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Öztürk PN, Çıplak B. Dummy. Int J Biol Macromol 2019; 132:1318-1326. [PMID: 30953723 DOI: 10.1016/j.ijbiomac.2019.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/02/2019] [Accepted: 04/02/2019] [Indexed: 11/19/2022]
Affiliation(s)
- Pembe Nur Öztürk
- Department of Biology, Faculty of Science, Akdeniz University 07058, Antalya, Turkey
| | - Battal Çıplak
- Department of Biology, Faculty of Science, Akdeniz University 07058, Antalya, Turkey.
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2
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Du S, Niu G, Nyman T, Wei M. Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae). PeerJ 2018; 6:e6131. [PMID: 30595984 PMCID: PMC6305119 DOI: 10.7717/peerj.6131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/17/2018] [Indexed: 01/27/2023] Open
Abstract
We describe Arge bella Wei & Du sp. nov., a large and beautiful species of Argidae from south China, and report its mitochondrial genome based on high-throughput sequencing data. We present the gene order, nucleotide composition of protein-coding genes (PCGs), and the secondary structures of RNA genes. The nearly complete mitochondrial genome of A. bella has a length of 15,576 bp and a typical set of 37 genes (22 tRNAs, 13 PCGs, and 2 rRNAs). Three tRNAs are rearranged in the A. bella mitochondrial genome as compared to the ancestral type in insects: trnM and trnQ are shuffled, while trnW is translocated from the trnW-trnC-trnY cluster to a location downstream of trnI. All PCGs are initiated by ATN codons, and terminated with TAA, TA or T as stop codons. All tRNAs have a typical cloverleaf secondary structure, except for trnS1. H821 of rrnS and H976 of rrnL are redundant. A phylogenetic analysis based on mitochondrial genome sequences of A. bella, 21 other symphytan species, two apocritan representatives, and four outgroup taxa supports the placement of Argidae as sister to the Pergidae within the symphytan superfamily Tenthredinoidea.
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Affiliation(s)
- Shiyu Du
- Central South University of Forestry and Technology, Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, China
| | - Gengyun Niu
- Jiangxi Normal University, Life Science College, Nanchang, Jiangxi, China
| | - Tommi Nyman
- Norwegian Institute of Bioeconomy Research, Department of Ecosystems in the Barents Region, Svanhovd Research Station, Svanvik, Norway
| | - Meicai Wei
- Central South University of Forestry and Technology, Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, China
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3
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Niu G, Korkmaz EM, Doğan Ö, Zhang Y, Aydemir MN, Budak M, Du S, Başıbüyük HH, Wei M. The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference. Int J Biol Macromol 2018; 124:185-199. [PMID: 30448489 DOI: 10.1016/j.ijbiomac.2018.11.129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/30/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
The Pamphilioidea represents a small superfamily of the phytophagous suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genomes (mitogenomes) of three pamphilioid species: Chinolyda flagellicornis (Pamphiliidae), Megalodontes spiraeae and M. cephalotes (Megalodontesidae) were newly sequenced using next generation sequencing and comparatively analysed with the previously reported symphytan mitogenomes. A positive AT skew (0.013) and a negative GC skew (-0.194) were found in pamphilioid mitogenome, and a deviation from strand asymmetry was also observed in the PCGs encoded on both strands. Several gene rearrangement events were observed in four tRNA gene clusters (WCY, IQM, ARNS1EF and TP clusters), which have not been reported from symphytan mitogenomes to date. As the most parsimonious explanation, compared with the inferred insect ancestral mitogenome architecture, the occurrence of gene rearrangements in pamphilioid mitogenomes requires totally five evolutionary steps, including four transpositions and one inversion. The predicted secondary structures of tRNAs, rrnS and rrnL genes are mostly consistent with reported hymenopteran species. Phylogenetic analyses recovered the monophyly of superfamily Pamphilioidea and indicated the relationship Tenthredinoidea + (Pamphilioidea + (Cephoidea + (Orussoidea + Apocrita))) with strong nodal supports.
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Affiliation(s)
- Gengyun Niu
- College of Life Sciences, Jiangxi Normal University, 99 Ziyang Road, Nanchang 330022, PR China
| | - Ertan Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey.
| | - Özgül Doğan
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Yaoyao Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, PR China
| | - Merve Nur Aydemir
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Shiyu Du
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Central South University of Forestry and Technology, 498 South Shaoshan Road, Changsha 410004, PR China
| | | | - Meicai Wei
- College of Life Sciences, Jiangxi Normal University, 99 Ziyang Road, Nanchang 330022, PR China
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4
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Song N, Lin A, Zhao X. Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data. PLoS One 2018; 13:e0191826. [PMID: 29381758 PMCID: PMC5790268 DOI: 10.1371/journal.pone.0191826] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/11/2018] [Indexed: 01/21/2023] Open
Abstract
It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Aili Lin
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xincheng Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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5
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Hellmuth M, Hernandez-Rosales M, Long Y, Stadler PF. Inferring phylogenetic trees from the knowledge of rare evolutionary events. J Math Biol 2017; 76:1623-1653. [PMID: 29218395 DOI: 10.1007/s00285-017-1194-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 11/16/2017] [Indexed: 10/18/2022]
Abstract
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters. In this contribution we analyze the phylogenetic information content from a combinatorial point of view by considering the binary relation on the set of taxa defined by the existence of a single event separating two taxa. We show that the graph-representation of this relation must be a tree. Moreover, we characterize completely the relationship between the tree of such relations and the underlying phylogenetic tree. With directed operations such as tandem-duplication-random-loss events in mind we demonstrate how non-symmetric information constrains the position of the root in the partially reconstructed phylogeny.
