyxum, which possesses a partitioned mt genome, the five mt genomes were encoded on single circular chromosomes. An mt plasmid was found in M. wulii, as described previously in Kudoa iwatai. In all new myxozoan genomes, five protein-coding genes (cob, cox1, cox2, nad1, and nad5) and two rRNAs (rnl and rns) were recognized, but no tRNA. We found that Myxobolus and Thelohanellus species shared unidentified reading frames, supporting the view that these mt open reading frames are functional. Our phylogenetic reconstructions based on the five conserved mt genes agree with previously published trees based on the 18S rRNA gene. CONCLUSIONS Our results suggest that the loss of cytochrome oxidase genes is not a characteristic of all myxobolids, the ancestral myxozoan mt genome was likely encoded on a single circular chromosome, and mt plasmids exist in a few lineages. Our findings indicate that myxozoan mt sequences are poor markers for reconstructing myxozoan phylogenetic relationships because of their fast-evolutionary rates and the abundance of repeated elements, which complicates assembly.
Collapse
Affiliation(s)
| | - Dayana Yahalomi
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Noam Bracha
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Michal Haddas-Sasson
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Stephen D Atkinson
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jerri L Bartholomew
- Department of Microbiology, Oregon State University, 97331, Corvallis, OR, USA
| | - Jin Yong Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, 6997801, Tel Aviv, Israel.
| |
Collapse
|
5
|
Sterling-Montealegre RA, Prada CF. Variability and evolution of gene order rearrangement in mitochondrial genomes of arthropods (except Hexapoda). Gene 2024; 892:147906. [PMID: 37844850 DOI: 10.1016/j.gene.2023.147906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
In the species-rich Phylum Arthropoda, the mitochondrial genome is relatively well conserved both in terms of number and order of genes. However, specific clades have a 'typical' gene order that differs from the putative arthropod ancestral arrangement. The aim of this work was to compare the rate of mitochondrial gene rearrangements at inter- and intra-taxonomic levels in the Arthropoda and to postulate the most parsimonious ancestral orders representing the four major arthropod lineages. For this purpose, we performed a comparative genomic analysis of arthropod mitochondrial genomes available in the NCBI database. Using a combination of bioinformatics methods that examined mitochondrial gene rearrangements in 464 species of arthropods from three subphyla (Chelicerata, Myriapoda, and Crustacea [except Hexapoda, previously analyzed]), we observed differences in the rate of rearrangement within major lineages. A higher rate of mitochondrial genome rearrangement was observed in Crustacea and Chelicerata compared to Myriapoda. Likewise, early branching clades exhibit less variability in mitochondrial genome order than late branching clades, within each subphylum. We identified 'hot regions' in the mitochondrial genome of each studied subphylum, and postulated the most likely ancestral gene order in each subphylum and taxonomic order. Our work provides new evidence on the evolutionary dynamics of mitochondrial genome gene order in arthropods and new mitochondrial genome architectures in different taxonomic divisions within each major lineage of arthropods.
Collapse
Affiliation(s)
| | - Carlos Fernando Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia.
| |
Collapse
|
6
|
Su CY, Zhu DH, Abe Y, Ide T, Liu Z. The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae). PeerJ 2023; 11:e15865. [PMID: 37810770 PMCID: PMC10557937 DOI: 10.7717/peerj.15865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/17/2023] [Indexed: 10/10/2023] Open
Abstract
Mitochondrial genomes (mitogenomes) have been widely used in comparative and evolutionary genomics, molecular evolution, phylogenetics, and population genetics, but very limited information is available for the family Cynipidae. In this report, we describe the mitogenome of Dryocosmus liui Pang, Su et Zhu, providing the first complete mitogenomic data for a cynipid gall wasp species. The mitogenome of D. liui is 16,819 bp in length, and contains the typical set of 37 genes. Two control regions were detected, with the second being a perfect inverted repeat of the major portion of the first. Gene rearrangements were found in transfer RNA (tRNA) genes, protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes, compared with the putative ancestral mitogenome. Similar to two other Cynipidae species with mitogenome data available, D. liui has a novel tRNA gene cluster trnL1-trnI-trnL2-trnW-trnM-trnQ between nad1 and nad2. Phylogenetic analysis based on sequences of PCGs and rRNA genes with D. liui included obtained topologies identical to previous studies supporting the a relationship of (Cynipoidea , (Platygastroidea, Proctotrupoidea)) within the monophyletic Proctotrupomorpha and (Cynipidae, Figitidae), Ibaliidae) within the Cynipoidea.
Collapse
Affiliation(s)
- Cheng-Yuan Su
- Laboratory of Insect Behavior and Evolutionary Ecology, College of Life Science and Technology, Central South University of Forestry & Technology (CSUFT), Changsha, Hunan, China
| | - Dao-Hong Zhu
- Laboratory of Insect Behavior and Evolutionary Ecology, College of Life Science and Technology, Central South University of Forestry & Technology (CSUFT), Changsha, Hunan, China
| | - Yoshihisa Abe
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Kyushu, Japan
| | - Tatsuya Ide
- Department of Zoology, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Zhiwei Liu
- Biological Sciences Department, Eastern Illinois University, Charleston, IL, United States of America
| |
Collapse
|
7
|
Dong Y, Jelocnik M, Gillett A, Valenza L, Conroy G, Potvin D, Shao R. Mitochondrial Genome Fragmentation Occurred Multiple Times Independently in Bird Lice of the Families Menoponidae and Laemobothriidae. Animals (Basel) 2023; 13:2046. [PMID: 37370555 DOI: 10.3390/ani13122046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Mitochondrial (mt) genome fragmentation has been discovered in all five parvorders of parasitic lice (Phthiraptera). To explore whether minichromosomal characters derived from mt genome fragmentation are informative for phylogenetic studies, we sequenced the mt genomes of 17 species of bird lice in Menoponidae and Laemobothriidae (Amblycera). Four species of Menoponidae (Actornithophilus sp. 1 ex [pied oystercatcher], Act. sp. 2 ex [masked lapwing], Austromenopon sp. 2 ex [sooty tern and crested tern], Myr. sp. 1 ex [satin bowerbird]) have fragmented mt genomes, whereas the other 13 species retain the single-chromosome mt genomes. The two Actornithophilus species have five and six mt minichromosomes, respectively. Aus. sp. 2 ex [sooty tern and crested tern] has two mt minichromosomes, in contrast to Aus. sp. 1 ex [sooty shearwater], which has a single mt chromosome. Myr. sp. 1 ex [satin bowerbird] has four mt minichromosomes. When mapped on the phylogeny of Menoponidae and Laemobothriidae, it is evident that mt genome fragmentation has occurred multiple times independently among Menoponidae and Laemobothriidae species. We found derived mt minichromosomal characters shared between Myrsidea species, between Actornithophilus species, and between and among different ischnoceran genera, respectively. We conclude that while mt genome fragmentation as a general feature does not unite all the parasitic lice that have this feature, each independent mt genome fragmentation event does produce minichromosomal characters that can be informative for phylogenetic studies of parasitic lice at different taxonomic levels.
Collapse
Affiliation(s)
- Yalun Dong
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia
| | - Martina Jelocnik
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia
| | - Amber Gillett
- Australia Zoo Wildlife Hospital, 1638 Steve Irwin Way, Beerwah, QLD 4519, Australia
| | - Ludovica Valenza
- Australia Zoo Wildlife Hospital, 1638 Steve Irwin Way, Beerwah, QLD 4519, Australia
| | - Gabriel Conroy
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia
| | - Dominique Potvin
- School of Science, Technology and Engineering, University of the Sunshine Coast, 1 Moreton Parade, Petrie, QLD 4502, Australia
| | - Renfu Shao
- Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556, Australia
| |
Collapse
|
8
|
Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
Collapse
Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
| |
Collapse
|
9
|
Johnson KP. Genomic Approaches to Uncovering the Coevolutionary History of Parasitic Lice. Life (Basel) 2022; 12:life12091442. [PMID: 36143478 PMCID: PMC9501036 DOI: 10.3390/life12091442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary New sequencing technologies have now made it possible to sequence entire genomes for a diversity of life on earth. Parasites comprise nearly half of all species. Lice are one important group of parasites of birds and mammals, including humans. Genome sequencing approaches have been applied to this group of parasites to uncover patterns of diversification. These patterns can be compared to the patterns of diversification in their hosts. Key findings from these studies have revealed that parasitic lice likely originated on birds and then switched to mammals multiple times. Within groups of birds and mammals, the evolutionary trees of lice match those for mammal hosts more than those for birds. Genomic approaches have also revealed that individual birds and mammals harbor distinct populations of lice. Thus, these new techniques allow for the study of patterns of diversification at a wide variety of scales. Abstract Next-generation sequencing technologies are revolutionizing the fields of genomics, phylogenetics, and population genetics. These new genomic approaches have been extensively applied to a major group of parasites, the lice (Insecta: Phthiraptera) of birds and mammals. Two louse genomes have been assembled and annotated to date, and these have opened up new resources for the study of louse biology. Whole genome sequencing has been used to assemble large phylogenomic datasets for lice, incorporating sequences of thousands of genes. These datasets have provided highly supported trees at all taxonomic levels, ranging from relationships among the major groups of lice to those among closely related species. Such approaches have also been applied at the population scale in lice, revealing patterns of population subdivision and inbreeding. Finally, whole genome sequence datasets can also be used for additional study beyond that of the louse nuclear genome, such as in the study of mitochondrial genome fragmentation or endosymbiont function.
