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Jain K, Panigrahi M, Nayak SS, Rajawat D, Sharma A, Sahoo SP, Bhushan B, Dutt T. The evolution of contemporary livestock species: Insights from mitochondrial genome. Gene 2024; 927:148728. [PMID: 38944163 DOI: 10.1016/j.gene.2024.148728] [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: 04/16/2024] [Revised: 06/05/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.
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Affiliation(s)
- Karan Jain
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | | | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Tapanainen R, Aasumets K, Fekete Z, Goffart S, Dufour E, L O Pohjoismäki J. Species-specific variation in mitochondrial genome tandem repeat polymorphisms in hares (Lepus spp., Lagomorpha, Leporidae) provides insight into their evolution. Gene 2024; 926:148644. [PMID: 38851366 DOI: 10.1016/j.gene.2024.148644] [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: 03/09/2024] [Revised: 04/23/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
The non-coding regions of the mitochondrial DNAs (mtDNAs) of hares, rabbits, and pikas (Lagomorpha) contain short (∼20 bp) and long (130-160 bp) tandem repeats, absent in related mammalian orders. In the presented study, we provide in-depth analysis for mountain hare (Lepus timidus) and brown hare (L. europaeus) mtDNA non-coding regions, together with a species- and population-level analysis of tandem repeat variation. Mountain hare short tandem repeats (SRs) as well as other analyzed hare species consist of two conserved 10 bp motifs, with only brown hares exhibiting a single, more variable motif. Long tandem repeats (LRs) also differ in sequence and copy number between species. Mountain hares have four to seven LRs, median value five, while brown hares exhibit five to nine LRs, median value six. Interestingly, introgressed mountain hare mtDNA in brown hares obtained an intermediate LR length distribution, with median copy number being the same as with conspecific brown hare mtDNA. In contrast, transfer of brown hare mtDNA into cultured mtDNA-less mountain hare cells maintained the original LR number, whereas the reciprocal transfer caused copy number instability, suggesting that cellular environment rather than the nuclear genomic background plays a role in the LR maintenance. Due to their dynamic nature and separation from other known conserved sequence elements on the non-coding region of hare mitochondrial genomes, the tandem repeat elements likely to represent signatures of ancient genetic rearrangements. clarifying the nature and dynamics of these rearrangements may shed light on the possible role of NCR repeated elements in mitochondria and in species evolution.
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Affiliation(s)
- Riikka Tapanainen
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Koit Aasumets
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Zsófia Fekete
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland; Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Steffi Goffart
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
| | - Jaakko L O Pohjoismäki
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland.
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Dong X, Liu Y, Chen Y, Ping X, Ren Z, Zhang Y. A chromosome-level genome assembly of Cape hare (Lepus capensis). Sci Data 2024; 11:1081. [PMID: 39362891 PMCID: PMC11449922 DOI: 10.1038/s41597-024-03953-2] [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: 08/01/2024] [Accepted: 09/26/2024] [Indexed: 10/05/2024] Open
Abstract
The Cape hare (Lepus capensis) is among the most widely distributed hare species globally, inhabiting extensive regions across Africa, the Middle East, and Central Asia. However, evolutionary and genetic research on L. capensis was seriously impeded by the absence of a reference genome. Here, we assembled and constructed a chromosome-level genome of L. capensis (with scaffolds anchored to 25 chromosomes and a total assembled length of 2.9 Gb, achieving a contig N50 length of 124.44 Mb) using PacBio HiFi sequencing and Hi-C assembly technology. Evaluation using BUSCO indicated the genome assembly to be 98.2% complete. The de novo prediction revealed that repetitive sequences constitute 46.13% of the entire genome, and long interspersed nuclear elements (LINEs) constituted the largest portion. We annotated a total of 13, 868 protein-coding genes using transcriptomes from two tissues (muscle and skin). This high-quality reference genome serves as a valuable genomic resource for advancing genetic studies in this species.
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Affiliation(s)
- Xianggui Dong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Yu Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuan Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xinxin Ping
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhanjun Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yuanyuan Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Chen H, Chen Y, Wang Z, Wu D, Chen P, Chen Y. The Complete Mitochondrial Genome of the Siberian Scoter Melanitta stejnegeri and Its Phylogenetic Relationship in Anseriformes. Int J Mol Sci 2024; 25:10181. [PMID: 39337666 PMCID: PMC11432269 DOI: 10.3390/ijms251810181] [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: 08/26/2024] [Revised: 09/19/2024] [Accepted: 09/20/2024] [Indexed: 09/30/2024] Open
Abstract
The Siberian Scoter (Melanitta stejnegeri) is a medium sea duck distinct from M. deglandi due to the absence of hybridization and differences in morphological characteristics. However, knowledge of its phylogenetic relationships within Anseriformes is limited due to a lack of molecular data. In this study, the complete mitogenome of M. stejnegeri was firstly sequenced, then annotated and used to reconstruct the phylogenetic relationships of 76 Anseriformes species. The complete mitogenome of M. stejnegeri is 16,631 bp and encodes 37 typical genes: 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 non-coding control region. Its mitogenome organization is similar to that of other Anseriformes species. The phylogenetic relationships within the genus Melanitta are initially clarified, with M. americana at the base. M. stejnegeri and M. deglandi are sister groups, clustering with M. fusca and M. perspicillata in order. Phylogenetic analysis suggests that Mareca falcata and M. strepera are sister groups, differing from previous studies. Results firstly indicate that Clangula hyemalis and Somateria mollissima are sister groups, suggesting a potentially skewed phylogenetic relationship may have been overlooked in earlier analyses relying solely on mitochondrial genomes. Our results provide new mitogenome data to support further phylogenetic and taxonomic studies of Anseriformes.
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Affiliation(s)
- Huimin Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yaqin Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Zhenqi Wang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Dawei Wu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Pan Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yanhong Chen
- The Anhui Provincial Key Laboratory of Biodiversity Conservation and Ecological Security in the Yangtze River Basin, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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Yi C, Shu X, Wang L, Yin J, Wang Y, Wang Y, Zhang H, He Q, Zhao M. The first report of complete mitogenomes of two endangered species of genus Propomacrus (Coleoptera: Scarabaeidae: Euchirinae) and phylogenetic implications. PLoS One 2024; 19:e0310559. [PMID: 39292737 PMCID: PMC11410235 DOI: 10.1371/journal.pone.0310559] [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: 03/11/2024] [Accepted: 09/03/2024] [Indexed: 09/20/2024] Open
Abstract
To understand the mitochondrial genome structure of two endangered and long-armed scarab beetles, Propomacrus davidi and Propomacrus bimucronatus, their complete mitogenomes were sequenced for the first time in this study. The complete mitogenomes of P. davidi and P. bimucronatus were 18, 042 bp and 18, 104 bp in length, respectively. The gene orders of their mitogenomes were highly consistent with other Coleopteran species, and the typical ATN was used as the start codon in most protein coding genes. The incomplete stop codon T was used in cox1, cox2, and nad5, and TAN was used as a complete stop codon in most protein coding genes. All predicted tRNAs could form a typical cloverleaf secondary structure, except that trnS1 lacked the dihydrouridine arm. Based on the maximum likelihood and the Bayesian inference methods, phylogenetic trees of 50 species were reconstructed. The results showed that P. davidi, P. bimucronatus, Cheirotonus jansoni and Cheirotonus gestroi clustered in the same branch, and were the most closely related. The results supported that subfamily Euchirinae is a monophyletic group of Scarabaeidae, which was consistent with the morphological classification. These molecular data enriched the complete mitogenome database of Euchirinae, and improved our understanding of the phylogenetic relationship and evolutionary characteristics of these two endangered species.
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Affiliation(s)
- Chuanhui Yi
- Yunnan Institute of Biological Diversity, Southwest Forestry University, Kunming, Yunnan Province, P.R. China
| | - Xu Shu
- Department of Forest Conservation, College of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan Province, P.R. China
| | - Lingmin Wang
- Department of Forest Conservation, College of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan Province, P.R. China
| | - Jing Yin
- Department of Forest Conservation, College of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan Province, P.R. China
| | - Youhui Wang
- Department of Forest Conservation, College of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan Province, P.R. China
| | - Yuchen Wang
- Department of Forest Conservation, College of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan Province, P.R. China
| | - Honghui Zhang
- Department of Forest Conservation, College of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan Province, P.R. China
| | - Qiuju He
- Department of Forest Conservation, College of Biodiversity Conservation, Southwest Forestry University, Kunming, Yunnan Province, P.R. China
| | - Min Zhao
- Division of Resource Insects, Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, Yunnan Province, P.R. China
- Key Laboratory of Breeding and Utilization of Resource Insects, National Forestry and Grassland Administration, Kunming, Yunnan Province, P.R. China
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Liu Q, Xu S, He J, Cai W, Wang X, Song F. Full-Length Transcriptome Profiling of the Complete Mitochondrial Genome of Sericothrips houjii (Thysanoptera: Thripidae: Sericothripinae) Featuring Extensive Gene Rearrangement and Duplicated Control Regions. INSECTS 2024; 15:700. [PMID: 39336667 PMCID: PMC11432214 DOI: 10.3390/insects15090700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/06/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024]
Abstract
The mitochondrial genome (mitogenome) of Thysanoptera has extensive gene rearrangement, and some species have repeatable control regions. To investigate the characteristics of the gene expression, transcription and post-transcriptional processes in such extensively gene-rearranged mitogenomes, we sequenced the mitogenome and mitochondrial transcriptome of Sericothrips houjii to analyze. The mitogenome was 14,965 bp in length and included two CRs contains 140 bp repeats between COIII-trnN (CR1) and trnT-trnP (CR2). Unlike the putative ancestral arrangement of insects, S. houjii exhibited only six conserved gene blocks encompassing 14 genes (trnL2-COII, trnD-trnK, ND2-trnW, ATP8-ATP6, ND5-trnH-ND4-ND4L and trnV-lrRNA). A quantitative transcription map showed the gene with the highest relative expression in the mitogenome was ND4-ND4L. Based on analyses of polycistronic transcripts, non-coding RNAs (ncRNAs) and antisense transcripts, we proposed a transcriptional model of this mitogenome. Both CRs contained the transcription initiation sites (TISs) and transcription termination sites (TTSs) of both strands, and an additional TIS for the majority strand (J-strand) was found within antisense lrRNA. The post-transcriptional cleavage processes followed the "tRNA punctuation" model. After the cleavage of transfer RNAs (tRNAs), COI and ND3 matured as bicistronic mRNA COI/ND3 due to the translocation of intervening tRNAs, and the 3' untranslated region (UTR) remained in the mRNAs for COII, COIII, CYTB and ND5. Additionally, isoform RNAs of ND2, srRNA and lrRNA were identified. In summary, the relative mitochondrial gene expression levels, transcriptional model and post-transcriptional cleavage process of S. houjii are notably different from those insects with typical mitochondrial gene arrangements. In addition, the phylogenetic tree of Thripidae including S. houjii was reconstructed. Our study provides insights into the phylogenetic status of Sericothripinae and the transcriptional and post-transcriptional regulation processes of extensively gene-rearranged insect mitogenomes.
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Affiliation(s)
- Qiaoqiao Liu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510640, China
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shiwen Xu
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jia He
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
- Ningxia Key Lab of Plant Disease and Pest Control, Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, China
| | - Wanzhi Cai
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xingmin Wang
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510640, China
| | - Fan Song
- MOA Key Lab of Pest Monitoring and Green Management, Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China
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Kuo YY, Chang JC, Li YH, Huang YF, Wu TY, Nai YS. The Complete Mitochondrial Genome and Phylogenetic Analysis of Rhagastis binoculata (Matsumura, 1909) (Lepidoptera: Sphingidae). Genes (Basel) 2024; 15:1171. [PMID: 39336762 PMCID: PMC11430935 DOI: 10.3390/genes15091171] [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: 07/28/2024] [Revised: 09/01/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024] Open
Abstract
The mitochondrial genome (mitogenome) Rhagastis binoculata (Matsumura, 1909), an endemic moth species in Taiwan, was sequenced and analyzed. The complete circular mitogenome of R. binoculata is 15,303 bp and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an AT-rich control region. The mitogenome has an overall nucleotide composition of 41.2% A, 11.9% C, 7.5% G, and 39.4% T, with an AT content of 80.6%. Of the protein-coding genes (PCGs), 12 start with ATG, ATT, and ATC, and COX1 starts with a "CGA" codon. All of the stop codons are "TAA, TAG, or T". Our phylogenetic analysis of 21 species of Sphingidae insects suggests that R. binoculata is clustered with Rhagastis mongoliana, which belongs to the subfamily Macroglossinae.
