1
|
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
|
2
|
Bett VK, Macon A, Vicoso B, Elkrewi M. Chromosome-Level Assembly of Artemia franciscana Sheds Light on Sex Chromosome Differentiation. Genome Biol Evol 2024; 16:evae006. [PMID: 38245839 PMCID: PMC10827361 DOI: 10.1093/gbe/evae006] [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: 09/21/2023] [Revised: 11/27/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.
Collapse
Affiliation(s)
| | - Ariana Macon
- Institute of Science and Technology Austria (ISTA), Klosterneuburg 3400, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria (ISTA), Klosterneuburg 3400, Austria
| | - Marwan Elkrewi
- Institute of Science and Technology Austria (ISTA), Klosterneuburg 3400, Austria
| |
Collapse
|
3
|
Palmisano JN, Farrell TM, Gustafson TM, Fitak RR. The mitochondrial genome of the pentastome parasite Raillietiella orientalis Hett, 1915 (Raillietiellida; Raillietiellidae) with notes on its phylogenetic position. Mitochondrial DNA B Resour 2023; 8:756-759. [PMID: 37475776 PMCID: PMC10355681 DOI: 10.1080/23802359.2023.2224461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/07/2023] [Indexed: 07/22/2023] Open
Abstract
In this study we sequenced and annotated the complete mitochondrial genome of the invasive reptile parasite Raillietiella orientalis using Illumina DNA sequencing. The length of the mitogenome was 15,320 bp and had a GC content of 33.1%. The mitogenome contained 13 protein-coding genes, two ribosomal RNA genes, and 22 tRNA genes, the order of which was diagnostic of Pancrustacean mitogenomes. A phylogenetic tree constructed from the 13 protein-coding genes of R. orientalis and 26 other Pancrustacean mitogenomes supported the placement of R. orientalis as part of the monophyletic subclass Pentastomida within the Maxillopoda and sister to the subclass Branchiura.
Collapse
Affiliation(s)
| | | | | | - Robert R. Fitak
- Department of Biology, University of Central Florida, Orlando, FL, USA
| |
Collapse
|
4
|
Lin YJ, Zhang LH, Ma Y, Storey KB, Yu DN, Zhang JY. Novel Gene Rearrangements in Mitochondrial Genomes of four families of Praying Mantises (Insecta, Mantodea) and Phylogenetic Relationships of Mantodea. Gene 2023; 880:147603. [PMID: 37422176 DOI: 10.1016/j.gene.2023.147603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/10/2023]
Abstract
The mitochondrial genome (mitogenome) plays an important role in phylogenetic studies of many species. The mitogenomes of many praying mantis groups have been well-studied, but mitogenomes of special mimic praying mantises, especially Acanthopoidea and Galinthiadoidea species, are still sorely lacking in the NCBI database. The present study analyzes five mitogenomes from four species of Acanthopoidea (Angela sp., Callibia diana, Coptopteryx sp., Raptrix fusca) and one of Galinthiadoidea (Galinthias amoena) that were sequenced by the primer-walking method. Among Angela sp. and Coptopteryx sp., three gene rearrangements were detected in ND3-A-R-N-S-E-F and COX1-L2-COX2 gene regions, two of which were novel. In addition, individual tandem repeats were found in control regions of four mitogenomes (Angela sp., C. diana, Coptopteryx sp., G. amoena). For those, plausible explanations were derived from the tandem duplication-random loss (TDRL) model and the slipped-strand mispairing model. One potential motif was found in Acanthopidae that was seen as a synapomorphy. Several conserved block sequences (CBSs) were detected within Acanthopoidea that paved the way for the design of specific primers. Via BI and ML analysis, based on four datasets (PCG12, PCG12R, PCG123, PCG123R), the merged phylogenetic tree within Mantodea was reconstructed. This showed that the monophyly of Acanthopoidea was supported and that the PCG12R dataset was the most suitable for reconstructing the phylogenetic tree within Mantodea.
