1
|
Lan G, Yu J, Liu J, Zhang Y, Ma R, Zhou Y, Zhu B, Wei W, Liu J, Qi G. Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae). Genes (Basel) 2024; 15:90. [PMID: 38254979 PMCID: PMC10815732 DOI: 10.3390/genes15010090] [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: 11/09/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Tarsiger indicus (Vieillot, 1817), the White-browed Bush Robin, is a small passerine bird widely distributed in Asian countries. Here, we successfully sequenced its mitogenome using the Illumina Novaseq 6000 platform (Illumina, San Diego, CA, USA) for PE 2 × 150 bp sequencing. Combined with other published mitogenomes, we conducted the first comprehensive comparative mitogenome analysis of Muscicapidae birds and reconstructed the phylogenetic relationships between Muscicapidae and related groups. The T. indicus mitogenome was 16,723 bp in size, and it possessed the typical avian mitogenome structure and organization. Most PCGs of T. indicus were initiated strictly with the typical start codon ATG, while COX1 and ND2 were started with GTG. RSCU statistics showed that CUA, CGA, and GCC were relatively high frequency in the T. indicus mitogenome. T. cyanurus and T. indicus shared very similar mitogenomic features. All 13 PCGs of Muscicapidae mitogenomes had experienced purifying selection. Specifically, ATP8 had the highest rate of evolution (0.13296), whereas COX1 had the lowest (0.01373). The monophylies of Muscicapidae, Turdidae, and Paradoxornithidae were strongly supported. The clade of ((Muscicapidae + Turdidae) + Sturnidae) in Passeriformes was supported by both Bayesian Inference and Maximum likelihood analyses. The latest taxonomic status of many passerine birds with complex taxonomic histories were also supported. For example, Monticola gularis, T. indicus, and T. cyanurus were allocated to Turdidae in other literature; our phylogenetic topologies clearly supported their membership in Muscicapidae; Paradoxornis heudei, Suthora webbiana, S. nipalensis, and S. fulvifrons were formerly classified into Muscicapidae; we supported their membership in Paradoxornithidae; Culicicapa ceylonensis was originally classified as a member of Muscicapidae; our results are consistent with a position in Stenostiridae. Our study enriches the genetic data of T. indicus and provides new insights into the molecular phylogeny and evolution of passerine birds.
Collapse
Affiliation(s)
- Guanwei Lan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Jiaojiao Yu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Juan Liu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Yue Zhang
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Rui Ma
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Yanshan Zhou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
| | - Biqing Zhu
- Administrative Bureau of Baihe National Nature Reserve, Ngawa 623400, China; (J.L.); (Y.Z.); (B.Z.)
| | - Wei Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China; (G.L.); (W.W.)
| | - Jiabin Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China; (J.Y.); (R.M.); (Y.Z.)
- Institute of Wildlife Conservation, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guilan Qi
- Animal Husbandry Institute, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
| |
Collapse
|
2
|
Gutiérrez EG, Ortega J, Savoie A, Baeza JA. The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates. BMC Genomics 2023; 24:527. [PMID: 37674108 PMCID: PMC10481570 DOI: 10.1186/s12864-023-09596-8] [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: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND The harsh conditions of high-altitude environments are known to drive the evolution of physiological and morphological traits in endothermic animals. These conditions are expected to result in the adaptive evolution of protein coding genes encoded in mitochondrial genomes that are vital for the oxidative phosphorylation pathway. In this study, we formally tested for signatures of adaptive evolution on mitochondrial protein coding genes in Tapirus pinchaque and other odd-toed ungulates inhabiting high-elevation environments. RESULTS The AT-rich mitochondrial genome of T. pinchaque is 16,750 bp long. A phylomitogenomic analysis supports the monophyly of the genus Tapirus and families in the Perissodactyla. The ratio of non-synonymous to synonymous substitutions demonstrated that all mitochondrial genes undergo purifying selection in T. pinchaque and other odd ungulates living at high elevations. Over this negative background selection, Branch Models suggested that cox3 and nad6 might be undergoing stronger purifying selection than other mitochondrial protein coding genes. Furthermore, Site Models suggested that one and four sites in nad2 and nad5, respectively, could be experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation of selection strength in nad6, evidence of episodic diversifying selection in cob, and revealed episodic positive/diversifying selection signatures for two sites in nad1, and one site each in nad2 and nad4. CONCLUSION The mitochondrial genome of T. pinchaque is an important genomic resource for conservation of this species and this study contributes to the understanding of adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates inhabiting high-altitude environments.