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Affiliation(s)
- Yu-Yun Kuo
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Ju-Chun Chang
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Yi-Hsuan Li
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung City 402202, Taiwan
| | - Yu-Feng Huang
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
| | - Tzong-Yuan Wu
- Department of Bioscience Technology, College of Science, Chung Yuan Christian University, Zhongli District, Taoyuan City 32023, Taiwan
| | - Yu-Shin Nai
- Department of Entomology, National Chung Hsing University, Taichung City 40227, Taiwan
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung City 402202, Taiwan
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Meng C, Cao S, Dong W, Gao C. The redescription and complete mitogenomes of two Oxycarenus species (Hemiptera, Oxycarenidae) and phylogenetic implications. Zookeys 2024; 1211:231-250. [PMID: 39279917 PMCID: PMC11393489 DOI: 10.3897/zookeys.1211.126013] [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: 04/24/2024] [Accepted: 07/29/2024] [Indexed: 09/18/2024] Open
Abstract
In this study, the two Oxycarenidae species, O.gossypii Horváth, 1926 and Oxycarenusbicolorheraldus Distant, 1904, are redescribed, and their complete mitogenomes are sequenced and analyzed. The phylogeny of Lygaeoidea is examined using 45 complete mitogenomes of lygaeoid species and four outgroup species. The gene orientation and arrangement of the two mitogenomes are found to be consistent with typical Lygaeoidea mitochondrial features, comprising 37 genes, including 13 PCGs, 22 tRNAs, 2 rRNAs, and a control region. Nucleotide composition of the species was biased towards A and T, with the gene order identical to the putative ancestral arrangement of insects. Start codons, stop codons, RNAs, relative synonymous codon usage (RSCU), and nucleotide diversity (Pi) of Oxycarenidae exhibited characteristics similar to other families in Lygaeoidea. Bayesian-inference (BI) and maximum-likelihood (ML) methods were employed to investigate phylogenetic relationships using PCG datasets from selected species. Phylogenetic analyses reveal slightly different topologies between BI and ML methods, with variation primarily concentrated in Colobathristidae and Rhyparochromidae. Our study confirms that the two sequenced Oxycarenidae species formed a single clade, and the position of Oxycarenidae remains stable in both ML and BI phylogenetic trees. These findings expand the mitochondrial genome databases of Lygaeoidea and provide valuable insights into the phylogenetic relationships within Lygaeoidea or Pentatomomorpha.
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Affiliation(s)
- Changjun Meng
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing, Jiangsu 210037, China Nanjing Forestry University Nanjing China
| | - Suyan Cao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing, Jiangsu 210037, China Nanjing Forestry University Nanjing China
| | - Wen Dong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing, Jiangsu 210037, China Nanjing Forestry University Nanjing China
| | - Cuiqing Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland, Nanjing Forestry University, Nanjing, Jiangsu 210037, China Nanjing Forestry University Nanjing China
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McElroy KE, Masonbrink R, Chudalayandi S, Severin AJ, Serb JM. A chromosome-level genome assembly of the disco clam, Ctenoides ales. G3 (BETHESDA, MD.) 2024; 14:jkae115. [PMID: 38805695 PMCID: PMC11373642 DOI: 10.1093/g3journal/jkae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 12/22/2023] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales (C. ales), which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and reported a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein-coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, is a valuable resource for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.
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Affiliation(s)
- Kyle E McElroy
- Department of Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Rick Masonbrink
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | | | - Andrew J Severin
- Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA
| | - Jeanne M Serb
- Department of Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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Klirs Y, Novosolov M, Gissi C, Garić R, Pupko T, Stach T, Huchon D. Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss. Genome Biol Evol 2024; 16:evae181. [PMID: 39162337 PMCID: PMC11384887 DOI: 10.1093/gbe/evae181] [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: 05/04/2024] [Revised: 07/19/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024] Open
Abstract
Sequencing the mitochondrial genome of the tunicate Oikopleura dioica is a challenging task due to the presence of long poly-A/T homopolymer stretches, which impair sequencing and assembly. Here, we report on the sequencing and annotation of the majority of the mitochondrial genome of O. dioica by means of combining several DNA and amplicon reads obtained by Illumina and MinIon Oxford Nanopore Technologies with public RNA sequences. We document extensive RNA editing, since all homopolymer stretches present in the mitochondrial DNA correspond to 6U-regions in the mitochondrial RNA. Out of the 13 canonical protein-coding genes, we were able to detect eight, plus an unassigned open reading frame that lacked sequence similarity to canonical mitochondrial protein-coding genes. We show that the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal. In addition to two very short rRNAs, we could only identify a single tRNA (tRNA-Met), suggesting multiple losses of tRNA genes, supported by a corresponding loss of mitochondrial aminoacyl-tRNA synthetases in the nuclear genome. Based on the eight canonical protein-coding genes identified, we reconstructed maximum likelihood and Bayesian phylogenetic trees and inferred an extreme evolutionary rate of this mitochondrial genome. The phylogenetic position of appendicularians among tunicates, however, could not be accurately determined.
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Affiliation(s)
- Yael Klirs
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Maria Novosolov
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
- Faculty of Health and Medical Sciences, GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Carmela Gissi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari 70126, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
- CoNISMa, Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma 00196, Italy
| | - Rade Garić
- Institute for Marine and Coastal Research, University of Dubrovnik, Dubrovnik 20000, Croatia
| | - Tal Pupko
- George S. Wise Faculty of Life Sciences, The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Thomas Stach
- Department of Molecular Parasitology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dorothée Huchon
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Steinhardt Museum of Natural History and National Research Center, Tel Aviv University, Tel Aviv 6997801, Israel
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Marturano G, Carli D, Cucini C, Carapelli A, Plazzi F, Frati F, Passamonti M, Nardi F. SmithHunter: a workflow for the identification of candidate smithRNAs and their targets. BMC Bioinformatics 2024; 25:286. [PMID: 39223476 PMCID: PMC11370224 DOI: 10.1186/s12859-024-05909-0] [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: 02/20/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND SmithRNAs (Small MITochondrial Highly-transcribed RNAs) are a novel class of small RNA molecules that are encoded in the mitochondrial genome and regulate the expression of nuclear transcripts. Initial evidence for their existence came from the Manila clam Ruditapes philippinarum, where they have been described and whose activity has been biologically validated through RNA injection experiments. Current evidence on the existence of these RNAs in other species is based only on small RNA sequencing. As a preliminary step to characterize smithRNAs across different metazoan lineages, a dedicated, unified, analytical workflow is needed. RESULTS We propose a novel workflow specifically designed for smithRNAs. Sequence data (from small RNA sequencing) uniquely mapping to the mitochondrial genome are clustered into putative smithRNAs and prefiltered based on their abundance, presence in replicate libraries and 5' and 3' transcription boundary conservation. The surviving sequences are subsequently compared to the untranslated regions of nuclear transcripts based on seed pairing, overall match and thermodynamic stability to identify possible targets. Ample collateral information and graphics are produced to help characterize these molecules in the species of choice and guide the operator through the analysis. The workflow was tested on the original Manila clam data. Under basic settings, the results of the original study are largely replicated. The effect of additional parameter customization (clustering threshold, stringency, minimum number of replicates, seed matching) was further evaluated. CONCLUSIONS The study of smithRNAs is still in its infancy and no dedicated analytical workflow is currently available. At its core, the SmithHunter workflow builds over the bioinformatic procedure originally applied to identify candidate smithRNAs in the Manila clam. In fact, this is currently the only evidence for smithRNAs that has been biologically validated and, therefore, the elective starting point for characterizing smithRNAs in other species. The original analysis was readapted using current software implementations and some minor issues were solved. Moreover, the workflow was improved by allowing the customization of different analytical parameters, mostly focusing on stringency and the possibility of accounting for a minimal level of genetic differentiation among samples.
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Affiliation(s)
| | - Diego Carli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Claudio Cucini
- Department of Life Sciences, University of Siena, 53100, Siena, Italy
| | - Antonio Carapelli
- Department of Life Sciences, University of Siena, 53100, Siena, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Francesco Frati
- Department of Life Sciences, University of Siena, 53100, Siena, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
| | - Francesco Nardi
- Department of Life Sciences, University of Siena, 53100, Siena, Italy
- National Biodiversity Future Center (NBFC), 90133, Palermo, Italy
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Yun SW, Park JY. Characterization of the complete mitochondrial genome of a newly discovered torrent catfish, Liobagrus geumgangensis, and their phylogenetic relationships. Genes Genomics 2024; 46:1123-1131. [PMID: 39126601 DOI: 10.1007/s13258-024-01552-4] [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: 05/28/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND A new Liobagrus fish was reported from the Korean Peninsula, but research on this taxon is lacking. Moreover, existing research on the mitogenome of the genus Liobagrus in Korea is very limited, and no studies have been conducted on structural characteristics of transfer RNA (tRNA) or gene order comparisons between taxa; instead, research has been restricted to basic phylogeny. OBJECTIVE The complete mitochondrial genome of Liobagrus geumgangensis was analyzed for the first time. We then aimed to reconstruct the phylogenetic relationships of the genus Liobagrus and estimate the divergence time of speciation events. METHODS We used a dissected fin clip from an adult of Liobagrus geumgangensis. Genomic DNA was extracted and analyzed with whole genome sequencing (WGS) and assembled by the NOVOPlasty method. The mitogenome sequence was annotated, and a genome map, tRNA structure, and phylogenetic tree were constructed using maximum likelihood analysis. In addition, divergence time was estimated. RESULTS The mitochondrial genome was 16,522 bp in length and comprised 37 genes. The overall base composition was 30.5% A, 25.5% T, 28.4% C, and 15.7% G. Most tRNAs exhibited the typical clover leaf shape, except trnS1. Phylogenetic analysis revealed that Liobagrus geumgangensis clustered within a clade with four other Liobagrus species exclusive to the southern region of the Korean Peninsula. Its divergence was estimated to have occurred during the late Miocene. CONCLUSION Characteristics of Liobagrus geumgangensis mitogenome were consistent with those of other torrent catfish species. Time scale estimation revealed distinct groupings, with some distributed across mainland Asia and others in the southern region of the Korean Peninsula. Notably, the Korean Peninsula group was identified as its own lineage, comprising entirely endemic species.
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Affiliation(s)
- Seung-Woon Yun
- Department of Biological Sciences, College of Natural Sciences, Jeonbuk National University, Jeonju, 54986, South Korea
| | - Jong-Young Park
- Department of Biological Sciences, College of Natural Sciences, Jeonbuk National University, Jeonju, 54986, South Korea.
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13
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Zhou G, Zhang H, Chen W, Li Z, Zhang X, Fu Y. Morphological observation, molecular identification and evolutionary analysis of Hydatigera kamiyai found in Neodon fuscus from the Qinghai-Tibetan plateau. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105629. [PMID: 38936527 DOI: 10.1016/j.meegid.2024.105629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/10/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Hydatigera kamiyai (H. kamiyai) is a new species within Hydatigera that has recently been resurrected. Voles and cats are hosts of H. kamiyai and have a certain impact on its health and economy. Moreover, the Qinghai-Tibetan plateau (QTP) is a research hotspot representing Earth's biodiversity, as its unique geographical environment and climatic conditions support the growth of a variety of mammals and provide favorable conditions for various parasites to complete their life history. The aim of this study was to reveal the phylogenetic relationships and divergence times of H. kamiyai strains isolated from Neodon fuscus on the QTP using morphological and molecular methods. In this study, we morphologically observed H. kamiyai and sequenced the whole mitochondrial genome. Then, we constructed phylogenetic trees with the maximum likelihood (ML) and Bayesian inference (BI) methods. The GTR alternative model was selected for divergence time analysis. These data demonstrated that the results were consistent with the general morphological characteristics of Hydatigera. The whole genome of H. kamiyai was 13,822 bp in size, and the A + T content (73%) was greater than the G + C content (27%). The Ka/Ks values were all <1, indicating that all 13 protein-coding genes (13 PCGs) underwent purifying selection during the process of evolution. The phylogenetic tree generated based on the 13 PCGs, cytochrom oxidase subunit I (COI), 18S rRNA and 28S rRNA revealed close phylogenetic relationships between H. kamiyai and Hydatigera, with high node support for the relationship. The divergence time based on 13 PCGs indicated that H. kamiyai diverged approximately 11.3 million years ago (Mya) in the Miocene. Interestingly, it diverged later than the period of rapid uplift in the QTP. We also speculated that H. kamiyai differentiation was caused by host differentiation due to the favorable living conditions brought about by the uplift of the QTP. As there have been relatively few investigations on the mitochondrial genome of H. kamiyai, our study could provide factual support for further studies of H. kamiyai on the QTP. We also emphasized the importance of further studies of its hosts, Neodon fuscus and cats, which will be important for further understanding the life cycle of H. kamiyai.