Collapse
Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| |
Collapse
|
10
|
Independent evolution of highly variable, fragmented mitogenomes of parasitic lice. Commun Biol 2022; 5:677. [PMID: 35804150 PMCID: PMC9270496 DOI: 10.1038/s42003-022-03625-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/22/2022] [Indexed: 11/08/2022] Open
Abstract
The mitochondrial genomes (mitogenomes) of bilaterian animals are highly conserved structures that usually consist of a single circular chromosome. However, several species of parasitic lice (Insecta: Phthiraptera) possess fragmented mitogenomes, where the mitochondrial genes are present on separate, circular chromosomes. Nevertheless, the extent, causes, and consequences of this structural variation remain poorly understood. Here, we combined new and existing data to better understand the evolution of mitogenome fragmentation in major groups of parasitic lice. We found strong evidence that fragmented mitogenomes evolved many times within parasitic lice and that the level of fragmentation is highly variable, including examples of heteroplasmic arrangements. We also found a significant association between mitochondrial fragmentation and signatures of relaxed selection. Mitochondrial fragmentation was also associated with changes to a lower AT%, possibly due to differences in mutation biases. Together, our results provide a significant advance in understanding the process of mitogenome fragmentation and provide an important perspective on mitochondrial evolution in eukaryotes.
Collapse
|
11
|
Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies. Sci Rep 2022; 12:7028. [PMID: 35487927 PMCID: PMC9054809 DOI: 10.1038/s41598-022-10547-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/21/2022] [Indexed: 11/08/2022] Open
Abstract
Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.
Collapse
|
12
|
Complete Mitochondrial Genomes of Metcalfa pruinosa and Salurnis marginella (Hemiptera: Flatidae): Genomic Comparison and Phylogenetic Inference in Fulgoroidea. Curr Issues Mol Biol 2021; 43:1391-1418. [PMID: 34698117 PMCID: PMC8929015 DOI: 10.3390/cimb43030099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/30/2022] Open
Abstract
The complete mitochondrial genomes (mitogenomes) of two DNA barcode-defined haplotypes of Metcalfa pruinosa and one of Salurnis marginella (Hemiptera: Flatidae) were sequenced and compared to those of other Fulgoroidea species. Furthermore, the mitogenome sequences were used to reconstruct phylogenetic relationships among fulgoroid families. The three mitogenomes, including that of the available species of Flatidae, commonly possessed distinctive structures in the 1702-1836 bp A+T-rich region, such as two repeat regions at each end and a large centered nonrepeat region. All members of the superfamily Fulgoroidea, including the Flatidae, consistently possessed a motiflike sequence (TAGTA) at the ND1 and trnS2 junction. The phylogenetic analyses consistently recovered the familial relationships of (((((Ricaniidae + Issidae) + Flatidae) + Fulgoridae) + Achilidae) + Derbidae) in the amino acid-based analysis, with the placement of Cixiidae and Delphacidae as the earliest-derived lineages of fulgoroid families, whereas the monophyly of Delphacidae was not congruent between tree-constructing algorithms.
Collapse
|
13
|
Spradling TA, Place AC, Campbell AL, Demastes JW. Mitochondrial genome of Geomydoecus aurei, a pocket-gopher louse. PLoS One 2021; 16:e0254138. [PMID: 34314423 PMCID: PMC8315533 DOI: 10.1371/journal.pone.0254138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/18/2021] [Indexed: 11/28/2022] Open
Abstract
Parasitic lice demonstrate an unusual array of mitochondrial genome architectures and gene arrangements. We characterized the mitochondrial genome of Geomydoecus aurei, a chewing louse (Phthiraptera: Trichodectidae) found on pocket gophers (Rodentia: Geomyidae) using reads from both Illumina and Oxford Nanopore sequencing coupled with PCR, cloning, and Sanger sequencing to verify structure and arrangement for each chromosome. The genome consisted of 12 circular mitochondrial chromosomes ranging in size from 1,318 to 2,088 nucleotides (nt). Total genome size was 19,015 nt. All 37 genes typical of metazoans (2 rRNA genes, 22 tRNA genes, and 13 protein-coding genes) were present. An average of 26% of each chromosome was composed of non-gene sequences. Within the non-gene region of each chromosome, there was a 79-nt nucleotide sequence that was identical among chromosomes and a conserved sequence with secondary structure that was always followed by a poly-T region. We hypothesize that these regions may be important in the initiation of transcription and DNA replication, respectively. The G. aurei genome shares 8 derived gene clusters with other chewing lice of mammals, but in G. aurei, genes on several chromosomes are not contiguous.
Collapse
Affiliation(s)
- Theresa A. Spradling
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa, United States of America
| | - Alexandra C. Place
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa, United States of America
| | - Ashley L. Campbell
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa, United States of America
| | - James W. Demastes
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa, United States of America
| |
Collapse
|
14
|
Nie Y, Fu YT, Zhang Y, Deng YP, Wang W, Tu Y, Liu GH. Highly rearranged mitochondrial genome in Falcolipeurus lice (Phthiraptera: Philopteridae) from endangered eagles. Parasit Vectors 2021; 14:269. [PMID: 34016171 PMCID: PMC8139141 DOI: 10.1186/s13071-021-04776-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background Fragmented mitochondrial (mt) genomes and extensive mt gene rearrangements have been frequently reported from parasitic lice (Insecta: Phthiraptera). However, relatively little is known about the mt genomes from the family Philopteridae, the most species-rich family within the suborder Ischnocera. Methods Herein, we use next-generation sequencing to decode the mt genome of Falcolipeurus suturalis and compare it with the mt genome of F. quadripustulatus. Phylogenetic relationships within the family Philopteridae were inferred from the concatenated 13 protein-coding genes of the two Falcolipeurus lice and members of the family Philopteridae using Bayesian inference (BI) and maximum likelihood (ML) methods. Results The complete mt genome of F. suturalis is a circular, double-stranded DNA molecule 16,659bp in size that contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and three non-coding regions. The gene order of the F. suturalis mt genome is rearranged relative to that of F. quadripustulatus, and is radically different from both other louse species and the putative ancestral insect. Phylogenetic analyses revealed clear genetic distinctiveness between F. suturalis and F. quadripustulatus (Bayesian posterior probabilities=1.0 and bootstrapping frequencies=100), and that the genus Falcolipeurus is sister to the genus Ibidoecus (Bayesian posterior probabilities=1.0 and bootstrapping frequencies=100). Conclusions These datasets help to better understand gene rearrangements in lice and the phylogenetic position of Falcolipeurus and provide useful genetic markers for systematic studies of bird lice. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04776-5.
Collapse
Affiliation(s)
- Yu Nie
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yi-Tian Fu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yu Zhang
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Yuan-Ping Deng
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Wei Wang
- School of Science and Engineering, GeneCology Research Centre, Animal Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Ya Tu
- Beijing Wildlife Rescue and Rehabilitation Center, Beijing, 101300, China.
| | - Guo-Hua Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128, Hunan, China.
| |
Collapse
|
15
|
Moreno-Carmona M, Cameron SL, Prada Quiroga CF. How are the mitochondrial genomes reorganized in Hexapoda? Differential evolution and the first report of convergences within Hexapoda. Gene 2021; 791:145719. [PMID: 33991648 DOI: 10.1016/j.gene.2021.145719] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/13/2021] [Accepted: 05/10/2021] [Indexed: 11/28/2022]
Abstract
The evolution of the Hexapoda mitochondrial genome has been the focus of several genetic and evolutionary studies over the last decades. However, they have concentrated on certain taxonomic orders of economic or health importance. The recent increase of mitochondrial genomes sequencing of diverse taxonomic orders generates an important opportunity to clarify the evolution of this group of organisms. However, there is no comparative study that investigates the evolution of the Hexapoda mitochondrial genome. In order to verify the level of rearrangement and the mitochondrial genome evolution, we performed a comparative genomic analysis of the Hexapoda mitochondrial genome available in the NCBI database. Using a combination of bioinformatics methods to carefully examine the mitochondrial gene rearrangements in 1198 Hexapoda species belonging to 32 taxonomic orders, we determined that there is a great variation in the rate of rearrangement by gene and by taxonomic order. A higher rate of genetic reassortment is observed in Phthiraptera, Thysanoptera, Protura, and Hymenoptera; compared to other taxonomic orders. Twenty-four events of convergence in the genetic order between different taxonomic orders were determined, most of them not previously reported; which proves the great evolutionary dynamics within Hexapoda.
Collapse
Affiliation(s)
- Manuela Moreno-Carmona
- Grupo de investigación de Biología y ecología de artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia
| | - Stephen L Cameron
- Department of Entomology, Purdue University, 901 West State Street, West Lafayette, IN 47907, USA
| | - Carlos Fernando Prada Quiroga
- Grupo de investigación de Biología y ecología de artrópodos, Facultad de Ciencias, Universidad del Tolima, Colombia.
| |
Collapse
|
16
|
Sweet AD, Johnson KP, Cao Y, de Moya RS, Skinner RK, Tan M, Virrueta Herrera S, Cameron SL. Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera. Gene 2020; 768:145312. [PMID: 33220346 DOI: 10.1016/j.gene.2020.145312] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/03/2020] [Accepted: 11/13/2020] [Indexed: 11/28/2022]
Abstract
Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.