Collapse
Affiliation(s)
- Edgar G Gutiérrez
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Avery Savoie
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA.
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA.
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
| |
Collapse
|
3
|
Zhao D, Guo Y, Gao Y. Natural selection drives the evolution of mitogenomes in Acrossocheilus. PLoS One 2022; 17:e0276056. [PMID: 36227932 PMCID: PMC9560497 DOI: 10.1371/journal.pone.0276056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
The mitochondrial genome plays a crucial role in the balance of energy and heat production in organisms and, thus, may be under natural selection due to its potential role in adaptive divergence and speciation. Here, we studied natural selection on the mitogenome of Acrossocheilus (Cypriniformes: Cyprinidae), a genus of fish that inhabits a broad latitudinal distribution ranging from the tropics and subtropics through temperate regions. Specifically, we used 25 published mitogenome sequences of Acrossocheilus species to investigate phylogenetic relationships in this genus and detected signals of positive selection on 13 protein-coding, mitochondrial genes. We found that relaxed purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, we also found evidence of diversifying selection on some codons, indicating episodes of positive selection. Additionally, we analyzed the mitogenomic data within an environmental modeling framework and found that the Ka/Ks ratio of ATP6 may correlated with a mean diurnal temperature range (p = 0.0449), while the Ka/Ks ratio of COX2 may correlated with precipitation during the driest month (p = 0.00761). These results suggest that the mitogenomes of Acrossocheilus species may be involved in evolutionary adaptations to different habitats. Based on this, we believe that our study provides a new insight into the role of the mitochondrial genome of Acrossocheilus species in adaptation to different environments. During our study, we also discovered several cases of paraphyly and polyphyly among accessions of species and their putative synonyms. Thus, our study suggests that a careful reassessment of the taxonomy of Acrossocheilus is using high-quality molecular data merited.
Collapse
Affiliation(s)
- Dan Zhao
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Yudong Guo
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
| | - Yang Gao
- Fisheries College, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- * E-mail:
| |
Collapse
|
4
|
Complete Mitogenomes of Polypedates Tree Frogs Unveil Gene Rearrangement and Concerted Evolution within Rhacophoridae. Animals (Basel) 2022; 12:ani12182449. [PMID: 36139309 PMCID: PMC9494961 DOI: 10.3390/ani12182449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Duplicated control regions have been reported several times in the tree frog family Rhacophoridae, and previous studies have mostly relied on sequence analysis to reconstruct their evolution. This is the first study to employ a phylogenetic method to demonstrate the existence of concerted and parallel evolution succinctly and intuitively in the duplicated control regions of the family Rhacophoridae. Phylogenetic relationships were also used to illustrate the parallel evolution of ATP8 loss of function in the genus Polypedates. In general, this study elucidated the evolutionary patterns and pathways of mitochondrial gene rearrangement of the family Rhacophoridae from a phylogenetic perspective, which aids in understanding the evolutionary history of this fascinating tree frog taxon from a molecular evolution standpoint. Abstract New developments in sequencing technology and nucleotide analysis have allowed us to make great advances in reconstructing anuran phylogeny. As a clade of representative amphibians that have radiated from aquatic to arboreal habitats, our understanding of the systematic status and molecular biology of rhacophorid tree frogs is still limited. We determined two new mitogenomes for the genus Polypedates (Rhacophoridae): P. impresus and P. mutus. We conducted comparative and phylogenetic analyses using our data and seven other rhacophorid mitogenomes. The mitogenomes of the genera Polypedates, Buergeria, and Zhangixalus were almost identical, except that the ATP8 gene in Polypedates had become a non-coding region; Buergeria maintained the legacy “LTPF” tRNA gene cluster compared to the novel “TLPF” order in the other two genera; and B. buergeri and Z. dennysi had no control region (CR) duplication. The resulting phylogenetic relationship supporting the above gene rearrangement pathway suggested parallel evolution of ATP8 gene loss of function (LoF) in Polypedates and CR duplication with concerted evolution of paralogous CRs in rhacophorids. Finally, conflicting topologies in the phylograms of 185 species reflected the advantages of phylogenetic analyses using multiple loci.