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Affiliation(s)
- Guoyan Zhou
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Haining Zhang
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Wangkai Chen
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Zhi Li
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Xueyong Zhang
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Yong Fu
- Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China; Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China.
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14
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Chai S, Chong Y, Yin D, Qiu Q, Xu S, Yang G. Genomic insights into adaptation to bipedal saltation and desert-like habitats of jerboas. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2003-2015. [PMID: 38902451 DOI: 10.1007/s11427-023-2516-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/20/2023] [Indexed: 06/22/2024]
Abstract
Jerboas is a lineage of small rodents displaying atypical mouse-like morphology with elongated strong hindlimbs and short forelimbs. They have evolved obligate bipedal saltation and acute senses, and been well-adapted to vast desert-like habitats. Using a newly sequenced chromosome-scale genome of the Mongolian five-toed jerboa (Orientallactaga sibirica), our comparative genomic analyses and in vitro functional assays showed that the genetic innovations in both protein-coding and non-coding regions played an important role in jerboa morphological and physiological adaptation. Jerboa-specific amino acid substitutions, and segment insertions/deletions (indels) in conserved non-coding elements (CNEs) were found in components of proteoglycan biosynthesis pathway (XYLT1 and CHSY1), which plays an important role in limb development. Meanwhile, we found specific evolutionary changes functionally associated with energy or water metabolism (e.g., specific amino acid substitutions in ND5 and indels in CNEs physically near ROR2) and senses (e.g., expansion of vomeronasal receptors and the FAM136A gene family) in jerboas. Further dual-luciferase reporter assay verified that some of the CNEs with jerboa-specific segment indels exerted a significantly different influence on luciferase activity, suggesting changes in their regulatory function in jerboas. Our results revealed the potential molecular mechanisms underlying jerboa adaptation since the divergence from the Eocene-Oligocene transition, and provided more resources and new insights to enhance our understanding of the molecular basis underlying the phenotypic diversity and the environmental adaptation of mammals.
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Affiliation(s)
- Simin Chai
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Yujie Chong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Daiqing Yin
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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15
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Wang X, Ren X, Teng X, Feng C, Xing Z, Wang S, Zheng L, Qu J, Wang L. Complete mitochondrial genome and phylogenetic analysis of Mancinella alouina. Mol Biol Rep 2024; 51:942. [PMID: 39196421 DOI: 10.1007/s11033-024-09778-x] [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: 03/14/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024]
Abstract
BACKGROUND The Muricidae family in the Class Gastropoda comprises numerous species with a vast range of morphological features and a worldwide presence. The phylogeny of the Muricidae has been analyzed in previous studies; however, the evolutionary relationships among the main branches of the Muricidae remain unknown. METHODS AND RESULTS In the present study, the mitochondrial genome of Mancinella alouina was sequenced. The mitochondrial genome was found to be 16,671 bp in length and made up of 37 genes (13 protein-coding genes, 22 transfer RNA and 2 ribosomal RNA genes). The genome has an A-T-rich region (66.5% A + T content) and all of the PCGs use the ATN start codon and the TAG or TAA stop codons. The mitochondrial gene arrangement of Mancinella alouina is similar to that of other Muricidae, except for Ocinebrellus inornatus and Ceratostoma burnetti. On the basis of a flexible molecular clock model, time-calibrated phylogenetic results indicate that the genus Mancinella diverged roughly 18.09 Mya, and that the family Muricidae emerged in the Late Cretaceous. CONCLUSIONS This study reveals the structural and sequence information features of the mitochondrial genome of Mancinella alouina. This study provides evidence for the relationships within the family Muricidae at the molecular level, and infer the divergence time. The results of phylogenetic analyses strongly support the current classification.
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Affiliation(s)
- Xumin Wang
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Xiaoyu Ren
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Xindong Teng
- Qingdao International Travel Healthcare Center, Qingdao, 266071, China
| | - Chunyu Feng
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Zhikai Xing
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Shuang Wang
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Li Zheng
- Ministry of Natural Resources, The First Institute of Oceanography, Qingdao, 266061, Shandong, China
| | - Jiangyong Qu
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China.
| | - Lijun Wang
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China.
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16
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Zhang D, Jin WD, Xu HF, Li XB, Jiang YW, Li DQ, Lin XL. Characteristics and Comparative Analysis of Six Mitogenomes of Genus Kiefferulus Goetghebuer, 1922 (Diptera: Chironomidae). INSECTS 2024; 15:646. [PMID: 39336614 PMCID: PMC11432734 DOI: 10.3390/insects15090646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024]
Abstract
Chironomidae is a cosmopolitan and species-rich family of insects, with many species serving as useful indicators of aquatic ecosystem health. In this study, we newly sequenced six species of Kiefferulus Goetghebuer, 1922 (Chironomidae: Chironominae) by high-throughput sequencing technology. We analyzed characters of the mitochondrial genome, including the sequence length, nucleotide composition, and evolutionary rates of this genus. The size of the newly obtained sequences ranged from 15,588 to 15,767 bp, and all of them included 22 tRNAs, 13 PCGs, 2 rRNAs, and 1 CR. The CR showed the highest AT content relative to the PCGs, rRNAs, and tRNAs. Relative synonymous codon usage analysis showed that UUA, UUU, and AUU are the preferred codons. The ratio of nonsynonymous (Ka) to synonymous (Ks) substitution rates showed that all Ka/Ks of PCGs were lower than 1, with ATP8 having the highest evolution rate, while COX1 exhibited the lowest evolution rate. We reconstructed the phylogenetic relationship of the genus Kiefferulus based on eight species (six ingroups and two outgroups), using five matrices and employing Maximum likelihood and Bayesian inference approaches. Phylogenetic analysis of the Kiefferulus showed that six species within this genus were classified into a monophyletic clade.
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Affiliation(s)
- Dan Zhang
- Characteristic Laboratory of Forensic Science in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan 250014, China
| | - Wei-Dong Jin
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Hai-Feng Xu
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Xue-Bo Li
- Characteristic Laboratory of Forensic Science in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan 250014, China
| | - Yong-Wei Jiang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Dai-Qing Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiao-Long Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
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17
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Liu W, Wang C, Wang J, Tang Y, Pei W, Ge X, Yan C. Phylogenetic and Comparative Analysis of Cryptochironomus, Demicryptochironomus and Harnischia Inferred from Mitogenomes (Diptera: Chironomidae). INSECTS 2024; 15:642. [PMID: 39336610 PMCID: PMC11432083 DOI: 10.3390/insects15090642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 09/30/2024]
Abstract
(1) Background: Mitochondrial genomes have been extensively employed as a crucial marker in numerous dipteran families for understanding phylogenetics and systematics relations, thereby playing a pivotal role in molecular biology studies. The phylogenetic relationship of the Harnischia generic complex remains contentious due to the paucity of taxonomic and molecular data. Specifically, the evolutionary relationships among Cryptochironomus, Demicryptochironomus, and Harnischia are still unclear. (2) Methods: In this study, Polypedilum and Endochironomus were used as outgroups to analyze phylogenetic relationships among Cryptochironomus, Demicryptochironomus, and Harnischia, mitogenomes of four Cryptochironomus, two Demicryptochironomus, two Harnischia, and two Cladopelma were newly sequenced. Subsequently, we conducted a thorough analysis of the nucleotide composition, sequence length, and evolutionary rate. (3) Results: All mitogenomes exhibited structural conservation, with all genes consistently arranged in the identical order as that of the ancestral mitogenome. Nucleotide composition varied significantly among different genes, and the control region displayed the highest A + T content. All protein-coding genes undergo rigorous purification selection, with the ATP8 gene exhibiting the most rapid evolutionary rate among them. Utilizing Bayesian Inference (BI) and Maximum Likelihood (ML) methods across various databases, we reconstructed the phylogenetic relationships among the genera within the Harnischia generic complex, drawing insights from an analysis of 14 mitochondrial genomes. (4) Conclusions: Our results showed that the monophyly of the genera Harnischia was well supported in all topologies; Cryptochironomus is sister to Demicryptochironomus.
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Affiliation(s)
- Wenbin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Chengyan Wang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Jingyuan Wang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Yaning Tang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Wenxuan Pei
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Xinyu Ge
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
| | - Chuncai Yan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin 300387, China
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18
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Zheng X, Lin X, Zhang X, Huang X, Yue X, Pu J. Complete mitochondrial genome of Penicillidia dufourii (Diptera: Hippoboscoidea: Nycteribiidae) and phylogenetic relationship. Parasitol Res 2024; 123:302. [PMID: 39158739 DOI: 10.1007/s00436-024-08321-y] [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: 05/31/2024] [Accepted: 08/08/2024] [Indexed: 08/20/2024]
Abstract
Penicillidia dufourii (Westwood 1834) is a specialized parasite categorized under family Nycteribiidae that prefers to parasitize the body surface of various bats under the genus Myotis. Many species of the family Nycteribiidae are carriers of various pathogens; however, research on P. dufourii remains scarce, and studies on its molecular identification and population genetic structure are still lacking. In this study, the complete mitochondrial genome of P. dufourii was elucidated for the first time using Illumina sequencing. The mitochondrial genome is 15,354 bp in size and encodes approximately 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Analysis of 13 protein-coding genes revealed that UUA, UCA, CGA, and GGA were the most common codons, while nad4L had the fastest evolutionary rate and cox1 the slowest. Phylogenetic analysis based on the mitochondrial genome indicated that P. dufourii is clustered with other species of the family Nycteribiidae and is most closely related to Nycteribia parvula and Phthiridium szechuanum.
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Affiliation(s)
- Xiaoyan Zheng
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Xiaoxia Lin
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Xianzheng Zhang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Xiaobin Huang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China.
| | - Xinke Yue
- School of Life Sciences, Yunnan Normal University, Kunming, 650000, China.
| | - Ju Pu
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
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Yang P, Guo W, Wei C, Wang X, Wang Y, Wang J. Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Triplophysa microphthalma. BIOLOGY 2024; 13:608. [PMID: 39194546 DOI: 10.3390/biology13080608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/07/2024] [Accepted: 08/09/2024] [Indexed: 08/29/2024]
Abstract
The complete mitochondrial genome has been extensively utilized in studies related to phylogenetics, offering valuable perspectives on evolutionary relationships. The mitochondrial genome of the fine-eyed plateau loach, Triplophysa microphthalma, has not attracted much attention, although this species is endemic to China. In this study, we characterized the mitochondrial genome of T. microphthalma and reassessed the classification status of its genus. The complete mitochondrial genome of T. microphthalma was 16,591 bp and contained thirty-seven genes, including thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and twenty-two transfer RNA genes (tRNAs). All but one of the thirteen PCGs had the regular start codon ATG; the gene cox1 started with GTG. Six PCGs had incomplete stop codons (T--). These thirteen PCGs are thought to have evolved under purifying selection, and the mitogenome shared a high degree of similarity with the genomes of species within the genus Leptobotia. All tRNA genes exhibited the standard clover-shaped structure, with the exception of the trnS1 gene, which lacked a DHU stem. A phylogenetic analysis indicated that T. microphthalma was more closely related to species within the genus Triplophysa than to those in Barbatula. The present study contributes valuable genomic information for T. microphthalma, and offers new perspectives on the phylogenetic relationships among species of Triplophysa and Barbatula. The findings also provide essential data that can inform the management and conservation strategies for T. microphthalma and other species of Triplophysa and Barbatula.