Collapse
Affiliation(s)
- Andrew D Sweet
- Department of Entomology, Purdue University, West Lafayette, IN, USA; Department of Biological Sciences, Arkansas State University, State University, AR, USA.
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Yanghui Cao
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Robert S de Moya
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA; Department of Entomology, University of Illinois, Urbana, IL, USA
| | - Rachel K Skinner
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA; Department of Entomology, University of Illinois, Urbana, IL, USA
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA; Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, USA
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
17
|
Martinů J, Štefka J, Poosakkannu A, Hypša V. "Parasite turnover zone" at secondary contact: A new pattern in host-parasite population genetics. Mol Ecol 2020; 29:4653-4664. [PMID: 32985035 DOI: 10.1111/mec.15653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/22/2020] [Accepted: 09/11/2020] [Indexed: 01/13/2023]
Abstract
We describe here a new pattern of population genetic structure in a host-parasite system that can arise after secondary contact of previously isolated populations. Due to different generation times, and therefore different tempos of molecular evolution, the host and parasite populations reach different degrees of genetic differentiation during their separation (e.g., in refugia). Consequently, upon secondary contact, the host populations are able to re-establish a single panmictic population across the area of contact, while the parasite populations stop their dispersal at the secondary contact zone and create a narrow hybrid zone. From the host's perspective, the parasite's hybrid zone functions on a microevolutionary scale as a "parasite turnover zone": while the hosts are passing from area A to area B, their parasites turn genetically from the area A genotypes to the area B genotypes. We demonstrate this novel pattern with a model composed of Apodemus mice and Polyplax lice by comparing maternally inherited markers (complete mitochondrial genomes, and complete genomes of the vertically transmitted symbiont Legionella polyplacis) with single nucleotide polymorphisms derived from louse genomic data. We discuss the circumstances that may lead to this pattern and possible reasons why it has been overlooked in studies of host-parasite population genetics.
Collapse
Affiliation(s)
- Jana Martinů
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.,Institute of Parasitology, Biology Centre CAS, v.v.i., České Budějovice, Czech Republic
| | - Jan Štefka
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.,Institute of Parasitology, Biology Centre CAS, v.v.i., České Budějovice, Czech Republic
| | - Anbu Poosakkannu
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| |
Collapse
|
18
|
Estrada-Souza IM, Sánchez-Montes S, Romero-Salas D, Cruz-Romero A, Aguilar-Domínguez M, Pérez-Brígido CD, Hermida-Lagunes J, Morales-Diaz J, Saelao P, Becker I, Pérez de León AA. Integrative taxonomic description of the chewing louse Tricholipeurus lipeuroides infesting Odocoileus virginianus veraecrucis white-tailed deer in Veracruz, Mexico. Parasitol Res 2020; 119:3203-3209. [PMID: 32820383 DOI: 10.1007/s00436-020-06855-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/16/2020] [Indexed: 10/23/2022]
Abstract
Chewing lice (Phthiraptera: Amblycera, Ischnocera) represent a component of the ectoparasite fauna associated with large sized mammals as deers. However, the diversity of chewing louse species infesting deer remains to be fully characterized in the Neotropics. Little is known about the chewing lice infesting the extant fourteen subspecies of white-tailed deer (Odocoileus virginianus) in Mexico. Known to infest white-tailed deer (WTD) in Canada and the United States (U.S.), Tricholipeurus lipeuroides is a chewing louse species that was originally described in the nineteenth century infesting O. v. mexicanus in Mexico. For the first time, infestation of O. v. veraecrucis, a Neotropical WTD subspecies in Mexico, with T. lipeuroides is reported herein. An integrative taxonomic approach was taken by combining morphological and molecular analyses to describe the T. lipeuroides infestion of O. v. veraecrucis. Ecological parameters of the T. lipeuroides infestations were also calculated. The prevalence was 91.7% of the 56 O. v. veraecrucis (29 females and 27 males) inspected while under chemical restraint that were sampled at 3 sites in the central region of Veracruz state in Mexico. The amplification and sequencing of previously reported T. lipeuroides Cytochrome Oxidase Subunit I gene confirmed the identity of all the chewing louse life stages. These results are discussed in the context of comparative analyses on the emergence of novel chewing lice-deer associations.
Collapse
Affiliation(s)
- Iris M Estrada-Souza
- Laboratorio de Parasitología, Rancho "Torreón del Molino", Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Circunvalación y Yáñez s/n, C.P. 91710, Veracruz, Mexico
| | - Sokani Sánchez-Montes
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Facultad de Ciencias Biológicas Agropecuarias, Universidad Veracruzana, Tuxpam, Veracruz, Mexico
| | - Dora Romero-Salas
- Laboratorio de Parasitología, Rancho "Torreón del Molino", Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Circunvalación y Yáñez s/n, C.P. 91710, Veracruz, Mexico.
| | - Anabel Cruz-Romero
- Laboratorio de Parasitología, Rancho "Torreón del Molino", Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Circunvalación y Yáñez s/n, C.P. 91710, Veracruz, Mexico
| | - Mariel Aguilar-Domínguez
- Laboratorio de Parasitología, Rancho "Torreón del Molino", Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Circunvalación y Yáñez s/n, C.P. 91710, Veracruz, Mexico
| | | | - Javier Hermida-Lagunes
- Laboratorio de Parasitología, Rancho "Torreón del Molino", Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Circunvalación y Yáñez s/n, C.P. 91710, Veracruz, Mexico
| | - Jorge Morales-Diaz
- Laboratorio de Parasitología, Rancho "Torreón del Molino", Facultad de Medicina Veterinaria y Zootecnia, Universidad Veracruzana, Circunvalación y Yáñez s/n, C.P. 91710, Veracruz, Mexico
| | - Perot Saelao
- USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, 2700 Fredericksburg Road, Kerrville, TX, USA
| | - Ingeborg Becker
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Adalberto A Pérez de León
- USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory and Veterinary Pest Genomics Center, 2700 Fredericksburg Road, Kerrville, TX, USA.
| |
Collapse
|
19
|
Sweet AD, Johnson KP, Cameron SL. Mitochondrial genomes of Columbicola feather lice are highly fragmented, indicating repeated evolution of minicircle-type genomes in parasitic lice. PeerJ 2020; 8:e8759. [PMID: 32231878 PMCID: PMC7098387 DOI: 10.7717/peerj.8759] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/16/2020] [Indexed: 01/21/2023] Open
Abstract
Most animals have a conserved mitochondrial genome structure composed of a single chromosome. However, some organisms have their mitochondrial genes separated on several smaller circular or linear chromosomes. Highly fragmented circular chromosomes (“minicircles”) are especially prevalent in parasitic lice (Insecta: Phthiraptera), with 16 species known to have between nine and 20 mitochondrial minicircles per genome. All of these species belong to the same clade (mammalian lice), suggesting a single origin of drastic fragmentation. Nevertheless, other work indicates a lesser degree of fragmentation (2–3 chromosomes/genome) is present in some avian feather lice (Ischnocera: Philopteridae). In this study, we tested for minicircles in four species of the feather louse genus Columbicola (Philopteridae). Using whole genome shotgun sequence data, we applied three different bioinformatic approaches for assembling the Columbicola mitochondrial genome. We further confirmed these approaches by assembling the mitochondrial genome of Pediculus humanus from shotgun sequencing reads, a species known to have minicircles. Columbicola spp. genomes are highly fragmented into 15–17 minicircles between ∼1,100 and ∼3,100 bp in length, with 1–4 genes per minicircle. Subsequent annotation of the minicircles indicated that tRNA arrangements of minicircles varied substantially between species. These mitochondrial minicircles for species of Columbicola represent the first feather lice (Philopteridae) for which minicircles have been found in a full mitochondrial genome assembly. Combined with recent phylogenetic studies of parasitic lice, our results provide strong evidence that highly fragmented mitochondrial genomes, which are otherwise rare across the Tree of Life, evolved multiple times within parasitic lice.
Collapse
Affiliation(s)
- Andrew D Sweet
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, United States of America
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| |
Collapse
|
20
|
Ono H, Yoshida MA. Direct RNA sequencing approach to compare non-model mitochondrial transcriptomes: An application to a cephalopod host and its mesozoan parasite. Methods 2020; 176:55-61. [PMID: 32151668 DOI: 10.1016/j.ymeth.2020.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 11/28/2022] Open
Abstract
To identify non-protein coding as well as truncated or premature RNA sequences expressed and obtain more complete transcriptome information, we combined the MinION direct RNA-sequencing of a conventional poly(A) RNA purification method with poly(A)-tagging of the non-coding RNA (ncRNA) fraction. This approach was applied to transcriptome sequencing of the dicyemid mesozoan, Dicyema misakiense, which has minicircular mitochondrial DNA molecules where each molecule encodes a single gene, as well as the host. Using informatics analysis, we distinguished dicyemid RNAs from those of the host squid. The poly(A) RNAs were assigned to host mitochondrial genes, host nuclear protein-coding genes, Dicyema nuclear protein-coding genes, and Dicyema mitochondrial genes in the decreasing order. Our poly(A)-tailing method recovered significantly more ncRNAs from the host compared with the sequencing of poly(A) RNAs. Furthermore, our method captured various lengths of squid mitochondrial DNA (mtDNA) transcripts at different steps of maturation including a read of 3,500 bp, which covers 21% of the squid mitochondrial genome, possibly a premature host RNA product. In contrast, shorter and less abundant reads were recovered from the dicyemid mitochondrial RNAs (mtRNAs). Even the longest read was 307 bp covering only a part of a minicircle. This study revealed significantly different modes of the mitochondrial transcription between a mesozoan and the host. Our approach to perform direct RNA-sequencing combined with the poly(A)-tailing reaction can be an effective method to fully capture non-poly(A) transcripts in a wide range of organisms.