Collapse
|
5
|
Liu Z, Wu S, Chen X, Zhang W, Zhou S, Wang X. The complete mitochondrial genome of the edible mushroom Pleurotus giganteus (Agaricales, Pleurotus) and insights into its phylogeny. Mitochondrial DNA B Resour 2022; 7:1313-1315. [PMID: 35874280 PMCID: PMC9297719 DOI: 10.1080/23802359.2022.2096418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Pleurotus giganteus (Berk.) Karunarathna & K.D. Hyde 2011 is one of the largest edible mushrooms integrating medicinal value and edible value. The complete mitochondrial genome of the edible fungus P. giganteus was published in this paper. It was determined using Pacbio and Illumina sequencing. The circular molecule is 102,950 bp in length, consisting of 30 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 24 transfer RNA (tRNA) genes. The base composition of the whole mitogenome is A (37.3%), T (37.7%), G (12.2%), and C (12.8%). The phylogenetic tree shows P. giganteus was the basal taxon in Pleurotus and closely related to Pleurotus citrinopileatus Singer 1990.
Collapse
Affiliation(s)
- Zengliang Liu
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Shengjin Wu
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xuefeng Chen
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wenlong Zhang
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Shuangyun Zhou
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaoguo Wang
- Microbiology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| |
Collapse
|
6
|
Noll D, Leon F, Brandt D, Pistorius P, Le Bohec C, Bonadonna F, Trathan PN, Barbosa A, Rey AR, Dantas GPM, Bowie RCK, Poulin E, Vianna JA. Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation. Sci Rep 2022; 12:3767. [PMID: 35260629 PMCID: PMC8904570 DOI: 10.1038/s41598-022-07562-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/21/2022] [Indexed: 12/21/2022] Open
Abstract
Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondrial genome may also be responsible for the discordance detected between nuclear- and mitochondrial-based phylogenies of gentoo penguin lineages.
Collapse
Affiliation(s)
- D Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile.,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile.,Facultad de Ciencias, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - F Leon
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - D Brandt
- Department of Integrative Biology, University of California, 3101 Valley Life Science Building, Berkeley, CA, 94720, USA
| | - P Pistorius
- Department of Zoology, 11DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Nelson Mandela University, Port Elizabeth, South Africa
| | - C Le Bohec
- CNRS, IPHC UMR 7178, Université de Strasbourg, 67000, Strasbourg, France.,Département de Biologie Polaire, Centre Scientifique de Monaco, 98000, Monaco City, Monaco
| | - F Bonadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier Cedex 5, France
| | | | - A Barbosa
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - A Raya Rey
- Centro Austral de Investigaciones Científicas - Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET), Ushuaia, Argentina.,Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Argentina.,Wildlife Conservation Society, Buenos Aires, Argentina
| | - G P M Dantas
- PPG in Vertebrate Biology, Pontificia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - R C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Science Building, Berkeley, CA, 94720, USA
| | - E Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile.,Facultad de Ciencias, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - J A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile. .,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile. .,Fondo de Desarrollo de Áreas Prioritarias (FONDAP), Center for Genome Regulation (CRG), Santiago, Chile.
| |
Collapse
|
7
|
Shi L, Liu L, Li X, Wu Y, Tian X, Shi Y, Wang Z. Phylogeny and evolution of Lasiopodomys in subfamily Arvivolinae based on mitochondrial genomics. PeerJ 2021; 9:e10850. [PMID: 33777513 PMCID: PMC7977381 DOI: 10.7717/peerj.10850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/06/2021] [Indexed: 01/02/2023] Open
Abstract
The species of Lasiopodomys Lataste 1887 with their related genera remains undetermined owing to inconsistent morphological characteristics and molecular phylogeny. To investigate the phylogenetic relationship and speciation among species of the genus Lasiopodomys, we sequenced and annotated the whole mitochondrial genomes of three individual species, namely Lasiopodomys brandtii Radde 1861, L. mandarinus Milne-Edwards 1871, and Neodon (Lasiopodomys) fuscus Büchner 1889. The nucleotide sequences of the circular mitogenomes were identical for each individual species of L. brandtii, L. mandarinus, and N. fuscus. Each species contained 13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs, with mitochondrial genome lengths of 16,557 bp, 16,562 bp, and 16,324 bp, respectively. The mitogenomes and PCGs showed positive AT skew and negative GC skew. Mitogenomic phylogenetic analyses suggested that L. brandtii, L. mandarinus, and L. gregalis Pallas 1779 belong to the genus Lasiopodomys, whereas N. fuscus belongs to the genus Neodon grouped with N. irene. Lasiopodomys showed the closest relationship with Microtus fortis Büchner 1889 and M. kikuchii Kuroda 1920, which are considered as the paraphyletic species of genera Microtus. TMRCA and niche model analysis revealed that Lasiopodomys may have first appeared during the early Pleistocene epoch. Further, L. gregalis separated from others over 1.53 million years ago (Ma) and then diverged into L. brandtii and L. mandarinus 0.76 Ma. The relative contribution of climatic fluctuations to speciation and selection in this group requires further research.