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Affiliation(s)
- Ping Yang
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wei Guo
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chao Wei
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China
| | - Xin Wang
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yixuan Wang
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China
| | - Jia Wang
- Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Biology, College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China
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Han Y, Xie Y, Hao Z, Mao J, Wang X, Chang Y, Tian Y. The Mitochondrial Genome of Ylistrum japonicum (Bivalvia, Pectinidae) and Its Phylogenetic Analysis. Int J Mol Sci 2024; 25:8755. [PMID: 39201441 PMCID: PMC11354973 DOI: 10.3390/ijms25168755] [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: 07/03/2024] [Revised: 08/06/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
The Ylistrum japonicum is a commercially valuable scallop known for its long-distance swimming abilities. Despite its economic importance, genetic and genomic research on this species is limited. This study presents the first complete mitochondrial genome of Y. japonicum. The mitochondrial genome is 19,475 bp long and encompasses 13 protein-coding genes, three ribosomal RNA genes, and 23 transfer RNA genes. Two distinct phylogenetic analyses were used to explore the phylogenetic position of the Y. japonicum within the family Pectinidae. Based on one mitochondrial phylogenetic analysis by selecting 15 Pectinidae species and additional outgroup taxa and one single gene phylogenetic analysis by 16S rRNA, two phylogenetic trees were constructed to provide clearer insights into the evolutionary placement of Y. japonicum within the family Pectinidae. Our analysis reveals that Ylistrum is a basal lineage to the Pectininae clade, distinct from its previously assigned tribe, Amusiini. This study offers critical insights into the genetic makeup and evolutionary history of Y. japonicum, enhancing our knowledge of this economically vital species.
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Affiliation(s)
| | | | | | | | | | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China; (Y.H.); (Y.X.); (Z.H.); (J.M.); (X.W.)
| | - Ying Tian
- Key Laboratory of Mariculture & Stock Enhancement in North China Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China; (Y.H.); (Y.X.); (Z.H.); (J.M.); (X.W.)
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21
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Wang L, Liu J, Liu H, Wang Y, Rong H. The complete mitochondrial genome analysis of Locastra muscosalis (Walker, 1866) (Lepidoptera: Pyralidae) and phylogenetic implications. Mitochondrial DNA B Resour 2024; 9:995-999. [PMID: 39113746 PMCID: PMC11305046 DOI: 10.1080/23802359.2024.2387259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
The complete mitochondrial genome of Locastra muscosalis (Walker, 1866) was sequenced and characterized in this study, which was the first reported complete mitogenome of the genus Locastra. The mitogenome of L. muscosalis has a total length of 15,177 bp, encompassing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A-T rich region. Phylogenetic analysis revealed that L. muscosalis is closely associated with Orthaga euadrusalis. These data will serve as a valuable foundation for future investigations into the Epipaschiinae and Pyralidae evolutionary history.
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Affiliation(s)
- Laiyou Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
| | - Jiali Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Haosen Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yu Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Hua Rong
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
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Wang J, Kan S, Kong J, Nie L, Fan W, Ren Y, Reeve W, Mower JP, Wu Z. Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes. Genome Biol Evol 2024; 16:evae177. [PMID: 39190481 PMCID: PMC11354287 DOI: 10.1093/gbe/evae177] [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] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Repeats can mediate rearrangements and recombination in plant mitochondrial genomes and plastid genomes. While repeat accumulations are linked to heightened evolutionary rates and complex structures in specific lineages, debates persist regarding the extent of their influence on sequence and structural evolution. In this study, 75 Plantago plastomes were analyzed to investigate the relationships between repeats, nucleotide substitution rates, and structural variations. Extensive repeat accumulations were associated with significant rearrangements and inversions in the large inverted repeats (IRs), suggesting that repeats contribute to rearrangement hotspots. Repeats caused infrequent recombination that potentially led to substoichiometric shifting, supported by long-read sequencing. Repeats were implicated in elevating evolutionary rates by facilitating localized hypermutation, likely through DNA damage and repair processes. This study also observed a decrease in nucleotide substitution rates for loci translocating into IRs, supporting the role of biased gene conversion in maintaining lower substitution rates. Combined with known parallel changes in mitogenomes, it is proposed that potential dysfunction in nuclear-encoded genes associated with DNA replication, recombination, and repair may drive the evolution of Plantago organellar genomes. These findings contribute to understanding how repeats impact organellar evolution and stability, particularly in rapidly evolving plant lineages.
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Affiliation(s)
- Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
- College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Marine College, Shandong University, Weihai 264209, China
| | - Jiali Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Liyun Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Weishu Fan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonglin Ren
- College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Wayne Reeve
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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23
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Cheng WX, Wang J, Mao ML, Lu YB, Zou JX. The mitochondrial genome of Bottapotamon fukienense (Brachiura: Potamidae) is fragmented into two chromosomes. BMC Genomics 2024; 25:755. [PMID: 39095713 PMCID: PMC11295360 DOI: 10.1186/s12864-024-10657-9] [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: 03/30/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND China is the hotspot of global freshwater crab diversity, but their wild populations are facing severe pressures associated with anthropogenic factors, necessitating the need to map their taxonomic and genetic diversity and design conservation policies. RESULTS Herein, we sequenced the mitochondrial genome of a Chinese freshwater crab species Bottapotamon fukienense, and found that it is fragmented into two chromosomes. We confirmed that fragmentation was not limited to a single specimen or population. Chromosome 1 comprised 15,111 base pairs (bp) and there were 26 genes and one pseudogene (pseudo-nad1) encoded on it. Chromosome 2 comprised 8,173 bp and there were 12 genes and two pseudogenes (pseudo-trnL2 and pseudo-rrnL) encoded on it. Combined, they comprise the largest mitogenome (23,284 bp) among the Potamidae. Bottapotamon was the only genus in the Potamidae dataset exhibiting rearrangements of protein-coding genes. Bottapotamon fukienense exhibited average rates of sequence evolution in the dataset and did not differ in selection pressures from the remaining Potamidae. CONCLUSIONS This is the first experimentally confirmed fragmentation of a mitogenome in crustaceans. While the mitogenome of B. fukienense exhibited multiple signs of elevated mitogenomic architecture evolution rates, including the exceptionally large size, duplicated genes, pseudogenisation, rearrangements of protein-coding genes, and fragmentation, there is no evidence that this is matched by elevated sequence evolutionary rates or changes in selection pressures.
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Affiliation(s)
- Wang-Xinjun Cheng
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Jun Wang
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Mei-Lin Mao
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Yuan-Biao Lu
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China
| | - Jie-Xin Zou
- Research Laboratory of Freshwater Crustacean Decapoda & Paragonimus, School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi Province, 330031, China.
- Provincial Key Laboratory for Drug Targeting and Drug Screening, Jiangxi Medical College, Nanchang University, Nanchang, 330031, China.
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24
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Zhan L, Chen Y, He J, Guo Z, Wu L, Storey KB, Zhang J, Yu D. The Phylogenetic Relationships of Major Lizard Families Using Mitochondrial Genomes and Selection Pressure Analyses in Anguimorpha. Int J Mol Sci 2024; 25:8464. [PMID: 39126033 PMCID: PMC11312734 DOI: 10.3390/ijms25158464] [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: 06/11/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism's energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed.
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Affiliation(s)
- Lemei Zhan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yuxin Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jingyi He
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Zhiqiang Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Lian Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada
| | - Jiayong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Laboratory of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Danna Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Laboratory of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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25
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Zheng S, Zhang C, Zhou J, Zhang S, Liu Y, Jin X, Wang Y, Liu B. Daphnia sp. (Branchiopoda: Cladocera) Mitochondrial Genome Gene Rearrangement and Phylogenetic Position Within Branchiopoda. Biochem Genet 2024; 62:3030-3051. [PMID: 38063953 DOI: 10.1007/s10528-023-10594-4] [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: 06/27/2023] [Accepted: 11/08/2023] [Indexed: 07/31/2024]
Abstract
In high-altitude (4500 m) freshwater lakes, Daphnia is the apex species and the dominant zooplankton. It frequently dwells in the same lake as the Gammarid. Branchiopoda, a class of Arthropoda, Crustacea, is a relatively primitive group in the subphylum Crustacea, which originated in the Cambrian period of the Paleozoic. The complete mitogenome sequence of Daphnia sp. (Branchiopoda: Cladocera) was sequenced and annotated in this study and deposited in GenBank. The sequence structure of this species was studied by comparing the original sequences with BLAST. In addition, we have also researched the mechanisms of their mitochondrial gene rearrangement by establishing a model. We have used the Bayesian inference [BI] and maximum likelihood [ML] methods to proceed with phylogenetic analysis inference, which generates identical phylogenetic topology that reveals the phylogenetic state of Daphnia. The complete mitogenome of Daphnia sp. shows that it was 15,254 bp in length and included two control regions (CRs) and 37 genes (13 protein-coding genes, 22 tRNAs and two ribosomal RNAs [16S and 12S]). In addition to tRNA-Ser (GCT), other tRNAs have a typical cloverleaf secondary structure. Meanwhile, the mitogenome of Daphnia sp. was clearly rearranged when compared to the mitogenome of typical Daphnia. In a word, we report a newly sequenced mitogenome of Daphnia sp. with a unique rearrangement phenomenon. These results will be helpful for further phylogenetic research and provide a foundation for future studies on the characteristics of the mitochondrial gene arrangement process in Daphnia.
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Affiliation(s)
- Sixu Zheng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Chi Zhang
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China.
| | - Jianshe Zhou
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, People's Republic of China
| | - Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, Guangzhou, 510300, Guangdong, China
| | - Yifan Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Xun Jin
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Yunpeng Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China
| | - Bingjian Liu
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, No.1, Haida South Road, Zhoushan, 316022, Zhejiang, People's Republic of China.
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26
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Kadam PS, Yang Z, Lu Y, Zhu H, Atiyas Y, Shah N, Fisher S, Nordgren E, Kim J, Issadore D, Eberwine J. Single-mitochondrion sequencing uncovers distinct mutational patterns and heteroplasmy landscape in mouse astrocytes and neurons. BMC Biol 2024; 22:162. [PMID: 39075589 PMCID: PMC11287894 DOI: 10.1186/s12915-024-01953-7] [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: 03/11/2024] [Accepted: 07/08/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Mitochondrial (mt) heteroplasmy can cause adverse biological consequences when deleterious mtDNA mutations accumulate disrupting "normal" mt-driven processes and cellular functions. To investigate the heteroplasmy of such mtDNA changes, we developed a moderate throughput mt isolation procedure to quantify the mt single-nucleotide variant (SNV) landscape in individual mouse neurons and astrocytes. In this study, we amplified mt-genomes from 1645 single mitochondria isolated from mouse single astrocytes and neurons to (1) determine the distribution and proportion of mt-SNVs as well as mutation pattern in specific target regions across the mt-genome, (2) assess differences in mtDNA SNVs between neurons and astrocytes, and (3) study co-segregation of variants in the mouse mtDNA. RESULTS (1) The data show that specific sites of the mt-genome are permissive to SNV presentation while others appear to be under stringent purifying selection. Nested hierarchical analysis at the levels of mitochondrion, cell, and mouse reveals distinct patterns of inter- and intra-cellular variation for mt-SNVs at different sites. (2) Further, differences in the SNV incidence were observed between mouse neurons and astrocytes for two mt-SNV 9027:G > A and 9419:C > T showing variation in the mutational propensity between these cell types. Purifying selection was observed in neurons as shown by the Ka/Ks statistic, suggesting that neurons are under stronger evolutionary constraint as compared to astrocytes. (3) Intriguingly, these data show strong linkage between the SNV sites at nucleotide positions 9027 and 9461. CONCLUSIONS This study suggests that segregation as well as clonal expansion of mt-SNVs is specific to individual genomic loci, which is important foundational data in understanding of heteroplasmy and disease thresholds for mutation of pathogenic variants.
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Affiliation(s)
- Parnika S Kadam
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zijian Yang
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Youtao Lu
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hua Zhu
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yasemin Atiyas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nishal Shah
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephen Fisher
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David Issadore
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - James Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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27
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Wei Z, Yang Y, Meng L, Zhang N, Liu S, Meng L, Li Y, Shao C. The Mitogenomic Landscape of Hexacorallia Corals: Insight into Their Slow Evolution. Int J Mol Sci 2024; 25:8218. [PMID: 39125787 PMCID: PMC11311739 DOI: 10.3390/ijms25158218] [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: 04/08/2024] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 08/12/2024] Open
Abstract
The utility of the mitochondrial genomes (mitogenomes) in analyzing the evolutionary history of animals has been proven. Five deep-sea corals (Bathypathes sp.1, Bathypathes sp.2, Schizopathidae 1, Trissopathes sp., and Leiopathes sp.) were collected in the South China Sea (SCS). Initially, the structures and collinearity of the five deep-sea coral mitogenomes were analyzed. The gene arrangements in the five deep-sea coral mitogenomes were similar to those in the order Antipatharia, which evidenced their conservation throughout evolutionary history. Additionally, to elucidate the slow evolutionary rates in Hexacorallia mitogenomes, we conducted comprehensive analyses, including examining phylogenetic relationships, performing average nucleotide identity (ANI) analysis, and assessing GC-skew dissimilarity combining five deep-sea coral mitogenomes and 522 reference Hexacorallia mitogenomes. Phylogenetic analysis using 13 conserved proteins revealed that species clustered together at the order level, and they exhibited interspersed distributions at the family level. The ANI results revealed that species had significant similarities (identity > 85%) within the same order, while species from different orders showed notable differences (identity < 80%). The investigation of the Hexacorallia mitogenomes also highlighted that the GC-skew dissimilarity was highly significant at the order level, but not as pronounced at the family level. These results might be attributed to the slow evolution rate of Hexacorallia mitogenomes and provide evidence of mitogenomic diversity. Furthermore, divergence time analysis revealed older divergence times assessed via mitogenomes compared with nuclear data, shedding light on significant evolutionary events shaping distinct orders within Hexacorallia corals. Those findings provide new insights into understanding the slow evolutionary rates of deep-sea corals in all lineages of Hexacorallia using their mitogenomes.