Collapse
Affiliation(s)
- Hiroki Ono
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Japan
| | - Masa-Aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Japan.
| |
Collapse
|
21
|
Jeong JS, Kim MJ, Kim I. The mitochondrial genome of the dung beetle, Copris tripartitus, with mitogenomic comparisons within Scarabaeidae (Coleoptera). Int J Biol Macromol 2020; 144:874-891. [DOI: 10.1016/j.ijbiomac.2019.09.165] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 11/25/2022]
|
22
|
Sun S, Sha Z, Wang Y. The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications. Ecol Evol 2019; 9:12390-12407. [PMID: 31788185 PMCID: PMC6875667 DOI: 10.1002/ece3.5542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/31/2019] [Accepted: 07/19/2019] [Indexed: 12/14/2022] Open
Abstract
Hydrothermal vents are considered as one of the most extremely harsh environments on the Earth. In this study, the complete mitogenomes of hydrothermal vent squat lobsters, Munidopsis lauensis and M. verrilli, were determined through Illumina sequencing and compared with other available mitogenomes of anomurans. The mitogenomes of M. lauensis (17,483 bp) and M. verrilli (17,636 bp) are the largest among all Anomura mitogenomes, while the A+T contents of M. lauensis (62.40%) and M. verrilli (63.99%) are the lowest. The mitogenomes of M. lauensis and M. verrilli display novel gene arrangements, which might be the result of three tandem duplication-random loss (tdrl) events from the ancestral pancrustacean pattern. The mitochondrial gene orders of M. lauensis and M. verrilli shared the most similarities with S. crosnieri. The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri. Positive selection analysis revealed that eighteen residues in seven genes (atp8, Cytb, nad3, nad4, nad4l, nad5, and nad6) of the hydrothermal vent anomurans were positively selected sites.
Collapse
Affiliation(s)
- Shao'e Sun
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Zhongli Sha
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yanrong Wang
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| |
Collapse
|
23
|
Song F, Li H, Liu GH, Wang W, James P, Colwell DD, Tran A, Gong S, Cai W, Shao R. Mitochondrial Genome Fragmentation Unites the Parasitic Lice of Eutherian Mammals. Syst Biol 2019; 68:430-440. [PMID: 30239978 PMCID: PMC6472445 DOI: 10.1093/sysbio/syy062] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 11/13/2022] Open
Abstract
Organelle genome fragmentation has been found in a wide range of eukaryotic lineages; however, its use in phylogenetic reconstruction has not been demonstrated. We explored the use of mitochondrial (mt) genome fragmentation in resolving the controversial suborder-level phylogeny of parasitic lice (order Phthiraptera). There are approximately 5000 species of parasitic lice in four suborders (Amblycera, Ischnocera, Rhynchophthirina, and Anoplura), which infest mammals and birds. The phylogenetic relationships among these suborders are unresolved despite decades of studies. We sequenced the mt genomes of eight species of parasitic lice and compared them with 17 other species of parasitic lice sequenced previously. We found that the typical single-chromosome mt genome is retained in the lice of birds but fragmented into many minichromosomes in the lice of eutherian mammals. The shared derived feature of mt genome fragmentation unites the eutherian mammal lice of Ischnocera (family Trichodectidae) with Anoplura and Rhynchophthirina to the exclusion of the bird lice of Ischnocera (family Philopteridae). The novel clade, namely Mitodivisia, is also supported by phylogenetic analysis of mt genome and cox1 gene sequences. Our results demonstrate, for the first time, that organelle genome fragmentation is informative for resolving controversial high-level phylogenies.
Collapse
Affiliation(s)
- Fan Song
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Guo-Hua Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province 410128, China
| | - Wei Wang
- School of Science and Engineering, GeneCology Research Centre, Animal Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Peter James
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Dutton Park, Queensland, Australia
| | - Douglas D Colwell
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | - Anette Tran
- School of Science and Engineering, GeneCology Research Centre, Animal Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Siyu Gong
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Key Laboratory of Pest Monitoring and Green Management, Ministry of Agriculture, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Renfu Shao
- School of Science and Engineering, GeneCology Research Centre, Animal Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| |
Collapse
|
24
|
Zhang SK, Shu JP, Wang YD, Liu YN, Peng H, Zhang W, Wang HJ. The complete mitochondrial genomes of two sibling species of camellia weevils (Coleoptera: Curculionidae) and patterns of Curculionini speciation. Sci Rep 2019; 9:3412. [PMID: 30833607 PMCID: PMC6399312 DOI: 10.1038/s41598-019-39895-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 02/01/2019] [Indexed: 11/09/2022] Open
Abstract
Complete mitochondrial genomes contain large and diverse datasets for species delineation. To better understand the divergence of the two morphologically indistinguishable weevil species in Curculionini, we first sequenced and compared their complete mitochondrial genomes. The complete mitochondrial genomes of Curculio chinensis and Curculio sp. were 19,713 bp with an A + T content of 76.61% and 19,216 bp with an A + T content of 76.85%, respectively. All 37 of the typical mitochondrial genes were determined in both species. The 13 protein sequences of the two species shared high homology (about 90%) except for ATP8 (73.08%). The differences in secondary structure of ATP8 were the number of possible proteins and nucleic acid binding sites. There were 22 and 15 mismatched base-pairs in the tRNA secondary structures from C. chinensis and Curculio sp., respectively. Maximum Likelihood and Bayesian analyses indicated that Curculio sp. is a novel species closely related to C. chinensis. The divergence time estimation suggests that Cryptorhynchinae and Curculionini lines diverged in the Cenozoic Period, while C. chinensis and Curculio sp. diverged at 6.7079 (95% CI 5-13) Mya. This study demonstrates the utility of using complete mitochondrial gene sets for phylogenetic analysis and enhances our understanding of the genetic basis for the evolution of the Curculionini.
Collapse
Affiliation(s)
- Shou-Ke Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, No. 1, Dongxiaofu Xiangshan Road, Haidian District, Beijing, 100091, P. R. China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| | - Jin-Ping Shu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China.
| | - Yang-Dong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, No. 1, Dongxiaofu Xiangshan Road, Haidian District, Beijing, 100091, P. R. China.
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China.
| | - Ya-Ning Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| | - Han Peng
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| | - Wei Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| | - Hao-Jie Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang District, Hangzhou, Zhejiang, 311400, P. R. China
| |
Collapse
|
25
|
Sweet AD, Johnson KP. The role of parasite dispersal in shaping a host–parasite system at multiple evolutionary scales. Mol Ecol 2018; 27:5104-5119. [DOI: 10.1111/mec.14937] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/13/2018] [Accepted: 10/23/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Andrew D. Sweet
- Illinois Natural History Survey, Prairie Research Institute University of Illinois at Urbana‐Champaign Champaign Illinois
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute University of Illinois at Urbana‐Champaign Champaign Illinois
| |
Collapse
|
26
|
Johnson KP, Dietrich CH, Friedrich F, Beutel RG, Wipfler B, Peters RS, Allen JM, Petersen M, Donath A, Walden KKO, Kozlov AM, Podsiadlowski L, Mayer C, Meusemann K, Vasilikopoulos A, Waterhouse RM, Cameron SL, Weirauch C, Swanson DR, Percy DM, Hardy NB, Terry I, Liu S, Zhou X, Misof B, Robertson HM, Yoshizawa K. Phylogenomics and the evolution of hemipteroid insects. Proc Natl Acad Sci U S A 2018; 115:12775-12780. [PMID: 30478043 PMCID: PMC6294958 DOI: 10.1073/pnas.1815820115] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.
Collapse
Affiliation(s)
- Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820;
| | - Christopher H Dietrich
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Frank Friedrich
- Institut für Zoologie, Universität Hamburg, 20146 Hamburg, Germany
| | - Rolf G Beutel
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Benjamin Wipfler
- Institut für Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
- Center of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Ralph S Peters
- Center of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Julie M Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
- Department of Biology, University of Nevada, Reno, NV 89557
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Kimberly K O Walden
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Alexey M Kozlov
- Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
- Institute of Evolutionary Biology and Ecology, University of Bonn, 53121 Bonn, Germany
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Karen Meusemann
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
- Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, 79104 Freiburg, Germany
- Australian National Insect Collection, Commonwealth Scientific and Industrial Research Organisation National Research Collections Australia, Acton, ACT 2601 Canberra, Australia
| | - Alexandros Vasilikopoulos
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN 47907
| | | | - Daniel R Swanson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820
| | - Diana M Percy
- Department of Life Sciences, Natural History Museum, London, SW7 5BD United Kingdom
- Department of Botany, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Nate B Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Irene Terry
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province, People's Republic of China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | | |
Collapse
|
27
|
The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum. ACTA ACUST UNITED AC 2018; 4. [PMID: 30105092 DOI: 10.1017/pao.2018.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.