Collapse
Affiliation(s)
- Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Likuan Liu
- School of Life Sciences, Qinghai Normal University, Xining, Qinghai, China
| | - Xiujuan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
8
|
Colihueque N, Gantz A, Parraguez M. Revealing the biodiversity of Chilean birds through the COI barcode approach. Zookeys 2021; 1016:143-161. [PMID: 33628081 PMCID: PMC7892532 DOI: 10.3897/zookeys.1016.51866] [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: 03/09/2020] [Accepted: 12/20/2020] [Indexed: 11/12/2022] Open
Abstract
The mitochondrial cytochrome c oxidase subunit I (COI) gene is an effective molecular tool for the estimation of genetic variation and the identification of bird species. This molecular marker is used to differentiate among Chilean bird species by analyzing barcodes for 76 species (197 individuals), comprising 28 species with no previous barcode data and 48 species with sequences retrieved from the BOLD and GenBank databases. The DNA barcodes correctly identified 94.7% of the species analyzed (72 of 76 species). Mean intraspecific K2P distance was 0.3% (range 0-8.7%). Within the intraspecific divergence range, three species, Phrygilus gayi, Sephanoides sephanoides and Curaeus curaeus, showed relatively high intraspecific divergence (1.5-8.7%), possibly due to the presence of a species complex or geographic isolation of sub-populations. Mean interspecific K2P distance was 24.7% (range 1.3-43.5%). Consequently, the intraspecific K2P distance showed limited overlap with interspecific K2P distance. The mean intraspecific divergence in our study was similar to that found in temperate regions of South America (0.24%). However, it was approximately one order of magnitude lower than values reported for bird species in tropical regions of northern South America (1.8-2.13%). This result suggests that bird species from Chile show low levels of genetic structure and divergence. The small overlap between intra- and inter-specific distances implies that COI barcodes could be used as an effective tool to identify nearly all the Chilean bird species analyzed.
Collapse
Affiliation(s)
- Nelson Colihueque
- Laboratorio de Biología Molecular y Citogenética, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avenida Alcalde Fuchslocher 1305, Casilla 933, Osorno, Chile Universidad de Los Lagos Osorno Chile
| | - Alberto Gantz
- Laboratorio de Ecología, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile Universidad de Los Lagos Osorno Chile
| | - Margarita Parraguez
- Laboratorio de Genética, Acuicultura y Biodiversidad, Universidad de Los Lagos, Osorno, Chile Universidad de Los Lagos Osorno Chile
| |
Collapse
|
9
|
Chen C, Wang J, Li Q, Fu R, Jin X, Huang W, Lu D. Mitogenomes of Two Phallus Mushroom Species Reveal Gene Rearrangement, Intron Dynamics, and Basidiomycete Phylogeny. Front Microbiol 2020; 11:573064. [PMID: 33193177 PMCID: PMC7644776 DOI: 10.3389/fmicb.2020.573064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/05/2020] [Indexed: 11/13/2022] Open
Abstract
Phallus indusiatus and Phallus echinovolvatus are edible bamboo mushrooms with pharmacological properties. We sequenced, assembled, annotated, and compared the mitogenomes of these species. Both mitogenomes were composed of circular DNA molecules, with sizes of 89,139 and 50,098 bp, respectively. Introns were the most important factor in mitogenome size variation within the genus Phallus. Phallus indusiatus, P. echinovolvatus, and Turbinellus floccosus in the subclass Phallomycetidae have conservative gene arrangements. Large-scale gene rearrangements were observed in species representing 42 different genera of Basidiomycetes. A variety of intron position classes were found in the 44 Basidiomycete species analyzed. A novel group II intron from the P. indusiatus mitogenome was compared with other fungus species containing the same intron, and we demonstrated that the insertion sites of the intron had a base preference. Phylogenetic analyses based on combined gene datasets yielded well-supported Bayesian posterior probability (BPP = 1) topologies. This indicated that mitochondrial genes are reliable molecular markers for analyzing the phylogenetic relationships of the Basidiomycetes. This is the first study of the mitogenome of the genus Phallus, and it increases our understanding of the population genetics and evolution of bamboo mushrooms and related species.