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Affiliation(s)
- Zhanfei Wei
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
| | - Yang Yang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Lihui Meng
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China;
| | - Nannan Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
| | - Liang Meng
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.Y.); (N.Z.); (S.L.)
| | - Yang Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China;
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28
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Zhu Y, Yan S, Ma P, Zhang Y, Zuo C, Ma X, Zhang Z. Comparative mitochondrial genome analysis provides new insights into the classification of Modiolinae. Mol Biol Rep 2024; 51:823. [PMID: 39023631 DOI: 10.1007/s11033-024-09767-0] [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: 05/07/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Mitochondrial genomes have become a powerful tool for studying molecular genetics and phylogeny of mollusks. Currently, the position of Modiolinae within Mytilidae and the taxonomic and phylogenetic relationships within Modiolinae were still controversial. This study focuses on the complete mitochondrial genomes of two species: Modiolus modulaides (Röding, 1798) and Modiolus auriculatus Krauss, 1848, which have not been sequenced before. METHODS AND RESULTS We assembled and characterized the mitochondrial genomes of M. modulaides and M. auriculatus and then analyzed the phylogenetic relationships. The mitochondrial genomes of M. modulaides and M. auriculatus were 15,422 bp and 16,027 bp, respectively. Both of them were composed of 36 functional genes, including 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. All protein-coding genes showed A + T bias, positive GC skews, and negative AT skews in nucleotide composition. Phylogenetic analysis based on the mitochondrial genomes showed that Modiolinae and Bathymodiolinae clustered together to form a sister relationship. Seven Modiolinae species were divided into two clades: L1 (M. modulaides, M. auriculatus and Modiolus philippinarum Hanley, 1843) and L2 [Modiolus modiolus (Linnaeus, 1758), Modiolus kurilensis Bernard, 1983, Modiolus nipponicus (Oyama, 1950), and Modiolus comptus (Sowerby III, 1915)]. The divergence time of the two clades was approximately 105.75 Ma. Furthermore, the transfer RNA gene rearrangement, longer genetic distance, and greater genetic differentiation were confirmed between the L1 and L2 clades, as well as differences in the external characteristics of the shells of the two clades. CONCLUSIONS Based on the molecular data, it was speculated that species from the L1 clade might belong to other genera or new genera. This study provides molecular information for further taxonomic and phylogenetic studies of Mytilidae.
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Affiliation(s)
- Yi Zhu
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaojing Yan
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Peizhen Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Yifei Zhang
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenxia Zuo
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- College of Life Sciences, Qingdao University, Qingdao, 266000, China
| | - Xiaojie Ma
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Zhang
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Yuan B, He G, Dong W. The first complete mitochondrial genome of the genus Laelaps with novel gene arrangement reveals extensive rearrangement and phylogenetics in the superfamily Dermanyssoidea. EXPERIMENTAL & APPLIED ACAROLOGY 2024:10.1007/s10493-024-00943-2. [PMID: 39017744 DOI: 10.1007/s10493-024-00943-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 06/26/2024] [Indexed: 07/18/2024]
Abstract
We collected 56 specimens of Laelaps chini from the endemic Hengduan Mountain rat species (Eothenomys miletus) and obtained the first complete mitochondrial genome of L. chini by next-generation sequencing (NGS). The L. chini mitogenome is 16,507 bp in size and contains 37 genes and a control region of 2380 bp in length. The L. chini mitogenome has a high AT content and a compact arrangement with four overlapping regions ranging from 1 to 2 bp and 16 spacer regions ranging from 1 to 48 bp. We analyzed 13 protein-coding genes of L. chini mitogenome and found that protein-coding genes in the L. chini mitogenome preferred codons ending in A/U and codon usage pattern was mainly influenced by natural selection. Cox1 has the slowest evolution rate and cox3 has the fastest evolution rate. We combined the mitochondrial genome of eight species of gamasid mites in the superfamily Dermanyssoidea from Genbank and the L. chini mitochondrial genome to analyze its rearrangement patterns and breakpoint numbers. We found that the L. chini mitogenome showed a novel arrangement pattern and nine species of gamasid mites in the superfamily Dermanyssoidea, which have been sequenced complete mitochondrial genomes to date, all showed different degrees of rearrangement. Laelaps chini, Echinolaelaps echidninus and Echinolaelaps fukinenensis were closely related species based on genetic distance and phylogenetic analyses. Notably they are clustered with Varroa destructor of the family Varroidae, suggesting that the family Varroidae is more closely related to the family Laelapidae, but more data are needed to test whether Varroa can be classified under the family Laelapidae. The L. chini mitogenome is the first complete mitochondrial genome for the genus Laelaps, and contributes to further exploration of the mitochondrial gene rearrangements and phylogeny for the superfamily Dermanyssoidea.
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Affiliation(s)
- Bili Yuan
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Gangxian He
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Wenge Dong
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China.
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Zhang CH, Wang HY, Wang Y, Chi ZH, Liu YS, Zu GH. The first two complete mitochondrial genomes for the genus Anagyrus (Hymenoptera, Encyrtidae) and their phylogenetic implications. Zookeys 2024; 1206:81-98. [PMID: 39006402 PMCID: PMC11245640 DOI: 10.3897/zookeys.1206.121923] [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: 02/29/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024] Open
Abstract
Anagyrus, a genus of Encyrtidae (Hymenoptera, Chalcidoidea), represents a successful group of parasitoid insects that attack various mealybug pests of agricultural and forestry plants. Until now, only 20 complete mitochondrial genomes have been sequenced, including those in this study. To enrich the diversity of mitochondrial genomes in Encyrtidae and to gain insights into their phylogenetic relationships, the mitochondrial genomes of two species of Anagyrus were sequenced, and the mitochondrial genomes of these species were compared and analyzed. Encyrtid mitochondrial genomes exhibit similarities in nucleotide composition, gene organization, and control region patterns. Comparative analysis of protein-coding genes revealed varying molecular evolutionary rates among different genes, with six genes (ATP8, ND2, ND4L, ND6, ND4 and ND5) showing higher rates than others. A phylogenetic analysis based on mitochondrial genome sequences supports the monophyly of Encyrtidae; however, the two subfamilies, Encyrtinae and Tetracneminae, are non-monophyletic. This study provides valuable insights into the phylogenetic relationships within the Encyrtidae and underscores the utility of mitochondrial genomes in the systematics of this family.
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Affiliation(s)
- Cheng-Hui Zhang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Hai-Yang Wang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Yan Wang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Zhi-Hao Chi
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Yue-Shuo Liu
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Guo-Hao Zu
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
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Sun CH, Lu CH, Wang ZJ. Comparison and phylogenetic analysis of the mitochondrial genomes of Synodontis eupterus and Synodontis polli. Sci Rep 2024; 14:15393. [PMID: 38965284 PMCID: PMC11224264 DOI: 10.1038/s41598-024-65809-4] [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: 05/21/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
We aimed to distinguish Synodontis eupterus and Synodontis polli. We performed sequencing and bioinformatic analysis of their mitochondrial genomes and constructed a phylogenetic tree of Mochokidae fish using maximum likelihood and Bayesian methods based on protein-coding gene (PCG) sequences of 14 Mochokidae species. The total length of the S. eupterus mitochondrial genome was 16,579 bp, including 13 (PCGs), 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (56.0%). The total length of the S. polli mitochondrial genome was 16,544 bp, including 13 PCGs, 22 tRNA genes, two rRNA genes, and one D-loop, with an AT-biased nucleotide composition (55.0%). In both species, except for COI, PCGs use ATG as the starting codon, the vast majority use TAG or TAA as the ending codon, and a few use incomplete codons (T - or TA -) as the ending codon. Phylogenetic analysis showed that S. eupterus and Synodontis clarias converged into one branch, S. polli and Synodontis petricola converged into one branch, Mochokiella paynei, Mochokus brevis, and nine species of the genus Synodontis converged into one branch, and M. paynei clustered with the genus Synodontis. This study lays a foundation for rebuilding a clearer Mochokidae fish classification system.
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Affiliation(s)
- Cheng-He Sun
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Chang-Hu Lu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Zi-Jian Wang
- Agriculture and Rural Bureau of Gaochun District, Nanjing, 211300, China
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da Silva FS, do Nascimento BLS, Cruz ACR, da Silva SP, Aragão CF, Dias DD, Silva LHDSE, Reis LAM, Reis HCF, Chagas LLD, Rosa Jr. JW, Vieira DBR, Brandão RCF, Medeiros DBDA, Nunes Neto JP. Sequencing and Description of the Mitochondrial Genome of Orthopodomyia fascipes (Diptera: Culicidae). Genes (Basel) 2024; 15:874. [PMID: 39062653 PMCID: PMC11276460 DOI: 10.3390/genes15070874] [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: 05/03/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 07/28/2024] Open
Abstract
The genus Orthopodomyia Theobald, 1904 (Diptera: Culicidae) comprises 36 wild mosquito species, with distribution largely restricted to tropical and temperate areas, most of which are not recognized as vectors of epidemiological importance due to the lack of information related to their bionomy and involvement in the cycle transmission of infectious agents. Furthermore, their evolutionary relationships are not completely understood, reflecting the scarcity of genetic information about the genus. Therefore, in this study, we report the first complete description of the mitochondrial genome of a Neotropical species representing the genus, Orthopodomyia fascipes Coquillet, 1906, collected in the Brazilian Amazon region. Using High Throughput Sequencing, we obtained a mitochondrial sequence of 15,598 bp, with an average coverage of 418.5×, comprising 37 functional subunits and a final portion rich in A + T, corresponding to the control region. The phylogenetic analysis, using Maximum Likelihood and Bayesian Inference based on the 13 protein-coding genes, corroborated the monophyly of Culicidae and its two subfamilies, supporting the proximity between the tribes Orthopodomyiini and Mansoniini, partially disagreeing with previous studies based on the use of molecular and morphological markers. The information generated in this study contributes to a better understanding of the taxonomy and evolutionary history of the genus and other groups of Culicidae.
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Affiliation(s)
- Fábio Silva da Silva
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Bruna Laís Sena do Nascimento
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Ana Cecília Ribeiro Cruz
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Sandro Patroca da Silva
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Carine Fortes Aragão
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Daniel Damous Dias
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Lucas Henrique da Silva e Silva
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Lúcia Aline Moura Reis
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Hanna Carolina Farias Reis
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Liliane Leal das Chagas
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - José Wilson Rosa Jr.
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Durval Bertram Rodrigues Vieira
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Roberto Carlos Feitosa Brandão
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Daniele Barbosa de Almeida Medeiros
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
| | - Joaquim Pinto Nunes Neto
- Graduate Program in Parasitary Biology in the Amazon Region, Center of Biological and Health Sciences, State University of Pará, Belém 66095-663, Brazil; (F.S.d.S.); (A.C.R.C.); (D.D.D.); (L.H.d.S.e.S.); (L.A.M.R.); (H.C.F.R.); (D.B.d.A.M.)
- Evandro Chagas Institute—IEC/MS/SVSA, Department of Arbovirology and Hemorragic Fevers, Ananindeua 67030-000, Brazil; (B.L.S.d.N.); (S.P.d.S.); (C.F.A.); (L.L.d.C.); (J.W.R.J.); (D.B.R.V.); (R.C.F.B.)