Collapse
|
28
|
Kim T, Kern E, Park C, Nadler SA, Bae YJ, Park JK. The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda). Sci Rep 2018; 8:7482. [PMID: 29749383 PMCID: PMC5945635 DOI: 10.1038/s41598-018-25759-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/27/2018] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial genes and whole mitochondrial genome sequences are widely used as molecular markers in studying population genetics and resolving both deep and shallow nodes in phylogenetics. In animals the mitochondrial genome is generally composed of a single chromosome, but mystifying exceptions sometimes occur. We determined the complete mitochondrial genome of the millipede-parasitic nematode Ruizia karukerae and found its mitochondrial genome consists of two circular chromosomes, which is highly unusual in bilateral animals. Chromosome I is 7,659 bp and includes six protein-coding genes, two rRNA genes and nine tRNA genes. Chromosome II comprises 7,647 bp, with seven protein-coding genes and 16 tRNA genes. Interestingly, both chromosomes share a 1,010 bp sequence containing duplicate copies of cox2 and three tRNA genes (trnD, trnG and trnH), and the nucleotide sequences between the duplicated homologous gene copies are nearly identical, suggesting a possible recent genesis for this bipartite mitochondrial genome. Given that little is known about the formation, maintenance or evolution of abnormal mitochondrial genome structures, R. karukerae mtDNA may provide an important early glimpse into this process.
Collapse
Affiliation(s)
- Taeho Kim
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Elizabeth Kern
- Division of EcoScience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Steven A Nadler
- Department of Entomology and Nematology, University of California, Davis, CA, 95616, USA
| | - Yeon Jae Bae
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Joong-Ki Park
- Division of EcoScience, Ewha Womans University, Seoul, 03760, Republic of Korea.
| |
Collapse
|
29
|
Chen L, Chen PY, Xue XF, Hua HQ, Li YX, Zhang F, Wei SJ. Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). Sci Rep 2018; 8:7034. [PMID: 29728615 PMCID: PMC5935716 DOI: 10.1038/s41598-018-25338-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/20/2018] [Indexed: 12/01/2022] Open
Abstract
Animal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma. Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.
Collapse
Affiliation(s)
- Long Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng-Yan Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,Department of Entomology, South China Agricultural University, Guangzhou, 510640, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hai-Qing Hua
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan-Xi Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Fan Zhang
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| |
Collapse
|
30
|
Shao R, Li H, Barker SC, Song S. The Mitochondrial Genome of the Guanaco Louse, Microthoracius praelongiceps: Insights into the Ancestral Mitochondrial Karyotype of Sucking Lice (Anoplura, Insecta). Genome Biol Evol 2018; 9:431-445. [PMID: 28164215 PMCID: PMC5381627 DOI: 10.1093/gbe/evx007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2017] [Indexed: 11/13/2022] Open
Abstract
Fragmented mitochondrial (mt) genomes have been reported in 11 species of sucking lice (suborder Anoplura) that infest humans, chimpanzees, pigs, horses, and rodents. There is substantial variation among these lice in mt karyotype: the number of minichromosomes of a species ranges from 9 to 20; the number of genes in a minichromosome ranges from 1 to 8; gene arrangement in a minichromosome differs between species, even in the same genus. We sequenced the mt genome of the guanaco louse, Microthoracius praelongiceps, to help establish the ancestral mt karyotype for sucking lice and understand how fragmented mt genomes evolved. The guanaco louse has 12 mt minichromosomes; each minichromosome has 2-5 genes and a non-coding region. The guanaco louse shares many features with rodent lice in mt karyotype, more than with other sucking lice. The guanaco louse, however, is more closely related phylogenetically to human lice, chimpanzee lice, pig lice, and horse lice than to rodent lice. By parsimony analysis of shared features in mt karyotype, we infer that the most recent common ancestor of sucking lice, which lived ∼75 Ma, had 11 minichromosomes; each minichromosome had 1-6 genes and a non-coding region. As sucking lice diverged, split of mt minichromosomes occurred many times in the lineages leading to the lice of humans, chimpanzees, and rodents whereas merger of minichromosomes occurred in the lineage leading to the lice of pigs and horses. Together, splits and mergers of minichromosomes created a very complex and dynamic mt genome organization in the sucking lice.
Collapse
Affiliation(s)
- Renfu Shao
- GeneCology Research Centre, School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Stephen C Barker
- Parasitology Section, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Simon Song
- GeneCology Research Centre, School of Science and Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| |
Collapse
|
31
|
Zhang LP, Yu DN, Storey KB, Cheng HY, Zhang JY. Higher tRNA gene duplication in mitogenomes of praying mantises (Dictyoptera, Mantodea) and the phylogeny within Mantodea. Int J Biol Macromol 2018; 111:787-795. [DOI: 10.1016/j.ijbiomac.2018.01.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/30/2017] [Accepted: 01/03/2018] [Indexed: 12/21/2022]
|
32
|
Mitochondrial phylogenomics and genome rearrangements in the barklice (Insecta: Psocodea). Mol Phylogenet Evol 2018; 119:118-127. [DOI: 10.1016/j.ympev.2017.10.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 11/19/2022]
|
33
|
Novel insights into mitochondrial gene rearrangement in thrips (Insecta: Thysanoptera) from the grass thrips, Anaphothrips obscurus. Sci Rep 2017; 7:4284. [PMID: 28655921 PMCID: PMC5487348 DOI: 10.1038/s41598-017-04617-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/17/2017] [Indexed: 11/29/2022] Open
Abstract
We sequenced the mitochondrial (mt) genome of the grass thrips, Anaphothrips obscurus, which is highly rearranged and differs from the four thrips species reported previously in the arrangement of both tRNA genes and a protein-coding gene, nad3, and in the copy number of the control region (CR). We reconstructed the phylogeny of the thrips with mt genome sequences, and used it as a framework to gain insights into mt genome evolution in thrips. It is evident that A. obscurus is less rearranged in mt genome organization than the other four known thrips. nad3 is in its ancestral location in A. obscurus but was translocated in other four thrips. Also, A. obscurus has one CR, which is ancestral to hexapods whereas other thrips have two or three CRs. All of the five thrips whose mt genomes have been sequenced to date are from the subfamily Thripinae, which represents about a quarter of the species richness in the order Thysanoptera. The high variation in mt genome organization observed in a subfamily challenges our knowledge about animal mt genomes. It remains to be investigated why mt genomes evolved so fast in the subfamily Thripinae and how mt genomes evolved in other lineages of thrips.
Collapse
|
34
|
Evolution and inheritance of animal mitochondrial DNA: rules and exceptions. ACTA ACUST UNITED AC 2017; 24:2. [PMID: 28164041 PMCID: PMC5282644 DOI: 10.1186/s40709-017-0060-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 01/10/2017] [Indexed: 12/17/2022]
Abstract
Mitochondrial DNA (mtDNA) has been studied intensely for “its own” merit. Its role for the function of the cell and the organism remains a fertile field, its origin and evolution is an indispensable part of the evolution of life and its interaction with the nuclear DNA is among the most important cases of genome synergism and co-evolution. Also, mtDNA was proven one of the most useful tools in population genetics and molecular phylogenetics. In this article we focus on animal mtDNA and discuss briefly how our views about its structure, function and transmission have changed, how these changes affect the information we have accumulated through its use in the fields of phylogeny and population structure and what are the most important questions that remain open for future research.
Collapse
|
35
|
The Complete Mitochondrial Genome of Aleurocanthus camelliae: Insights into Gene Arrangement and Genome Organization within the Family Aleyrodidae. Int J Mol Sci 2016; 17:ijms17111843. [PMID: 27827992 PMCID: PMC5133843 DOI: 10.3390/ijms17111843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/27/2016] [Accepted: 11/01/2016] [Indexed: 11/24/2022] Open
Abstract
There are numerous gene rearrangements and transfer RNA gene absences existing in mitochondrial (mt) genomes of Aleyrodidae species. To understand how mt genomes evolved in the family Aleyrodidae, we have sequenced the complete mt genome of Aleurocanthus camelliae and comparatively analyzed all reported whitefly mt genomes. The mt genome of A. camelliae is 15,188 bp long, and consists of 13 protein-coding genes, two rRNA genes, 21 tRNA genes and a putative control region (GenBank: KU761949). The tRNA gene, trnI, has not been observed in this genome. The mt genome has a unique gene order and shares most gene boundaries with Tetraleurodes acaciae. Nineteen of 21 tRNA genes have the conventional cloverleaf shaped secondary structure and two (trnS1 and trnS2) lack the dihydrouridine (DHU) arm. Using ARWEN and homologous sequence alignment, we have identified five tRNA genes and revised the annotation for three whitefly mt genomes. This result suggests that most absent genes exist in the genomes and have not been identified, due to be lack of technology and inference sequence. The phylogenetic relationships among 11 whiteflies and Drosophila melanogaster were inferred by maximum likelihood and Bayesian inference methods. Aleurocanthus camelliae and T. acaciae form a sister group, and all three Bemisia tabaci and two Bemisia afer strains gather together. These results are identical to the relationships inferred from gene order. We inferred that gene rearrangement plays an important role in the mt genome evolved from whiteflies.