Collapse
Affiliation(s)
- Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Jian Wang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Qiang Li
- School of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Rongtao Fu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Daihua Lu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China.,Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture, Chengdu, China
| |
Collapse
|
10
|
The role of selection in the evolution of marine turtles mitogenomes. Sci Rep 2020; 10:16953. [PMID: 33046778 PMCID: PMC7550602 DOI: 10.1038/s41598-020-73874-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Abstract
Sea turtles are the only extant chelonian representatives that inhabit the marine environment. One key to successful colonization of this habitat is the adaptation to different energetic demands. Such energetic requirement is intrinsically related to the mitochondrial ability to generate energy through oxidative phosphorylation (OXPHOS) process. Here, we estimated Testudines phylogenetic relationships from 90 complete chelonian mitochondrial genomes and tested the adaptive evolution of 13 mitochondrial protein-coding genes of sea turtles to determine how natural selection shaped mitochondrial genes of the Chelonioidea clade. Complete mitogenomes showed strong support and resolution, differing at the position of the Chelonioidea clade in comparison to the turtle phylogeny based on nuclear genomic data. Codon models retrieved a relatively increased dN/dS (ω) on three OXPHOS genes for sea turtle lineages. Also, we found evidence of positive selection on at least three codon positions, encoded by NADH dehydrogenase genes (ND4 and ND5). The accelerated evolutionary rates found for sea turtles on COX2, ND1 and CYTB and the molecular footprints of positive selection found on ND4 and ND5 genes may be related to mitochondrial molecular adaptation to stress likely resulted from a more active lifestyle in sea turtles. Our study provides insight into the adaptive evolution of the mtDNA genome in sea turtles and its implications for the molecular mechanism of oxidative phosphorylation.
Collapse
|
11
|
Liu D, Zhang Y, Zhang M, Yang J, Tang W. Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses. BMC Evol Biol 2020; 20:125. [PMID: 32957913 PMCID: PMC7507615 DOI: 10.1186/s12862-020-01683-8] [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: 02/11/2019] [Accepted: 09/07/2020] [Indexed: 11/10/2022] Open
Abstract
Background The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species. Results We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments. Conclusions This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.
Collapse
Affiliation(s)
- Dong Liu
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China. .,Key Laboratory of Exploration and Utilization Aquatic Genetic Resources, Ministry of Education, Shanghai, 201306, China. .,Shanghai Ocean University, National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306, China.
| | - Yuanyuan Zhang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, University of Georgia, GA, 30602, USA
| | - Jinquan Yang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China
| | - Wenqiao Tang
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai, 201306, China.,Key Laboratory of Exploration and Utilization Aquatic Genetic Resources, Ministry of Education, Shanghai, 201306, China.,Shanghai Ocean University, National Demonstration Center for Experimental Fisheries Science Education, Shanghai, 201306, China
| |
Collapse
|
12
|
Wilson RE, Sonsthagen SA, Smé N, Gharrett AJ, Majewski AR, Wedemeyer K, Nelson RJ, Talbot SL. Mitochondrial genome diversity and population mitogenomics of polar cod (Boreogadus saida) and Arctic dwelling gadoids. Polar Biol 2020. [DOI: 10.1007/s00300-020-02703-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
13
|
Pan H, Cole TL, Bi X, Fang M, Zhou C, Yang Z, Ksepka DT, Hart T, Bouzat JL, Argilla LS, Bertelsen MF, Boersma PD, Bost CA, Cherel Y, Dann P, Fiddaman SR, Howard P, Labuschagne K, Mattern T, Miller G, Parker P, Phillips RA, Quillfeldt P, Ryan PG, Taylor H, Thompson DR, Young MJ, Ellegaard MR, Gilbert MTP, Sinding MHS, Pacheco G, Shepherd LD, Tennyson AJD, Grosser S, Kay E, Nupen LJ, Ellenberg U, Houston DM, Reeve AH, Johnson K, Masello JF, Stracke T, McKinlay B, Borboroglu PG, Zhang DX, Zhang G. High-coverage genomes to elucidate the evolution of penguins. Gigascience 2020; 8:5571031. [PMID: 31531675 PMCID: PMC6904868 DOI: 10.1093/gigascience/giz117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. RESULTS Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. CONCLUSIONS We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.