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Xiang H, Zhou Q, Li W, Shu J, Gu Z, Jiang W. Insights into phylogenetic positions and distribution patterns: Complete mitogenomes of two sympatric Asian horned toads in Boulenophrys (Anura: Megophryidae). Ecol Evol 2024; 14:e11687. [PMID: 38994208 PMCID: PMC11237341 DOI: 10.1002/ece3.11687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/06/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Boulenophrys sangzhiensis and Boulenophrys tuberogranulata, two narrow-distributed toad species within the Megophryidae family in southern China, are experiencing population declines due to habitat loss and degradation. Despite their critical conservation status, the two species remain largely overlooked in public and scientific spheres. This study presented the first sequencing, assembly, and annotation of the complete mitogenomes of both species using next-generation sequencing. The mitogenome of B. sangzhiensis was 16,950 bp, while that of B. tuberogranulata was 16,841 bp, each comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a noncoding control region (D-loop). The gene content, nucleotide composition, and evolutionary rates of each mitogenome were analyzed. Both mitogenomes exhibited negative AT skew and GC skew with high A + T content. ATP8 exhibited the highest evolutionary rate, while COI had the lowest. A phylogenetic analysis based on 28 mitogenomes revealed two major clades of Megophryidae, supporting the classification of two subfamilies, Megophryinae and Leptobrachiinae. Within the subfamily Megophryinae, the genus Boulenophrys was divided into two species groups. Intriguingly, despite coexisting in Zhangjiajie City, B. sangzhiensis and B. tuberogranulata exhibited distinct origins from the two different species groups, underscoring the unique role of the coexisting area Zhangjiajie in driving their speciation and preserving their current populations. A parallel pattern was also identified in the Leptobrachiinae genus Leptobrachium within the same region. This study provided valuable data references and enhanced our understanding of the molecular characteristics of these threatened amphibian species.
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Affiliation(s)
- Hongmei Xiang
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoidesJishou UniversityZhangjiajieChina
| | - Qiang Zhou
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoidesJishou UniversityZhangjiajieChina
- College of Biology and Environmental SciencesJishou UniversityJishouChina
| | - Wei Li
- Zhangjiajie National Forest ParkZhangjiajieChina
| | - Juan Shu
- Zhangjiajie National Forest ParkZhangjiajieChina
| | - Zhirong Gu
- National Nature Reserve of BadagongshanZhangjiajieChina
| | - Wansheng Jiang
- Key Laboratory of Hunan Forest Products and Chemical Industry Engineering, National and Local United Engineering Laboratory of Integrative Utilization Technology of Eucommia ulmoidesJishou UniversityZhangjiajieChina
- College of Biology and Environmental SciencesJishou UniversityJishouChina
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Han F, Bi C, Zhao Y, Gao M, Wang Y, Chen Y. Unraveling the complex evolutionary features of the Cinnamomum camphora mitochondrial genome. PLANT CELL REPORTS 2024; 43:183. [PMID: 38922445 DOI: 10.1007/s00299-024-03256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024]
Abstract
KEY MESSAGE We reported the mitochondrial genome of Cinnamomum camphora for the first time, revealing frequent rearrangement events in the non-coding regions of Magnoliids mitochondrial genomes. As one of the representative species in the Lauraceae family of Magnoliids, Cinnamomum camphora holds significant economic and ecological value. In this study, the mitochondrial genome (mitogenome) of C. camphora was complete assembled and annotated using PacBio HiFi sequencing. The C. camphora mitogenome is characterized by a branch structure, spans 900,894 bp, and contains 43 protein-coding genes (PCGs), 24 tRNAs, and 3 rRNAs. Most of these PCGs are under purifying selection, with only two (ccmFc and rps7) exhibiting signs of positive selection. The C. camphora mitogenome contains numerous repetitive sequences and intracellular gene transfers, with a total of 36 mitochondrial plastid DNAs, amounting to a combined length of 23,816 bp. Comparative analysis revealed that the non-coding regions of Magnoliids mitogenomes have undergone frequent rearrangements during evolution, but the coding sequences remain highly conserved (more than 98% similarity for protein-coding sequences). Furthermore, a maximum-likelihood phylogenetic tree was reconstructed based on 25 PCGs from 23 plant mitogenomes. The analysis supports the closest relationship between C. camphora and C. chekiangense, consistent with the APG IV classification system. This study elucidates the unique evolutionary features of the C. camphora mitogenome, which will provide valuable insights into the study of genetics and evolution of the family Lauraceae.
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Affiliation(s)
- Fuchuan Han
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Changwei Bi
- State Key Laboratory of Tree Genetics and Breeding, Co-innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
| | - Yunxiao Zhao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Ming Gao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Yangdong Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China
| | - Yicun Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, No. 73, Daqiao Road, Fuyang, Hangzhou, 311400, Zhejiang, People's Republic of China.
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Aishan Z, Mu ZL, Li ZC, Luo XY, Huangfu N. The First Three Mitochondrial Genomes for the Characterization of the Genus Egeirotrioza (Hemiptera: Triozidae) and Phylogenetic Implications. Genes (Basel) 2024; 15:842. [PMID: 39062621 PMCID: PMC11275608 DOI: 10.3390/genes15070842] [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: 05/10/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
(1) Background: Mitochondrial genomes are important markers for the study of phylogenetics and systematics. Triozidae includes some primary pests of Populus euphratica. The phylogenetic relationships of this group remain controversial due to the lack of molecular data. (2) Methods: Mitochondria of Egeirotrioza Boselli were sequenced and assembled. We analyzed the sequence length, nucleotide composition, and evolutionary rate of Triozidae, combined with the 13 published mitochondrial genomes. (3) Results: The evolutionary rate of protein-coding genes was as follows: ATP8 > ND6 > ND5 > ND2 > ND4 > ND4L > ND1 > ND3 > APT6 > CYTB > COX3 > COX2 > COX1. We reconstructed the phylogenetic relationships of Triozidae based on 16 triozid mitochondrial genomes (thirteen ingroups and three outgroups) using the maximum likelihood (ML) and Bayesian inference (BI) approaches. The phylogenetic analysis of the 16 Triozidae mitochondrial genomes showed that Egeirotrioza was closely related to Leptynoptera. (4) Conclusions: We have identified 13 PCGs, 22 tRNAs, 2 rRNAs, and 1 control region (CR) of all newly sequenced mitochondrial genomes, which were the mitochondrial gene type in animals. The results of this study provide valuable genomic information for the study of psyllid species.
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Affiliation(s)
- Zhulidezi Aishan
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Z.A.); (Z.-L.M.); (Z.-C.L.)
| | - Ze-Lu Mu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Z.A.); (Z.-L.M.); (Z.-C.L.)
| | - Zi-Cong Li
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Z.A.); (Z.-L.M.); (Z.-C.L.)
| | - Xin-Yu Luo
- Department of Entomology, China Agricultural University, Beijing 100193, China;
| | - Ning Huangfu
- National Natural History Museum of China, Beijing 100050, China
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Liu Y, Liu H, Zhang F, Xu H. The initiation of mitochondrial DNA replication. Biochem Soc Trans 2024; 52:1243-1251. [PMID: 38884788 PMCID: PMC11346463 DOI: 10.1042/bst20230952] [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: 03/11/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
Mitochondrial DNA replication is initiated by the transcription of mitochondrial RNA polymerase (mtRNAP), as mitochondria lack a dedicated primase. However, the mechanism determining the switch between continuous transcription and premature termination to generate RNA primers for mitochondrial DNA (mtDNA) replication remains unclear. The pentatricopeptide repeat domain of mtRNAP exhibits exoribonuclease activity, which is required for the initiation of mtDNA replication in Drosophila. In this review, we explain how this exonuclease activity contributes to primer synthesis in strand-coupled mtDNA replication, and discuss how its regulation might co-ordinate mtDNA replication and transcription in both Drosophila and mammals.
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Affiliation(s)
- Yi Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Haibin Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Fan Zhang
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Hong Xu
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, U.S.A
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Kadam PS, Yang Z, Lu Y, Zhu H, Atiyas Y, Shah N, Fisher S, Nordgren E, Kim J, Issadore D, Eberwine J. Single-Mitochondrion Sequencing Uncovers Distinct Mutational Patterns and Heteroplasmy Landscape in Mouse Astrocytes and Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598906. [PMID: 38915628 PMCID: PMC11195285 DOI: 10.1101/2024.06.13.598906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Background Mitochondrial (mt) heteroplasmy can cause adverse biological consequences when deleterious mtDNA mutations accumulate disrupting 'normal' mt-driven processes and cellular functions. To investigate the heteroplasmy of such mtDNA changes we developed a moderate throughput mt isolation procedure to quantify the mt single-nucleotide variant (SNV) landscape in individual mouse neurons and astrocytes In this study we amplified mt-genomes from 1,645 single mitochondria (mts) isolated from mouse single astrocytes and neurons to 1. determine the distribution and proportion of mt-SNVs as well as mutation pattern in specific target regions across the mt-genome, 2. assess differences in mtDNA SNVs between neurons and astrocytes, and 3. Study cosegregation of variants in the mouse mtDNA. Results 1. The data show that specific sites of the mt-genome are permissive to SNV presentation while others appear to be under stringent purifying selection. Nested hierarchical analysis at the levels of mitochondrion, cell, and mouse reveals distinct patterns of inter- and intra-cellular variation for mt-SNVs at different sites. 2. Further, differences in the SNV incidence were observed between mouse neurons and astrocytes for two mt-SNV 9027:G>A and 9419:C>T showing variation in the mutational propensity between these cell types. Purifying selection was observed in neurons as shown by the Ka/Ks statistic, suggesting that neurons are under stronger evolutionary constraint as compared to astrocytes. 3. Intriguingly, these data show strong linkage between the SNV sites at nucleotide positions 9027 and 9461. Conclusion This study suggests that segregation as well as clonal expansion of mt-SNVs is specific to individual genomic loci, which is important foundational data in understanding of heteroplasmy and disease thresholds for mutation of pathogenic variants.
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Affiliation(s)
- Parnika S Kadam
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zijian Yang
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Youtao Lu
- Department of Biology, School of Arts and Sciences; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hua Zhu
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yasemin Atiyas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nishal Shah
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen Fisher
- Department of Biology, School of Arts and Sciences; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik Nordgren
- Department of Biology, School of Arts and Sciences; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Issadore
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Li Q, Jiang P, Li M, Du J, Sun J, Chen N, Wu Y, Chang Q, Hu C. Structure and Phylogenetic Relationships of Scolopacidae Mitogenomes (Charadriiformes: Scolopacidae). Curr Issues Mol Biol 2024; 46:6186-6198. [PMID: 38921040 PMCID: PMC11202466 DOI: 10.3390/cimb46060369] [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: 05/10/2024] [Revised: 06/09/2024] [Accepted: 06/15/2024] [Indexed: 06/27/2024] Open
Abstract
The family Scolopacidae presents a valuable subject for evolutionary research; however, molecular studies of Scolopacidae are still relatively understudied, and the phylogenetic relationships of certain species remain unclear. In this study, we sequenced and obtained complete mitochondrial DNA (mtDNA) from Actitis hypoleucos and partial mtDNA from Numenius arquata, Limosa limosa, and Limnodromus semipalmatus. The complete mtDNA contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 tRNA genes, and a control region. Scolopacidae contained three types of start codons and five types of stop codons (including one incomplete stop codon, T--). In 13 protein-coding genes, average uncorrected pairwise distances (Aupd) revealed that ATP8 was the least conserved while COX3 had the lowest evolutionary rate. The ratio of Ka/Ks suggested that all PCGs were under purifying selection. Using two methods (maximum likelihood and Bayesian inference) to analyze the phylogenetic relationships of the family Scolopacidae, it was found that the genera Xenus and Actitis were clustered into another sister group, while the genus Phalaropus is more closely related to the genus Tringa. The genera Limnodromus, Gallinago, and Scolopax form a monophyletic group. This study improves our understanding of the evolutionary patterns and phylogenetic relationships of the family Scolopacidae.
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Affiliation(s)
- Quanheng Li
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Peiyue Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Mingxuan Li
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Jingjing Du
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Jianxiang Sun
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Nuo Chen
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Yu Wu
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (M.L.); (J.D.); (J.S.); (N.C.); (Y.W.)
| | - Qing Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Chaochao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
- Analytical and Testing Center, Nanjing Normal University, Nanjing 210046, China
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39
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Gendron EMS, Qing X, Sevigny JL, Li H, Liu Z, Blaxter M, Powers TO, Thomas WK, Porazinska DL. Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection. BMC Genomics 2024; 25:615. [PMID: 38890582 PMCID: PMC11184840 DOI: 10.1186/s12864-024-10500-1] [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: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. RESULTS Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. CONCLUSIONS Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.
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Affiliation(s)
- Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA.
| | - Xue Qing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Hongmei Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyin Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | | | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - W Kelly Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
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40
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Siddika MA, Ahmed KA, Alam MS, Bushra J, Begum RA. Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama. Sci Rep 2024; 14:13820. [PMID: 38879694 PMCID: PMC11180200 DOI: 10.1038/s41598-024-64791-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/13/2024] [Indexed: 06/19/2024] Open
Abstract
The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.