Collapse
|
36
|
Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
Collapse
Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
| |
Collapse
|
37
|
Phillips WS, Brown AMV, Howe DK, Peetz AB, Blok VC, Denver DR, Zasada IA. The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers. BMC Genomics 2016; 17:706. [PMID: 27595608 PMCID: PMC5011991 DOI: 10.1186/s12864-016-3047-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/27/2016] [Indexed: 01/21/2023] Open
Abstract
Background The evolution of animal mitochondrial (mt) genomes has resulted in a highly conserved structure: a single compact circular chromosome approximately 14 to 20 kb long. Within the last two decades exceptions to this conserved structure, such as the division of the genome into multiple chromosomes, have been reported in a diverse set of metazoans. We report on the two circle multipartite mt genome of a newly described cyst nematode, Globodera ellingtonae. Results The G. ellingtonae mt genome was found to be comprised of two circles, each larger than any other multipartite circular mt chromosome yet reported, and both were larger than the single mt circle of the model nematode Caenorhabditis elegans. The genetic content of the genome was disproportionately divided between the two circles, although they shared a ~6.5 kb non-coding region. The 17.8 kb circle (mtDNA-I) contained ten protein-coding genes and two tRNA genes, whereas the 14.4 kb circle (mtDNA-II) contained two protein-coding genes, 20 tRNA genes and both rRNA genes. Perhaps correlated with this division of genetic content, the copy number of mtDNA-II was more than four-fold that of mtDNA-I in individual nematodes. The difference in copy number increased between second-stage and fourth-stage juveniles. Conclusions The segregation of gene types to different mt circles in G. ellingtonae could provide benefit by localizing gene functional types to independent transcriptional units. This is the first report of both two-circle and several-circle mt genomes within a single genus. The differential copy number associated with this multipartite mt organization could provide a model system for deconstructing mechanisms regulating mtDNA copy number both in somatic cells and during germline development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3047-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wendy S Phillips
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA.
| | - Amanda M V Brown
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Amy B Peetz
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA
| | - Vivian C Blok
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, UK
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Inga A Zasada
- Horticultural Crops Research Laboratory, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, USA
| |
Collapse
|
38
|
Pietan LL, Spradling TA, Demastes JW. The Mitochondrial Cytochrome Oxidase Subunit I Gene Occurs on a Minichromosome with Extensive Heteroplasmy in Two Species of Chewing Lice, Geomydoecus aurei and Thomomydoecus minor. PLoS One 2016; 11:e0162248. [PMID: 27589589 PMCID: PMC5010254 DOI: 10.1371/journal.pone.0162248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 08/21/2016] [Indexed: 12/02/2022] Open
Abstract
In animals, mitochondrial DNA (mtDNA) typically occurs as a single circular chromosome with 13 protein-coding genes and 22 tRNA genes. The various species of lice examined previously, however, have shown mitochondrial genome rearrangements with a range of chromosome sizes and numbers. Our research demonstrates that the mitochondrial genomes of two species of chewing lice found on pocket gophers, Geomydoecus aurei and Thomomydoecus minor, are fragmented with the 1,536 base-pair (bp) cytochrome-oxidase subunit I (cox1) gene occurring as the only protein-coding gene on a 1,916-1,964 bp minicircular chromosome in the two species, respectively. The cox1 gene of T. minor begins with an atypical start codon, while that of G. aurei does not. Components of the non-protein coding sequence of G. aurei and T. minor include a tRNA (isoleucine) gene, inverted repeat sequences consistent with origins of replication, and an additional non-coding region that is smaller than the non-coding sequence of other lice with such fragmented mitochondrial genomes. Sequences of cox1 minichromosome clones for each species reveal extensive length and sequence heteroplasmy in both coding and noncoding regions. The highly variable non-gene regions of G. aurei and T. minor have little sequence similarity with one another except for a 19-bp region of phylogenetically conserved sequence with unknown function.
Collapse
Affiliation(s)
- Lucas L. Pietan
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa, United States of America
| | - Theresa A. Spradling
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa, United States of America
| | - James W. Demastes
- Department of Biology, University of Northern Iowa, Cedar Falls, Iowa, United States of America
| |
Collapse
|
39
|
Shi Y, Chu Q, Wei DD, Qiu YJ, Shang F, Dou W, Wang JJ. The mitochondrial genome of booklouse, Liposcelis sculptilis (Psocoptera: Liposcelididae) and the evolutionary timescale of Liposcelis. Sci Rep 2016; 6:30660. [PMID: 27470659 PMCID: PMC4965752 DOI: 10.1038/srep30660] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/07/2016] [Indexed: 11/16/2022] Open
Abstract
Bilateral animals are featured by an extremely compact mitochondrial (mt) genome with 37 genes on a single circular chromosome. To date, the complete mt genome has only been determined for four species of Liposcelis, a genus with economic importance, including L. entomophila, L. decolor, L. bostrychophila, and L. paeta. They belong to A, B, or D group of Liposcelis, respectively. Unlike most bilateral animals, L. bostrychophila, L. entomophila and L. paeta have a bitipartite mt genome with genes on two chromosomes. However, the mt genome of L. decolor has the typical mt chromosome of bilateral animals. Here, we sequenced the mt genome of L. sculptilis, and identified 35 genes, which were on a single chromosome. The mt genome fragmentation is not shared by the D group of Liposcelis and the single chromosome of L. sculptilis differed from those of booklice known in gene content and gene arrangement. We inferred that different evolutionary patterns and rate existed in Liposcelis. Further, we reconstructed the evolutionary history of 21 psocodean taxa with phylogenetic analyses, which suggested that Liposcelididae and Phthiraptera have evolved 134 Ma and the sucking lice diversified in the Late Cretaceous.
Collapse
Affiliation(s)
- Yan Shi
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Qing Chu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Dan-Dan Wei
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Yuan-Jian Qiu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
| |
Collapse
|
40
|
Park JS, Kim MJ, Jeong SY, Kim SS, Kim I. Complete mitochondrial genomes of two gelechioids, Mesophleps albilinella and Dichomeris ustalella (Lepidoptera: Gelechiidae), with a description of gene rearrangement in Lepidoptera. Curr Genet 2016; 62:809-826. [PMID: 26952721 DOI: 10.1007/s00294-016-0585-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 02/20/2016] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
We sequenced the entire mitochondrial genome (mitogenome) of two gelechioids, Mesophleps albilinella and Dichomeris ustalella, and compared their genome organization and sequence composition to those of available gelechioid mitogenomes for an enhanced understanding of Gelechioidea genomic characteristics. We compared all available lepidopteran mitogenome arrangements, including that of M. albilinella, which is unique in Gelechioidea, to comprehend the extensiveness and mechanisms of gene rearrangement in Lepidoptera. The genomes of M. albilinella and D. ustalella are 15,274 and 15,410 bp in size, respectively, with the typical sets of mitochondrial (mt) genes. The COI gene begins with CGA (arginine) in all sequenced gelechioids, including M. albilinella and D. ustalella, reinforcing the feature as a synapomorphic trait, at least in the Gelechioidea. Each 353- and 321-bp long A + T-rich region of M. albilinella and D. ustalella contains one (D. ustalella) or two (M. albilinella) tRNA-like structures. The M. albilinella mitogenome has a unique gene arrangement among the Gelechioidea: ARNESF (the underline signifies an inverted gene) at the ND3 and ND5 junction, as opposed to the ARNSEF that is found in ancestral insects. An extensive search of available lepidopteran mitogenomes, including that of M. albilinella, turned up six rearrangements that differ from those of ancestral insects. Most of the rearrangements can be explained by the tandem duplication-random loss model, but inversion, which requires recombination, is also found in two cases, including M. albilinella. Excluding the MIQ rearrangement at the A + T-rich region and ND2 junction, which is found in nearly all Ditrysia, most of the remaining rearrangements found in Lepidoptera appear to be independently derived in that they are automorphic at several taxonomic scales, although current mitogenomic data are limited, particularly for congeneric data.
Collapse
Affiliation(s)
- Jeong Sun Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, 33, Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea
| | - Min Jee Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, 33, Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea
| | - Su Yeon Jeong
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, 33, Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea
| | - Sung Soo Kim
- Research Institute for East Asian Environment and Biology, Seoul, 24, Arisu-ro 25na-gil, Gangdong-gu, Seoul, 05207, Republic of Korea
| | - Iksoo Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, 33, Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea.
| |
Collapse
|
41
|
Fragmented mitochondrial genomes in two suborders of parasitic lice of eutherian mammals (Anoplura and Rhynchophthirina, Insecta). Sci Rep 2015; 5:17389. [PMID: 26617060 PMCID: PMC4663631 DOI: 10.1038/srep17389] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/29/2015] [Indexed: 11/26/2022] Open
Abstract
Parasitic lice (order Phthiraptera) infest birds and mammals. The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera. The sucking lice (suborder Anoplura) known, however, have fragmented mt genomes with 9–20 minichromosomes. We sequenced the mt genome of the elephant louse, Haematomyzus elephantis – the first species of chewing lice investigated from the suborder Rhynchophthirina. We identified 33 mt genes in the elephant louse, which were on 10 minichromosomes. Each minichromosome is 3.5–4.2 kb in size and has 2–6 genes. Phylogenetic analyses of mt genome sequences confirm that the elephant louse is more closely related to sucking lice than to the chewing lice in the Amblycera and Ischnocera. Our results indicate that mt genome fragmentation is shared by the suborders Anoplura and Rhynchophthirina. Nine of the 10 mt minichromosomes of the elephant louse differ from those of the sucking lice (Anoplura) known in gene content and gene arrangement, indicating that distinct mt karyotypes have evolved in Anoplura and Rhynchophthirina since they diverged ~92 million years ago.