Collapse
Affiliation(s)
- Hailin Pan
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Theresa L Cole
- Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, Canterbury 7640, New Zealand.,Department of Zoology, University of Otago, PO Box 56, Dunedin, Otago 9054, New Zealand
| | - Xupeng Bi
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Miaoquan Fang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Chengran Zhou
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhengtao Yang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Tom Hart
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Juan L Bouzat
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Lisa S Argilla
- The Wildlife Hospital Dunedin, School of Veterinary Nursing, Otago Polytechnic, Dunedin, Otago 9016, New Zealand
| | - Mads F Bertelsen
- Copenhagen Zoo, Roskildevej 38, DK-2000 Frederiksberg, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - P Dee Boersma
- Center for Ecosystem Sentinels, Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Charles-André Bost
- Centre d'Etudes Biologiques de Chizé (CEBC), UMR 7372 du CNRS-La Rochelle Université, 79360 Villiers-en-Bois, France
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé (CEBC), UMR 7372 du CNRS-La Rochelle Université, 79360 Villiers-en-Bois, France
| | - Peter Dann
- Research Department, Phillip Island Nature Parks, PO Box 97, Cowes, Phillip Island, Victoria, 3922, Australia
| | - Steven R Fiddaman
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK
| | - Pauline Howard
- Hornby Veterinary Centre, 7 Tower Street, Hornby, Christchurch, Canterbury 8042, New Zealand.,South Island Wildlife Hospital, Christchurch, Canterbury, New Zealand
| | - Kim Labuschagne
- National Zoological Garden, South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa
| | - Thomas Mattern
- Department of Zoology, University of Otago, PO Box 56, Dunedin, Otago 9054, New Zealand
| | - Gary Miller
- Division of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Patricia Parker
- Department of Biology, University of Missouri St. Louis, St Louis, MO 63121, USA
| | - Richard A Phillips
- British Antarctic Survey, Natural Environment Research Council, High Cross, Cambridge, UK
| | - Petra Quillfeldt
- Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Peter G Ryan
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa
| | - Helen Taylor
- Vet Services Hawkes Bay Ltd, 801 Heretaunga Street, Hastings, New Zealand.,Wairoa Farm Vets, 77 Queen Street, Wairoa 4108, New Zealand
| | - David R Thompson
- National Institute of Water and Atmospheric Research Ltd., Private Bag 14901, Kilbirnie, Wellington 6241, New Zealand
| | - Melanie J Young
- Department of Zoology, University of Otago, PO Box 56, Dunedin, Otago 9054, New Zealand
| | - Martin R Ellegaard
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen, Denmark
| | - George Pacheco
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5A, Copenhagen, Denmark
| | - Lara D Shepherd
- Museum of New Zealand Te Papa Tongarewa, PO Box 467, Wellington 6140, New Zealand
| | - Alan J D Tennyson
- Museum of New Zealand Te Papa Tongarewa, PO Box 467, Wellington 6140, New Zealand
| | - Stefanie Grosser
- Department of Zoology, University of Otago, PO Box 56, Dunedin, Otago 9054, New Zealand.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Emily Kay
- Wildbase, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.,Wellington Zoo, 200 Daniell St, Newtown, Wellington 6021, New Zealand
| | - Lisa J Nupen
- FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch 7701, South Africa.,National Zoological Gardens of South Africa, Pretoria, South Africa
| | - Ursula Ellenberg
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria, Australia.,Global Penguin Society, University of Washington, Seattle, WA, USA
| | - David M Houston
- Biodiversity Group, Department of Conservation, Auckland, New Zealand
| | - Andrew Hart Reeve
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.,Department of Biology, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kathryn Johnson
- Wildbase, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.,Wellington Zoo, 200 Daniell St, Newtown, Wellington 6021, New Zealand
| | - Juan F Masello
- Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Thomas Stracke
- South Island Wildlife Hospital, Christchurch, Canterbury, New Zealand
| | - Bruce McKinlay
- Biodiversity Group, Department of Conservation, Dunedin, New Zealand
| | - Pablo García Borboroglu
- Center for Ecosystem Sentinels, Department of Biology, University of Washington, Seattle, WA 98195, USA.,Global Penguin Society, Puerto Madryn 9120, Argentina.,CESIMAR CCT Cenpat-CONICET, Puerto Madryn 9120, Chubut, Argentina
| | - De-Xing Zhang
- Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Beijing 100101, China
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| |
Collapse
|
14
|
Colihueque N, Gantz A. Molecular genetic studies of Chilean avifauna: an overview about current progress. NEOTROPICAL BIOLOGY AND CONSERVATION 2019. [DOI: 10.3897/neotropical.14.e48588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The biodiversity of Chilean avifauna has been shaped by geological events, geographical factors and extreme climatic regimens. Molecular genetic studies developed to date have begun to provide valuable information to elucidate the effect of these factors on the evolutionary history of Chilean birds. We conducted a search in two bibliographic databases (PubMed and Scopus) over the period between 1998 and 2018 to identify the number and class of articles published in this research field. The quantification of specific research categories was also performed to assess progress in different molecular genetic issues of Chilean birds. Representative studies of the more active research areas: population structure, phylogeography, systematics and taxonomy and genetic diversity, were briefly commented on. Studies on genetic divergence analysis of cryptic species and the underlying genetics at molecular level of adaptive phenotypes in populations, were very scarce. Several types of mitochondrial and nuclear markers have been used, with COI plus D-loop and microsatellite loci, respectively, being the most widely-used markers. However, high-throughput analyses based on complete mitochondrial genomes have also been published. More than one hundred species have been analyzed; the most studied groups being penguins, followed by New World swallows. Although, to date, molecular genetic studies of Chilean birds still require further analysis, the studies available on some species or groups have provided important data to improve our understanding of the origin and evolution of this avifauna.