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Affiliation(s)
- Most Ayesha Siddika
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | | | - Mohammad Shamimul Alam
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Jannatul Bushra
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Rowshan Ara Begum
- Genetics and Molecular Biology Laboratory, Department of Zoology, University of Dhaka, Dhaka, 1000, Bangladesh
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41
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Dallagnol LC, Cônsoli FL. Evolutionary and phylogenetic insights from the mitochondrial genomic analysis of Diceraeus melacanthus and D. furcatus (Hemiptera: Pentatomidae). Sci Rep 2024; 14:12861. [PMID: 38834792 DOI: 10.1038/s41598-024-63584-w] [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: 01/23/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
The mitochondrial genomes of D. melacanthus and D. furcatus were sequenced and used to investigate the phylogenetic relationships with 54 species of Pentatomidae. Their mitogenomes are 17,197 and 15,444 bp-long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22/21 transfer RNA genes, with conserved gene arrangement. Leu, Lys, and Ser were the most common amino acids in their PCGs. PCGs evolutionary analysis indicated their mitogenomes are under purifying selection, and the most conserved genes are from the cytochrome complex, reinforcing their suitability as markers for molecular taxonomy. We identified 490 mtSSRs in 56 Pentatomidae species, with large variation and a positive correlation between mtSSR number and genome size. Three mtSSRs were identified in each Diceraeus species. Only the mtSSR in the nad6 (D. melacanthus) and nad4 (D. furcatus) appear to have application as molecular markers for species characterization. Phylogenetic analysis confirmed the monophyly of Pentatomidae. However, our analysis challenged the monophyly of Pentatominae and Podopinae. We also detected unexpected relationships among some tribes and genera, highlighting the complexity of the internal taxonomic structure of Pentatomidae. Both Diceraeus species were grouped in the same clade with the remaining Carpocorini analyzed.
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Affiliation(s)
- Lilian Cris Dallagnol
- Insect Interactions Laboratory, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Fernando Luís Cônsoli
- Insect Interactions Laboratory, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.
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42
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Waneka G, Broz AK, Wold-McGimsey F, Zou Y, Wu Z, Sloan DB. Disruption of recombination machinery alters the mutational landscape in plant organellar genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597120. [PMID: 38895361 PMCID: PMC11185577 DOI: 10.1101/2024.06.03.597120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made towards understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar targeted mutS homolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats in Arabidopsis thaliana. We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes of A. thaliana mutant lines lacking radA, recA1, or recA3. In contrast, osb2 and why2 mutants did not exhibit an increase in point mutations compared to wild type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data from A. thaliana organellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants and msh1 mutants. Finally, using long-read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Yi Zou
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Zhiqiang Wu
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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43
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Zhan L, He J, Meng S, Guo Z, Chen Y, Storey KB, Zhang J, Yu D. Mitochondrial Protein-Coding Gene Expression in the Lizard Sphenomorphus incognitus (Squamata:Scincidae) Responding to Different Temperature Stresses. Animals (Basel) 2024; 14:1671. [PMID: 38891717 PMCID: PMC11170996 DOI: 10.3390/ani14111671] [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: 05/06/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
In the context of global warming, the frequency of severe weather occurrences, such as unexpected cold spells and heat waves, will grow, as well as the intensity of these natural disasters. Lizards, as a large group of reptiles, are ectothermic. Their body temperatures are predominantly regulated by their environment and temperature variations directly impact their behavior and physiological activities. Frequent cold periods and heat waves can affect their biochemistry and physiology, and often their ability to maintain their body temperature. Mitochondria, as the center of energy metabolism, are crucial for maintaining body temperature, regulating metabolic rate, and preventing cellular oxidative damage. Here, we used RT-qPCR technology to investigate the expression patterns and their differences for the 13 mitochondrial PCGs in Sphenomorphus incognitus (Squamata:Scincidae), also known as the brown forest skink, under extreme temperature stress at 4 °C, 8 °C, 34 °C, and 38 °C for 24 h, compared to the control group at 25 °C. In southern China, for lizards, 4 °C is close to lethal, and 8 °C induces hibernation, while 34/38 °C is considered hot and environmentally realistic. Results showed that at a low temperature of 4 °C for 24 h, transcript levels of ATP8, ND1, ND4, COI, and ND4L significantly decreased, to values of 0.52 ± 0.08, 0.65 ± 0.04, 0.68 ± 0.10, 0.28 ± 0.02, and 0.35 ± 0.02, respectively, compared with controls. By contrast, transcript levels of COIII exhibited a significant increase, with a mean value of 1.86 ± 0.21. However, exposure to 8 °C for 24 h did not lead to an increase in transcript levels. Indeed, transcript levels of ATP6, ATP8, ND1, ND3, and ND4 were significantly downregulated, to 0.48 ± 0.11, 0.68 ± 0.07, 0.41 ± 0.08, 0.54 ± 0.10, and 0.52 ± 0.07, respectively, as compared with controls. Exposure to a hot environment of 34 °C for 24 h led to an increase in transcript levels of COI, COII, COIII, ND3, ND5, CYTB, and ATP6, with values that were 3.3 ± 0.24, 2.0 ± 0.2, 2.70 ± 1.06, 1.57 ± 0,08, 1.47 ± 0.13, 1.39 ± 0.56, and 1.86 ± 0.12, respectively, over controls. By contrast, ND4L exhibited a significant decrease (to 0.31 ± 0.01) compared with controls. When exposed to 38 °C, the transcript levels of the 13 PCGs significantly increased, ranging from a 2.04 ± 0.23 increase in ND1 to a 6.30 ± 0.96 rise in ND6. Under two different levels of cold and heat stress, the expression patterns of mitochondrial genes in S. incognitus vary, possibly associated with different strategies employed by this species in response to low and high temperatures, allowing for rapid compensatory adjustments in mitochondrial electron transport chain proteins in response to temperature changes. Furthermore, this underscores once again the significant role of mitochondrial function in determining thermal plasticity in reptiles.
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Affiliation(s)
- Lemei Zhan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Jingyi He
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Siqi Meng
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Zhiqiang Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Yuxin Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S5B6, Canada;
| | - Jiayong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
| | - Danna Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.Z.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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44
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Lopes-Lima M, Geist J, Egg S, Beran L, Bikashvili A, Van Bocxlaer B, Bogan AE, Bolotov IN, Chelpanovskaya OA, Douda K, Fernandes V, Gomes-Dos-Santos A, Gonçalves DV, Gürlek ME, Johnson NA, Karaouzas I, Kebapçı Ü, Kondakov AV, Kuehn R, Lajtner J, Mumladze L, Nagel KO, Neubert E, Österling M, Pfeiffer J, Prié V, Riccardi N, Sell J, Schneider LD, Shumka S, Sîrbu I, Skujienė G, Smith CH, Sousa R, Stöckl K, Taskinen J, Teixeira A, Todorov M, Trichkova T, Urbańska M, Välilä S, Varandas S, Veríssimo J, Vikhrev IV, Woschitz G, Zając K, Zając T, Zanatta D, Zieritz A, Zogaris S, Froufe E. Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications. Mol Phylogenet Evol 2024; 195:108046. [PMID: 38447924 DOI: 10.1016/j.ympev.2024.108046] [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: 09/17/2023] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
The global decline of freshwater mussels and their crucial ecological services highlight the need to understand their phylogeny, phylogeography and patterns of genetic diversity to guide conservation efforts. Such knowledge is urgently needed for Unio crassus, a highly imperilled species originally widespread throughout Europe and southwest Asia. Recent studies have resurrected several species from synonymy based on mitochondrial data, revealing U. crassus to be a complex of cryptic species. To address long-standing taxonomic uncertainties hindering effective conservation, we integrate morphometric, phylogenetic, and phylogeographic analyses to examine species diversity within the U. crassus complex across its entire range. Phylogenetic analyses were performed using cytochrome c oxidase subunit I (815 specimens from 182 populations) and, for selected specimens, whole mitogenome sequences and Anchored Hybrid Enrichment (AHE) data on ∼ 600 nuclear loci. Mito-nuclear discordance was detected, consistent with mitochondrial DNA gene flow between some species during the Pliocene and Pleistocene. Fossil-calibrated phylogenies based on AHE data support a Mediterranean origin for the U. crassus complex in the Early Miocene. The results of our integrative approach support 12 species in the group: the previously recognised Unio bruguierianus, Unio carneus, Unio crassus, Unio damascensis, Unio ionicus, Unio sesirmensis, and Unio tumidiformis, and the reinstatement of five nominal taxa: Unio desectusstat. rev., Unio gontieriistat. rev., Unio mardinensisstat. rev., Unio nanusstat. rev., and Unio vicariusstat. rev. Morphometric analyses of shell contours reveal important morphospace overlaps among these species, highlighting cryptic, but geographically structured, diversity. The distribution, taxonomy, phylogeography, and conservation of each species are succinctly described.
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Affiliation(s)
- M Lopes-Lima
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
| | - J Geist
- Aquatic Systems Biology, Technical University of Munich, TUM School of Life Sciences, Mühlenweg 22, 85354 Freising, Germany
| | - S Egg
- Aquatic Systems Biology, Technical University of Munich, TUM School of Life Sciences, Mühlenweg 22, 85354 Freising, Germany; Molecular Zoology, Technical University of Munich, TUM School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - L Beran
- Regional Office Kokořínsko - Máchův kraj Protected Landscape Area Administration, Nature Conservation Agency of the Czech Republic, Česká 149, CZ-27601 Mělnik, Czech Republic
| | - A Bikashvili
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - B Van Bocxlaer
- CNRS, Univ. Lille, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - A E Bogan
- North Carolina Museum of Natural Sciences, 11 West Jones Street, Raleigh, NC 27601 USA
| | - I N Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - O A Chelpanovskaya
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - K Douda
- Department of Zoology and Fisheries, FAFNR, Czech University of Life Sciences Prague, Kamýcká 129, CZ-16500 Prague, Czech Republic
| | - V Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - A Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - D V Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - M E Gürlek
- Burdur Vocational School of Food Agriculture and Livestock, Mehmet Akif Ersoy University, 15100 Burdur, Türkiye
| | - N A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - I Karaouzas
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - Ü Kebapçı
- Biology Department, Faculty of Science and Arts, Burdur Mehmet Akif Ersoy University, Burdur, Türkiye
| | - A V Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - R Kuehn
- Molecular Zoology, Technical University of Munich, TUM School of Life Sciences, Hans-Carl-von-Carlowitz-Platz 2, Freising, Germany
| | - J Lajtner
- Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - L Mumladze
- Institute of Zoology, Ilia State University, Cholokashvili ave. 3/5, 0162 Tbilisi, Georgia
| | - K-O Nagel
- Malacological Section, Senckenberg Research Institute and Natural History Museum Frankfurt/M., Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - E Neubert
- Natural History Museum, 3005 Bern, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - M Österling
- Institution of Environmental and Life Sciences, Karlstad University, Biology, 65188 Karlstad, Sweden
| | - J Pfeiffer
- National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue, Washington, DC, USA
| | - V Prié
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - N Riccardi
- CNR Water Research Institute, Largo Tonolli 50, 28922 Verbania, Italy
| | - J Sell
- Department of Genetics and Biosystematics, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - L D Schneider
- The Rural Economy and Agricultural Society, 305 96 Eldsberga, Sweden
| | - S Shumka
- Faculty Of Biotechnology and Food, Agricultural University of Tirana, Koder Kamez, Tirana 2029, Albania
| | - I Sîrbu
- Lucian Blaga University of Sibiu, Faculty of Sciences, 5-7 Dr. I. Rațiu St., 550012 Sibiu, Romania
| | - G Skujienė
- Department of Zoology, Institute of Biosciences, Life Sciences Center, Vilnius University, Saulėtekio av. 7, LT-10223 Vilnius, Lithuania
| | - C H Smith
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - R Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal
| | - K Stöckl
- Bavarian Academy for Nature Conservation and Landscape Management, Seethalerstrasse 6, 83410 Laufen, Germany
| | - J Taskinen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - A Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - M Todorov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - T Trichkova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000 Sofia, Bulgaria
| | - M Urbańska
- Department of Zoology, Poznań University of Life Sciences, ul. Wojska Polskiego 28, 60-637 Poznań, Poland
| | - S Välilä
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - S Varandas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; CITAB-UTAD - Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Forestry Department, Vila Real, Portugal
| | - J Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - I V Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences, Nikolsky Av. 20, 163020 Arkhangelsk, Russia
| | - G Woschitz
- IFIS - Ichthyological Research Initiative Styria, 1160 Vienna, Austria
| | - K Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - T Zając
- Institute of Nature Conservation, Polish Academy of Sciences, Al. Adama Mickiewicza 33, 31-120 Kraków, Poland
| | - D Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - A Zieritz
- School of Geography, University of Nottingham, University Park, Sir Clive Granger Building, Nottingham NG7 2RD, United Kingdom
| | - S Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Av., Anavyssos 19013, Greece
| | - E Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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Hu J, Sun Y, Li B, Liu Z, Wang Z, Gao Q, Guo M, Liu G, Zhao KT, Gao C. Strand-preferred base editing of organellar and nuclear genomes using CyDENT. Nat Biotechnol 2024; 42:936-945. [PMID: 37640945 DOI: 10.1038/s41587-023-01910-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/19/2023] [Indexed: 08/31/2023]
Abstract
Transcription-activator-like effector (TALE)-based tools for base editing of nuclear and organellar DNA rely on double-stranded DNA deaminases, which edit substrate bases on both strands of DNA, reducing editing precision. Here, we present CyDENT base editing, a CRISPR-free, strand-selective, modular base editor. CyDENT comprises a pair of TALEs fused with a FokI nickase, a single-strand-specific cytidine deaminase and an exonuclease to generate a single-stranded DNA substrate for deamination. We demonstrate effective base editing in nuclear, mitochondrial and chloroplast genomes. At certain mitochondrial sites, we show editing efficiencies of 14% and strand specificity of 95%. Furthermore, by exchanging the CyDENT deaminase with one that prefers editing GC motifs, we demonstrate up to 20% mitochondrial base editing at sites that are otherwise inaccessible to editing by other methods. The modular nature of CyDENT enables a suite of bespoke base editors for various applications.