Collapse
|
42
|
Herd KE, Barker SC, Shao R. The mitochondrial genome of the chimpanzee louse, Pediculus schaeffi: insights into the process of mitochondrial genome fragmentation in the blood-sucking lice of great apes. BMC Genomics 2015; 16:661. [PMID: 26335315 PMCID: PMC4557858 DOI: 10.1186/s12864-015-1843-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 08/14/2015] [Indexed: 11/16/2022] Open
Abstract
Background Blood-sucking lice in the genera Pediculus and Pthirus are obligate ectoparasites of great apes. Unlike most bilateral animals, which have 37 mitochondrial (mt) genes on a single circular chromosome, the sucking lice of humans have extensively fragmented mt genomes. The head louse, Pediculus capitis, and the body louse, Pe. humanus, have their 37 mt genes on 20 minichromosomes. The pubic louse, Pthirus pubis, has its 34 mt genes known on 14 minichromosomes. To understand the process of mt genome fragmentation in the sucking lice of great apes, we sequenced the mt genome of the chimpanzee louse, Pe. schaeffi, and compared it with the three human lice. Results We identified all of the 37 mt genes typical of bilateral animals in the chimpanzee louse; these genes are on 18 types of minichromosomes. Seventeen of the 18 minichromosomes of the chimpanzee louse have the same gene content and gene arrangement as their counterparts in the human head louse and the human body louse. However, five genes, cob, trnS1, trnN, trnE and trnM, which are on three minichromosomes in the human head louse and the human body louse, are together on one minichromosome in the chimpanzee louse. Conclusions Using the human pubic louse, Pt. pubis, as an outgroup for comparison, we infer that a single minichromosome has fragmented into three in the lineage leading to the human head louse and the human body louse since this lineage diverged from the chimpanzee louse ~6 million years ago. Our results provide insights into the process of mt genome fragmentation in the sucking lice in a relatively fine evolutionary scale. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1843-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kate E Herd
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
| | - Stephen C Barker
- Department of Parasitology, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
| | - Renfu Shao
- GeneCology Research Centre, Faculty of Science, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia.
| |
Collapse
|
43
|
Dickey AM, Kumar V, Morgan JK, Jara-Cavieres A, Shatters RG, McKenzie CL, Osborne LS. A novel mitochondrial genome architecture in thrips (Insecta: Thysanoptera): extreme size asymmetry among chromosomes and possible recent control region duplication. BMC Genomics 2015; 16:439. [PMID: 26055161 PMCID: PMC4460840 DOI: 10.1186/s12864-015-1672-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 05/29/2015] [Indexed: 11/19/2022] Open
Abstract
Background Multipartite mitochondrial genomes are very rare in animals but have been found previously in two insect orders with highly rearranged genomes, the Phthiraptera (parasitic lice), and the Psocoptera (booklice/barklice). Results We provide the first report of a multipartite mitochondrial genome architecture in a third order with highly rearranged genomes: Thysanoptera (thrips). We sequenced the complete mitochondrial genomes of two divergent members of the Scirtothrips dorsalis cryptic species complex. The East Asia 1 species has the single circular chromosome common to animals while the South Asia 1 species has a genome consisting of two circular chromosomes. The fragmented South Asia 1 genome exhibits extreme chromosome size asymmetry with the majority of genes on the large, 14.28 kb, chromosome and only nad6 and trnC on the 0.92 kb mini-circle chromosome. This genome also features paralogous control regions with high similarity suggesting a very recent origin of the nad6 mini-circle chromosome in the South Asia 1 cryptic species. Conclusions Thysanoptera, along with the other minor paraenopteran insect orders should be considered models for rapid mitochondrial genome evolution, including fragmentation. Continued use of these models will facilitate a greater understanding of recombination and other mitochondrial genome evolutionary processes across eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1672-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Aaron M Dickey
- Subtropical Insects Research Unit, US Horticultural Research Laboratory, Fort Pierce, USA. .,Mid-Florida Research & Education Center, University of Florida, Apopka, USA. .,Present Address: Agricultural Research Service, US Department of Agriculture, Clay Center, USA.
| | - Vivek Kumar
- Subtropical Insects Research Unit, US Horticultural Research Laboratory, Fort Pierce, USA. .,Mid-Florida Research & Education Center, University of Florida, Apopka, USA.
| | - J Kent Morgan
- Subtropical Insects Research Unit, US Horticultural Research Laboratory, Fort Pierce, USA. .,Present Address: J. Kent Morgan Consulting, Fort Pierce, USA.
| | | | - Robert G Shatters
- Subtropical Insects Research Unit, US Horticultural Research Laboratory, Fort Pierce, USA. .,US Department of Agriculture, Agricultural Research Service, Fort Pierce, USA.
| | - Cindy L McKenzie
- Subtropical Insects Research Unit, US Horticultural Research Laboratory, Fort Pierce, USA. .,US Department of Agriculture, Agricultural Research Service, Fort Pierce, USA.
| | - Lance S Osborne
- Mid-Florida Research & Education Center, University of Florida, Apopka, USA.
| |
Collapse
|
44
|
First comparative insight into the architecture of COI mitochondrial minicircle molecules of dicyemids reveals marked inter-species variation. Parasitology 2015; 142:1066-79. [PMID: 25877339 DOI: 10.1017/s0031182015000384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Dicyemids, poorly known parasites of benthic cephalopods, are one of the few phyla in which mitochondrial (mt) genome architecture departs from the typical ~16 kb circular metazoan genome. In addition to a putative circular genome, a series of mt minicircles that each comprises the mt encoded units (I-III) of the cytochrome c oxidase complex have been reported. Whether the structure of the mt minicircles is a consistent feature among dicyemid species is unknown. Here we analyse the complete cytochrome c oxidase subunit I (COI) minicircle molecule, containing the COI gene and an associated non-coding region (NCR), for ten dicyemid species, allowing for first time comparisons between species of minicircle architecture, NCR function and inferences of minicircle replication. Divergence in COI nucleotide sequences between dicyemid species was high (average net divergence = 31.6%) while within species diversity was lower (average net divergence = 0.2%). The NCR and putative 5' section of the COI gene were highly divergent between dicyemid species (average net nucleotide divergence of putative 5' COI section = 61.1%). No tRNA genes were found in the NCR, although palindrome sequences with the potential to form stem-loop structures were identified in some species, which may play a role in transcription or other biological processes.
Collapse
|
45
|
Abstract
In virtually all multicellular eukaryotes, mitochondria are transmitted exclusively through one parent, usually the mother. In this short review, we discuss some of the major consequences of uniparental transmission of mitochondria, including deleterious effects in males and selection for increased transmission through females. Many of these consequences, particularly sex ratio distortion, have well-studied parallels in other maternally transmitted genetic elements, such as bacterial endosymbionts of arthropods. We also discuss the consequences of linkage between mitochondria and other maternally transmitted genetic elements, including the role of cytonuclear incompatibilities in maintaining polymorphism. Finally, as a case study, we discuss a recently discovered maternally transmitted sex ratio distortion in an insect that is associated with extraordinarily divergent mitochondria.
Collapse
|
46
|
García LE, Sánchez-Puerta MV. Comparative and evolutionary analyses of Meloidogyne spp. Based on mitochondrial genome sequences. PLoS One 2015; 10:e0121142. [PMID: 25799071 PMCID: PMC4370701 DOI: 10.1371/journal.pone.0121142] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/12/2015] [Indexed: 01/11/2023] Open
Abstract
Molecular taxonomy and evolution of nematodes have been recently the focus of several studies. Mitochondrial sequences were proposed as an alternative for precise identification of Meloidogyne species, to study intraspecific variability and to follow maternal lineages. We characterized the mitochondrial genomes (mtDNAs) of the root knot nematodes M. floridensis, M. hapla and M. incognita. These were AT rich (81–83%) and highly compact, encoding 12 proteins, 2 rRNAs, and 22 tRNAs. Comparisons with published mtDNAs of M. chitwoodi, M. incognita (another strain) and M. graminicola revealed that they share protein and rRNA gene order but differ in the order of tRNAs. The mtDNAs of M. floridensis and M. incognita were strikingly similar (97–100% identity for all coding regions). In contrast, M. floridensis, M. chitwoodi, M. hapla and M. graminicola showed 65–84% nucleotide identity for coding regions. Variable mitochondrial sequences are potentially useful for evolutionary and taxonomic studies. We developed a molecular taxonomic marker by sequencing a highly-variable ~2 kb mitochondrial region, nad5-cox1, from 36 populations of root-knot nematodes to elucidate relationships within the genus Meloidogyne. Isolates of five species formed monophyletic groups and showed little intraspecific variability. We also present a thorough analysis of the mitochondrial region cox2-rrnS. Phylogenies based on either mitochondrial region had good discrimination power but could not discriminate between M. arenaria, M. incognita and M. floridensis.