Collapse
Affiliation(s)
- Yi-Jie Lin
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang Province, China.
| | - Li-Hua Zhang
- Taishun County Forestry Bureau, Wenzhou, Zhejiang Province, China.
| | - Yue Ma
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang Province, China.
| | | | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang Province, China; Department of Biology, Carleton University, Ottawa, Canada.
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang Province, China; Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China.
| |
Collapse
|
5
|
Schoenemann B, Clarkson ENK. The median eyes of trilobites. Sci Rep 2023; 13:3917. [PMID: 36890176 PMCID: PMC9995485 DOI: 10.1038/s41598-023-31089-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
Arthropods typically possess two types of eyes-compound eyes, and the ocellar, so called 'median eyes'. Only trilobites, an important group of arthropods during the Palaeozoic, seem not to possess median eyes. While compound eyes are in focus of many investigations, median eyes are not as well considered. Here we give an overview of the occurence of median eyes in the arthropod realm and their phylogenetic relationship to other ocellar eye-systems among invertebrates. We discuss median eyes as represented in the fossil record e.g. in arthropods of the Cambrian fauna, and document median eyes in trilobites the first time. We make clear that ocellar systems, homologue to median eyes and possibly their predecessors are the primordial visual system, and that the compound eyes evolved later. Furthermore, the original number of median eyes is two, as retained in chelicerates. Four, probably the consequence of a gene-dublication, can be found for example in basal crustaceans, three is a derived number by fusion of the central median eyes and characterises Mandibulata. Median eyes are present in larval trilobites, but lying below a probably thin, translucent cuticle, as described here, which explains why they have hitherto escaped detection. So this article gives a review about the complexity of representation and evolution of median eyes among arthropods, and fills the gap of missing median eyes in trilobites. Thus now the number of median eyes represented in an arthropod is an important tool to find its position in the phylogenetic tree.
Collapse
Affiliation(s)
- Brigitte Schoenemann
- Department of Biology, Institute of Zoology (Neurobiology, Animal Physiology), University of Cologne, 50674, Cologne, Germany.
| | - Euan N K Clarkson
- Grant Institute, School of Geosciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JW, UK
| |
Collapse
|
6
|
Conflicts in Mitochondrial Phylogenomics of Branchiopoda, with the First Complete Mitogenome of Laevicaudata (Crustacea: Branchiopoda). Curr Issues Mol Biol 2023; 45:820-837. [PMID: 36825999 PMCID: PMC9955068 DOI: 10.3390/cimb45020054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
Conflicting phylogenetic signals are pervasive across genomes. The potential impact of such systematic biases may be reduced by phylogenetic approaches accommodating for heterogeneity or by the exclusive use of homoplastic sites in the datasets. Here, we present the complete mitogenome of Lynceus grossipedia as the first representative of the suborder Laevicaudata. We employed a phylogenomic approach on the mitogenomic datasets representing all major branchiopod groups to identify the presence of conflicts and concordance across the phylogeny. We found pervasive phylogenetic conflicts at the base of Diplostraca. The homogeneity of the substitution pattern tests and posterior predictive tests revealed a high degree of compositional heterogeneity among branchiopod mitogenomes at both the nucleotide and amino acid levels, which biased the phylogenetic inference. Our results suggest that Laevicaudata as the basal clade of Phyllopoda was most likely an artifact caused by compositional heterogeneity and conflicting phylogenetic signal. We demonstrated that the exclusive use of homoplastic site methods combining the application of site-heterogeneous models produced correct phylogenetic estimates of the higher-level relationships among branchiopods.
Collapse
|
7
|
Wang Z, Xu X, Zheng Y, Wang J, Yu Q, Liu B. Taxonomic status and phylogenetic relationship of Anomura (Crustacea: Decapoda) based on mitochondrial sequences and gene order rearrangements. Gene X 2022; 851:147042. [DOI: 10.1016/j.gene.2022.147042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/26/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022] Open
|