Collapse
|
15
|
Yu F, Zhang Y, Song J, Liang J. The complete mitochondrial genome of a wild edible mushroom, Russula griseocarnosa. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3368-3369. [PMID: 33365997 PMCID: PMC7707367 DOI: 10.1080/23802359.2019.1674215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Russula griseocarnosa is a wild edible ectomycorrhizal mushroom in southern China. In this study, we assembled the complete mitochondrial genome of R. griseocarnosa. Its total length was 60995 bp with a GC content of 21% and contained a total of 52 genes, including 14 standard protein-coding genes, two rRNA genes, 21 tRNA genes and 15 free-standing open reading frames (ORFs). Phylogenetic analysis reflected that the evolutionary processes between R. griseocarnosa and some agaricomycetes.
Collapse
Affiliation(s)
- Fei Yu
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Yongjie Zhang
- College of Life Science, Shanxi University, Taiyuan, China
| | - Jie Song
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Junfeng Liang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| |
Collapse
|
16
|
Cole TL, Ksepka DT, Mitchell KJ, Tennyson AJD, Thomas DB, Pan H, Zhang G, Rawlence NJ, Wood JR, Bover P, Bouzat JL, Cooper A, Fiddaman SR, Hart T, Miller G, Ryan PG, Shepherd LD, Wilmshurst JM, Waters JM. Mitogenomes Uncover Extinct Penguin Taxa and Reveal Island Formation as a Key Driver of Speciation. Mol Biol Evol 2019; 36:784-797. [PMID: 30722030 DOI: 10.1093/molbev/msz017] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversification of penguins. We test this hypothesis using a fossil-calibrated phylogeny of mitochondrial genomes (mitogenomes) from all extant and recently extinct penguin taxa. Our temporal analysis demonstrates that numerous recent island-endemic penguin taxa diverged following the formation of their islands during the Plio-Pleistocene, including the Galápagos (Galápagos Islands), northern rockhopper (Gough Island), erect-crested (Antipodes Islands), Snares crested (Snares) and royal (Macquarie Island) penguins. Our analysis also reveals two new recently extinct island-endemic penguin taxa from New Zealand's Chatham Islands: Eudyptes warhami sp. nov. and a dwarf subspecies of the yellow-eyed penguin, Megadyptes antipodes richdalei ssp. nov. Eudyptes warhami diverged from the Antipodes Islands erect-crested penguin between 1.1 and 2.5 Ma, shortly after the emergence of the Chatham Islands (∼3 Ma). This new finding of recently evolved taxa on this young archipelago provides further evidence that the radiation of penguins over the last 5 Ma has been linked to island emergence. Mitogenomic analyses of all penguin species, and the discovery of two new extinct penguin taxa, highlight the importance of island formation in the diversification of penguins, as well as the extent to which anthropogenic extinctions have affected island-endemic taxa across the Southern Hemisphere's isolated archipelagos.