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Affiliation(s)
- Jiacheng Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | | | - Guanwen Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | | | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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Novotny MV, Xu W, Mulya A, Janocha AJ, Erzurum SC. Method for depletion of mitochondria DNA in human bronchial epithelial cells. MethodsX 2024; 12:102497. [PMID: 38089156 PMCID: PMC10711463 DOI: 10.1016/j.mex.2023.102497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/23/2023] [Indexed: 12/20/2023] Open
Abstract
Mitochondria are increasingly recognized to play a role in the airway inflammation of asthma. Model systems to study the role of mitochondrial gene expression in bronchial epithelium are lacking. Here, we create custom bronchial epithelial cell lines that are depleted of mitochondrial DNA. One week of ethidium bromide (EtBr) treatment led to ∼95 % reduction of mtDNA copy number (mtDNA-CN) in cells, which was further reduced by addition of 25 µM 2',3'-dideoxycytidin (ddC). Treatment for up to three weeks with EtBr and ddC led to near complete loss of mtDNA. The basal oxygen consumption rate (OCR) of mtDNA-depleted BET-1A and BEAS-2B cells dropped to near zero. Glycolysis measured by extracellular acidification rate (ECAR) increased ∼two-fold in cells when mtDNA was eliminated. BET-1A ρ0 and BEAS-2B ρ0 cells were cultured for two months, frozen and thawed, cultured for two more months, and maintained near zero mtDNA-CN. Mitochondrial DNA-depleted BET-1A ρ0 and BEAS-2B ρ0 cell lines are viable, lack the capacity for aerobic respiration, and increase glycolysis.•BET-1A and BEAS-2B cells were treated with ethidium bromide (EtBr) with or without 2',3'-dideoxycytidine (ddC) to create cells lacking mitochondrial DNA (mtDNA).•Cells' mtDNA copy number relative to nuclear DNA (nDNA) were verified by quantitative polymerase chain reaction (qPCR).•Cells were also assessed for oxidative phosphorylation by measures of oxygen consumption using the Seahorse analyzer.
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Affiliation(s)
| | | | | | | | - Serpil C. Erzurum
- Lerner Research Institute, USA
- Respiratory Institute: Cleveland Clinic, 9500 Euclid Avenue, NB2-21, Cleveland, OH 44195, USA
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Shah RA, Riyaz M, Ignacimuthu S, Sivasankaran K. Characterization and Molecular Phylogenetic Analysis of Subfamily Erebinae (Lepidoptera: Noctuoidea: Erebidae) Using Five Complete Mitochondrial Genomes. Biochem Genet 2024; 62:2224-2252. [PMID: 37891448 DOI: 10.1007/s10528-023-10528-0] [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: 07/20/2022] [Accepted: 09/07/2023] [Indexed: 10/29/2023]
Abstract
In this study, the complete mitogenomes of Sympis rufibasis, Lacera noctilio, Oxyodes scrobiculata, Mocis undata, and Artena dotata were newly sequenced to bring up-to-date the database using the next-generation sequencing methods. The gene order of all sequenced mitogenomes was identical consisting of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a non-coding A+T-rich region, which were common to other Lepidopteran insects. All protein-coding genes (PCGs) initiated with a canonical ATN codon and ended with TAN or an incomplete stop codon, single T. The A+T-rich region of S. rufibasis, L. noctilio, O. scrobiculata, M. undata, and A. dotata are 406 bp, 462 bp, 372 bp, 410 bp, and 406 bp long, respectively, containing number of characteristics that are distinctive to Noctuoidea moths. We analyzed concatenated amino acid sequences of protein-coding genes not including rRNAs, using Maximum Likelihood and Bayesian Inference methods. The phylogenetic analyses indicated that the tribe relationships within Erebinae were reconstructed as (Sypnini+((Erebini 1+Poaphilini 1)+((Euclidiini+Catocalini+(Hypopyrini+Erebini 2))+((Hulodini+(Poaphilini 2+Ophiusini))))). Phylogenetic analyses supported and confirmed the monophyly of the subfamilies' relationships as follows: (Hypeninae+Lymantriinae)+((Scoliopterginae+((Calpinae+Erebinae)+((Herminiinae+Aganainae)+Arctiinae)))) within Erebidae.
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Affiliation(s)
- Rauf Ahmad Shah
- Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola Collège, Chennai, Tamil Nadu, 600034, India
| | - Muzafar Riyaz
- Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola Collège, Chennai, Tamil Nadu, 600034, India
| | - Savarimuthu Ignacimuthu
- Xavier Research Foundation, St. Xavier's College, Palayamkottai, Tamil Nadu, 627002, India
- Creighton University, 2500 California Plaza, Omaha, USA
| | - Kuppusamy Sivasankaran
- Division of Taxonomy and Biodiversity, Entomology Research Institute, Loyola Collège, Chennai, Tamil Nadu, 600034, India.
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Hong YH, Yuan YN, Li K, Storey KB, Zhang JY, Zhang SS, Yu DN. Differential Mitochondrial Genome Expression of Four Hylid Frog Species under Low-Temperature Stress and Its Relationship with Amphibian Temperature Adaptation. Int J Mol Sci 2024; 25:5967. [PMID: 38892163 PMCID: PMC11172996 DOI: 10.3390/ijms25115967] [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: 05/06/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Extreme weather poses huge challenges for animals that must adapt to wide variations in environmental temperature and, in many cases, it can lead to the local extirpation of populations or even the extinction of an entire species. Previous studies have found that one element of amphibian adaptation to environmental stress involves changes in mitochondrial gene expression at low temperatures. However, to date, comparative studies of gene expression in organisms living at extreme temperatures have focused mainly on nuclear genes. This study sequenced the complete mitochondrial genomes of five Asian hylid frog species: Dryophytes japonicus, D. immaculata, Hyla annectans, H. chinensis and H. zhaopingensis. It compared the phylogenetic relationships within the Hylidae family and explored the association between mitochondrial gene expression and evolutionary adaptations to cold stress. The present results showed that in D. immaculata, transcript levels of 12 out of 13 mitochondria genes were significantly reduced under cold exposure (p < 0.05); hence, we put forward the conjecture that D. immaculata adapts by entering a hibernation state at low temperature. In H. annectans, the transcripts of 10 genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COX1, COX2 and ATP8) were significantly reduced in response to cold exposure, and five mitochondrial genes in H. chinensis (ND1, ND2, ND3, ND4L and ATP6) also showed significantly reduced expression and transcript levels under cold conditions. By contrast, transcript levels of ND2 and ATP6 in H. zhaopingensis were significantly increased at low temperatures, possibly related to the narrow distribution of this species primarily at low latitudes. Indeed, H. zhaopingensis has little ability to adapt to low temperature (4 °C), or maybe to enter into hibernation, and it shows metabolic disorder in the cold. The present study demonstrates that the regulatory trend of mitochondrial gene expression in amphibians is correlated with their ability to adapt to variable climates in extreme environments. These results can predict which species are more likely to undergo extirpation or extinction with climate change and, thereby, provide new ideas for the study of species extinction in highly variable winter climates.
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Affiliation(s)
- Yue-Huan Hong
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ya-Ni Yuan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ke Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Shu-Sheng Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Xu W, Tai J, He K, Xu T, Zhang G, Xu B, Liu H. Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis. Animals (Basel) 2024; 14:1598. [PMID: 38891645 PMCID: PMC11171051 DOI: 10.3390/ani14111598] [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: 04/28/2024] [Revised: 05/20/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Although the pencilfish is a globally popular economic fish in the aquarium market, its taxonomic classification could be further refined. In order to understand the taxonomy of species of the genus Nannostomus (Characiformes, Lebiasinidae) and their phylogenetic position within the order Characiformes, in this study, we characterized mitochondrial genomes (mitogenomes) from four Nannostomus species for the first time. The four mitogenomes exhibited the typical circular structure, with overall sizes varying from 16,661 bp to 16,690 bp. They contained 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 1 control region (CR). Nucleotide composition analysis suggested that the mitochondrial sequences were biased toward A and T. Bayesian inference and maximum likelihood analyses based on PCGs support the family Lebiasinidae classification, described using four Nannostomus species, clustering together with Lebiasina multimaculata from the same family. The results of this study support the current taxonomic classification of the family Lebiasinidae. Phylogenetic analysis also suggested that gene rearrangement would not significantly impact the phylogenetic relationships within the order Characiformes. These results might provide new data regarding the phylogeny and classification of the order Characiformes, thus providing a theoretical basis for the economic development of aquarium fish markets.
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Affiliation(s)
- Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Jingzhe Tai
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Ke He
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China;
| | - Tangjun Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Gaoji Zhang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Boyu Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (W.X.); (J.T.); (T.X.); (G.Z.); (B.X.)
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50
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Zhang X, Li C, Jiang L, Qiao G, Chen J. Characteristics and Comparative Analysis of Mitochondrial Genomes of the Aphid Genus Hyalopterus Koch (Hemiptera: Aphididae: Aphidinae). INSECTS 2024; 15:389. [PMID: 38921104 PMCID: PMC11204073 DOI: 10.3390/insects15060389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
Using Illumina sequencing technology, we generated complete mitochondrial genomes (mitogenomes) of three constituent species of the aphid genus Hyalopterus Koch, Hyalopterus amygdali (Blanchard), Hyalopterus arundiniformis Ghulamullah, and Hyalopterus pruni (Geoffroy). The sizes of the Hyalopterus mitogenomes range from 15,306 to 15,410 bp, primarily due to variations in the length of non-coding regions. The Hyalopterus mitogenomes consist of 37 coding genes arranged in the order of the ancestral insect mitogenome, a control region, and a repeat region between trnE and trnF. According to the COI-based analysis, one previously reported mitogenome of H. pruni should be assigned to H. arundiniformis. The gene order, nucleotide composition, and codon usage in the Hyalopterus mitogenomes are highly conserved and similar to those of other species of Aphidinae. The tandem repeat units differ in nucleotide composition, length, and copy number across three Hyalopterus species. Within the widespread Eurasian species H. arundiniformis, variation in repeat units among different geographic populations is observed, indicating that the repeat region may provide valuable insights for studying the intraspecific diversification of aphids. Phylogenetic analyses based on 28 complete mitogenomes of Aphidinae supported the monophyly of Aphidinae, Aphidini, Macrosiphini, and two subtribes of Aphidini. Hyalopterus was monophyletic. H. amygdali and H. pruni formed a sister group, while H. arundiniformis was placed basally. Characterization of the mitogenomes of Hyalopterus provides valuable resources for further comparative studies and for advancing our understanding of the aphid mitogenome architecture.
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Affiliation(s)
- Xiaolu Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cailing Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (X.Z.); (C.L.); (L.J.)
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