Collapse
Affiliation(s)
- Laura Evangelina García
- IBAM-CONICET and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Chacras de Coria, Mendoza, Argentina
| | - M. Virginia Sánchez-Puerta
- IBAM-CONICET and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Chacras de Coria, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Mendoza, Argentina
- * E-mail:
| |
Collapse
|
47
|
Lin R, Liu C, Shen B, Bai M, Ling J, Chen G, Mao Z, Cheng X, Xie B. Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales. BMC Microbiol 2015; 15:5. [PMID: 25636983 PMCID: PMC4360972 DOI: 10.1186/s12866-015-0341-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 01/08/2015] [Indexed: 11/10/2022] Open
Abstract
Background The fungus Pochonia chlamydosporia parasitizes nematode eggs and has become one of the most promising biological control agents (BCAs) for plant-parasitic nematodes, which are major agricultural pests that cause tremendous economic losses worldwide. The complete mitochondrial (mt) genome is expected to open new avenues for understanding the phylogenetic relationships and evolution of the invertebrate-pathogenic fungi in Hypocreales. Results The complete mitogenome sequence of P. chlamydosporia is 25,615 bp in size, containing the 14 typical protein-coding genes, two ribosomal RNA genes, an intronic ORF coding for a putative ribosomal protein (rps3) and a set of 23 transfer RNA genes (trn) which recognize codons for all amino acids. Sequence similarity studies and syntenic gene analyses show that 87.02% and 58.72% of P. chlamydosporia mitogenome sequences match 90.50% of Metarhizium anisopliae sequences and 61.33% of Lecanicillium muscarium sequences with 92.38% and 86.04% identities, respectively. A phylogenetic tree inferred from 14 mt proteins in Pezizomycotina fungi supports that P. chlamydosporia is most closely related to the entomopathogenic fungus M. anisopliae. The invertebrate-pathogenic fungi in Hypocreales cluster together and clearly separate from a cluster comprising plant-pathogenic fungi (Fusarium spp.) and Hypocrea jecorina. A comparison of mitogenome sizes shows that the length of the intergenic regions or the intronic regions is the major size contributor in most of mitogenomes in Sordariomycetes. Evolutionary analysis shows that rps3 is under positive selection, leading to the display of unique evolutionary characteristics in Hypocreales. Moreover, the variability of trn distribution has a clear impact on gene order in mitogenomes. Gene rearrangement analysis shows that operation of transposition drives the rearrangement events in Pezizomycotina, and most events involve in trn position changes, but no rearrangement was found in Clavicipitaceae. Conclusions We present the complete annotated mitogenome sequence of P. chlamydosporia. Based on evolutionary and phylogenetic analyses, we have determined the relationships between the invertebrate-pathogenic fungi in Hypocreales. The invertebrate-pathogenic fungi in Hypocreales referred to in this paper form a monophyletic group sharing a most recent common ancestor. Our rps3 and trn gene order results also establish a foundation for further exploration of the evolutionary trajectory of the fungi in Hypocreales. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0341-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Runmao Lin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chichuan Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Baoming Shen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. .,College of Plant Protection, Hunan Agricultural University, Changsha, Hunan Province, 410128, China.
| | - Miao Bai
- Key Laboratory for Crop Germplasm Innovation and Utilization of Hunan Province, Hunan Agricultural University, Changsha, Hunan Province, 410128, China.
| | - Jian Ling
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Guohua Chen
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhenchuan Mao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xinyue Cheng
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
48
|
Ma C, Wang Y, Wu C, Kang L, Liu C. The compact mitochondrial genome of Zorotypus medoensis provides insights into phylogenetic position of Zoraptera. BMC Genomics 2014; 15:1156. [PMID: 25529234 PMCID: PMC4367826 DOI: 10.1186/1471-2164-15-1156] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zoraptera, generally regarded as a member of Polyneoptera, represents one of the most enigmatic insect orders. Although phylogenetic analyses based on a wide array of morphological and/or nuclear data have been performed, the position of Zoraptera is still under debate. Mitochondrial genome (mitogenome) information is commonly considered to be preferable to reconstruct phylogenetic relationships, but no efforts have been made to incorporate it in Zorapteran phylogeny. To characterize Zoraptera mitogenome features and provide insights into its phylogenetic placement, here we sequenced, for the first time, one complete mitogenome of Zoraptera and reconstructed the phylogeny of Polyneoptera. RESULTS The mitogenome of Zorotypus medoensis with an A+T content of 72.50% is composed of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a noncoding A+T-rich region. The gene content and arrangement are identical to those considered ancestral for insects. This mitogenome shows a number of very unusual features. First, it is very compact, comprising 14,572 bp, and is the smallest among all known polyneopteran mitogenomes. Second, both noncoding sequences and coding genes exhibit a significant decrease in size compared with those of other polyneopterans. Third, Z. medoensis mitogenome has experienced an accelerated substitution rate. Fourth, truncated secondary structures of tRNA genes occur with loss of dihydrouridine (DHU) arm in trnC, trnR, and trnS(AGN) and loss of TΨC arm in trnH and trnT. The phylogenetic analyses based on the mitogenome sequence information indicate that Zoraptera, represented by Z. medoensis, is recovered as sister to Embioptera. However, both Zoraptera and Embioptera exhibit very long branches in phylogenetic trees. CONCLUSIONS Characterization of Z. medoensis mitogenome contributes to our understanding of the enigmatic Zoraptera. Mitogenome data demonstrate an overall strong resolution of deep-level phylogenies of Polyneoptera but not Insecta. It is preferable to expand taxon sampling of Zoraptera and other poorly represented orders in future to break up long branches.
Collapse
Affiliation(s)
- Chuan Ma
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yeying Wang
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chao Wu
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Le Kang
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chunxiang Liu
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Laboratory of Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| |
Collapse
|
49
|
Huang M, Wang Y, Liu X, Li W, Kang Z, Wang K, Li X, Yang D. The complete mitochondrial genome and its remarkable secondary structure for a stonefly Acroneuria hainana Wu (Insecta: Plecoptera, Perlidae). Gene 2014; 557:52-60. [PMID: 25499698 DOI: 10.1016/j.gene.2014.12.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/03/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
The Plecoptera (stoneflies) is a hemimetabolous order of insects, whose larvae are usually used as indicators for fresh water biomonitoring. Herein, we describe the complete mitochondrial (mt) genome of a stonefly species, namely Acroneuria hainana Wu belonging to the family Perlidae. This mt genome contains 13 PCGs, 22 tRNA-coding genes and 2 rRNA-coding genes that are conserved in most insect mt genomes, and it also has the identical gene order with the insect ancestral gene order. However, there are three special initiation codons of ND1, ND5 and COI in PCGs: TTG, GTG and CGA, coding for L, V and R, respectively. Additionally, the 899-bp control region, with 73.30% A+T content, has two long repeated sequences which are found at the 3'-end closing to the tRNA(Ile) gene. Both of them can be folded into a stem-loop structure, whose adjacent upstream and downstream sequences can be also folded into stem-loop structures. It is presumed that the four special structures in series could be associated with the D-loop replication. It might be able to adjust the replication speed of two replicate directions.
Collapse
Affiliation(s)
- Mingchao Huang
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Yuyu Wang
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Weihai Li
- Department of Plant Protection, Henan Institute of Science and Technology, Xinxiang, China
| | - Zehui Kang
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Kai Wang
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Xuankun Li
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
50
|
Babbucci M, Basso A, Scupola A, Patarnello T, Negrisolo E. Is it an ant or a butterfly? Convergent evolution in the mitochondrial gene order of Hymenoptera and Lepidoptera. Genome Biol Evol 2014; 6:3326-43. [PMID: 25480682 PMCID: PMC4466343 DOI: 10.1093/gbe/evu265] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2014] [Indexed: 11/18/2022] Open
Abstract
Insect mitochondrial genomes (mtDNA) are usually double helical and circular molecules containing 37 genes that are encoded on both strands. The arrangement of the genes is not constant for all species, and produces distinct gene orders (GOs) that have proven to be diagnostic in defining clades at different taxonomic levels. In general, it is believed that distinct taxa have a very low chance of sharing identically arranged GOs. However, examples of identical, homoplastic local rearrangements occurring in distinct taxa do exist. In this study, we sequenced the complete mtDNAs of the ants Formica fusca and Myrmica scabrinodis (Formicidae, Hymenoptera) and compared their GOs with those of other Insecta. The GO of F. fusca was found to be identical to the GO of Dytrisia (the largest clade of Lepidoptera). This finding is the first documented case of an identical GO shared by distinct groups of Insecta, and it is the oldest known event of GO convergent evolution in animals. Both Hymenoptera and Lepidoptera acquired this GO early in their evolution. Using a phylogenetic approach combined with new bioinformatic tools, the chronological order of the evolutionary events that produced the diversity of the hymenopteran GOs was determined. Additionally, new local homoplastic rearrangements shared by distinct groups of insects were identified. Our study showed that local and global homoplasies affecting the insect GOs are more widespread than previously thought. Homoplastic GOs can still be useful for characterizing the various clades, provided that they are appropriately considered in a phylogenetic and taxonomic context.
Collapse
Affiliation(s)
- Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| | - Andrea Basso
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy Department of Agronomy, Food, Natural Resources, Animal and Environment (DAFNE), University of Padova, Agripolis, Legnaro (PD), Italy Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| | - Antonio Scupola
- Natural History Museum (Museo di Storia Naturale), Verona, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| | - Enrico Negrisolo
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Agripolis, Legnaro (PD), Italy
| |
Collapse
|