Collapse
Affiliation(s)
- Theresa L Cole
- Department of Zoology, University of Otago, Dunedin, New Zealand.,Manaaki Whenua Landcare Research, Lincoln, Canterbury, New Zealand
| | | | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | | | - Daniel B Thomas
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Hailin Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,China National Genebank, BGI-Shenzhen, Shenzhen, Guangdong, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jamie R Wood
- Manaaki Whenua Landcare Research, Lincoln, Canterbury, New Zealand
| | - Pere Bover
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.,ARAID Foundation, IUCA-Grupo Aragosaurus, Universidad de Zaragoza, Zaragoza, Spain
| | - Juan L Bouzat
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | | | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Gary Miller
- Division of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA, Australia.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Peter G Ryan
- DST-NRF Centre of Excellence, FitzPatrick Institute of African Ornithology, University of Cape Town, Rondebosch, South Africa
| | - Lara D Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Janet M Wilmshurst
- Manaaki Whenua Landcare Research, Lincoln, Canterbury, New Zealand.,School of Environment, University of Auckland, Auckland, New Zealand
| | | |
Collapse
|
17
|
Li Q, Wang Q, Jin X, Chen Z, Xiong C, Li P, Liu Q, Huang W. Characterization and comparative analysis of six complete mitochondrial genomes from ectomycorrhizal fungi of the Lactarius genus and phylogenetic analysis of the Agaricomycetes. Int J Biol Macromol 2019; 121:249-260. [DOI: 10.1016/j.ijbiomac.2018.10.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 01/08/2023]
|
18
|
Contrasting phylogeographic pattern among Eudyptes penguins around the Southern Ocean. Sci Rep 2018; 8:17481. [PMID: 30504851 PMCID: PMC6269470 DOI: 10.1038/s41598-018-35975-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Since at least the middle-Miocene, the Antarctic Polar Front (APF) and the Subtropical Front (STF) appear to have been the main drivers of diversification of marine biota in the Southern Ocean. However, highly migratory marine birds and mammals challenge this paradigm and the importance of oceanographic barriers. Eudyptes penguins range from the Antarctic Peninsula to subantarctic islands and some of the southernmost subtropical islands. Because of recent diversification, the number of species remains uncertain. Here we analyze two mtDNA (HVRI, COI) and two nuclear (ODC, AK1) markers from 13 locations of five putative Eudyptes species: rockhopper (E. filholi, E. chrysocome, and E. moseleyi), macaroni (E. chrysolophus) and royal penguins (E. schlegeli). Our results show a strong phylogeographic structure among rockhopper penguins from South America, subantarctic and subtropical islands supporting the recognition of three separated species of rockhopper penguins. Although genetic divergence was neither observed among macaroni penguins from the Antarctic Peninsula and sub-Antarctic islands nor between macaroni and royal penguins, population genetic analyses revealed population genetic structure in both cases. We suggest that the APF and STF can act as barriers for these species. While the geographic distance between colonies might play a role, their impact/incidence on gene flow may vary between species and colonies.
Collapse
|
19
|
Li Q, Wang Q, Chen C, Jin X, Chen Z, Xiong C, Li P, Zhao J, Huang W. Characterization and comparative mitogenomic analysis of six newly sequenced mitochondrial genomes from ectomycorrhizal fungi (Russula) and phylogenetic analysis of the Agaricomycetes. Int J Biol Macromol 2018; 119:792-802. [PMID: 30076929 DOI: 10.1016/j.ijbiomac.2018.07.197] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/31/2018] [Accepted: 07/31/2018] [Indexed: 01/06/2023]
Abstract
In this study, the mitochondrial genomes of six Russula species were sequenced using next generation sequencing. The six mitogenomes were all composed of circular DNA molecules, with lengths ranging from 40,961 bp to 69,423 bp. The length and number of protein coding genes (PCGs), GC content, AT skew, and GC skew varied among the six mitogenomes. The increased number and total size of introns likely contributed to the size expansion of mitogenomes in some Russula species. Gene synteny analysis revealed some gene rearrangements among the six mitochondrial genomes. The nad4L gene had the lowest K2P genetic distance of the 15 core PCGs among the six Russula species, indicating that this gene was highly conserved. The Ka/Ks values for all 15 core PCGs were <1, suggesting that they were all subject to purifying selection. Phylogenetic analyses based on two gene datasets (15 core PCGs, and 15 core PCGs + rnl + rns) recovered identical and well-supported trees. In addition, cox1 was identified as a potential single-gene molecular marker for the phylogenetic analysis of relationships among Agaricomycetes species. This study provides the first report of mitogenomes from the Russulaceae family and facilitates the investigation of population genetics and evolution of other ectomycorrhizal fungi.
Collapse
Affiliation(s)
- Qiang Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Qiangfeng Wang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Cheng Chen
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, PR China
| | - Xin Jin
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Zuqin Chen
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Chuan Xiong
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Ping Li
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China
| | - Jian Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China.
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, Sichuan, PR China.
| |
Collapse
|