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Affiliation(s)
- Marc Hellmuth
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany.,Center for Bioinformatics, Saarland University, Building E 2.1, P.O. Box 151150, 66041, Saarbrücken, Germany
| | - Maribel Hernandez-Rosales
- CONACYT-Instituto de Matemáticas, UNAM Juriquilla, Blvd. Juriquilla 3001, 76230, Juriquilla, Querétaro, QRO, Mexico
| | - Yangjing Long
- Department of Mathematics and Computer Science, University of Greifswald, Walther-Rathenau-Straße 47, 17487, Greifswald, Germany. .,School of Mathematical Sciences, Central China Normal University, Luoyu Road 152, Wuhan, 430079, Hubei, China.
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center of Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany.,Max-Planck-Institute for Mathematics in the Sciences, Inselstraße 22, 04103, Leipzig, Germany.,Inst. f. Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090, Vienna, Austria.,Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM, 87501, USA
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Chen PY, Zheng BY, Liu JX, Wei SJ. Next-Generation Sequencing of Two Mitochondrial Genomes from Family Pompilidae (Hymenoptera: Vespoidea) Reveal Novel Patterns of Gene Arrangement. Int J Mol Sci 2016; 17:ijms17101641. [PMID: 27727175 PMCID: PMC5085674 DOI: 10.3390/ijms17101641] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 09/14/2016] [Accepted: 09/20/2016] [Indexed: 01/09/2023] Open
Abstract
Animal mitochondrial genomes have provided large and diverse datasets for evolutionary studies. Here, the first two representative mitochondrial genomes from the family Pompilidae (Hymenoptera: Vespoidea) were determined using next-generation sequencing. The sequenced region of these two mitochondrial genomes from the species Auplopus sp. and Agenioideus sp. was 16,746 bp long with an A + T content of 83.12% and 16,596 bp long with an A + T content of 78.64%, respectively. In both species, all of the 37 typical mitochondrial genes were determined. The secondary structure of tRNA genes and rRNA genes were predicted and compared with those of other insects. Atypical trnS1 using abnormal anticodons TCT and lacking D-stem pairings was identified. There were 49 helices belonging to six domains in rrnL and 30 helices belonging to three domains in rrns present. Compared with the ancestral organization, four and two tRNA genes were rearranged in mitochondrial genomes of Auplopus and Agenioideus, respectively. In both species, trnM was shuffled upstream of the trnI-trnQ-trnM cluster, and trnA was translocated from the cluster trnA-trnR-trnN-trnS1-trnE-trnF to the region between nad1 and trnL1, which is novel to the Vespoidea. In Auplopus, the tRNA cluster trnW-trnC-trnY was shuffled to trnW-trnY-trnC. Phylogenetic analysis within Vespoidea revealed that Pompilidae and Mutillidae formed a sister lineage, and then sistered Formicidae. The genomes presented in this study have enriched the knowledge base of molecular markers, which is valuable in respect to studies about the gene rearrangement mechanism, genomic evolutionary processes and phylogeny of Hymenoptera.
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Affiliation(s)
- Peng-Yan Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China.
| | - Bo-Ying Zheng
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Jing-Xian Liu
- Department of Entomology, South China Agricultural University, Guangzhou 510640, China.
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
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7
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Krakowetz CN, Sproat A, Lindsay LR, Chilton NB. Sequence variability in the mitochondrial 12S rRNA and tRNA Val genes of Ixodes scapularis (Acari: Ixodidae) individuals shown previously to be genetically invariant. Mol Cell Probes 2015; 29:177-81. [PMID: 25863143 DOI: 10.1016/j.mcp.2015.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 10/23/2022]
Abstract
The DNA sequences of the mitochondrial (mt) 12S rRNA and tRNA(Val) genes were characterized for 82 blacklegged ticks (Ixodes scapularis) that were genetically identical for Domains IV and V of the mt 16S rRNA gene. Thirty-one haplotypes, differed in sequence by 1-9 bp, were detected among the 82 ticks. Most nucleotide alterations in DNA sequence did not affect the stability of the secondary structures of the RNAs. The magnitude of the DNA sequence variation in the mt 12S rRNA and tRNA(Val) genes among blacklegged ticks suggests that this region of the mitochondrial genome has potential as a genetic marker for examining the population genetics and phylogeography of I. scapularis.
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Affiliation(s)
- Chantel N Krakowetz
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - Allison Sproat
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada
| | - L Robbin Lindsay
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB R3E 3R2, Canada
| | - Neil B Chilton
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada.
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8
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Two nearly complete mitogenomes of wheat stem borers, Cephus pygmeus (L.) and Cephus sareptanus Dovnar-Zapolskij (Hymenoptera: Cephidae): an unusual elongation of rrnS gene. Gene 2015; 558:254-64. [PMID: 25576223 DOI: 10.1016/j.gene.2014.12.069] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 12/24/2014] [Accepted: 12/31/2014] [Indexed: 11/23/2022]
Abstract
Two nearly complete mitochondrial genomes (mitogenomes) of wheat stem borers, Cephus pygmeus and Cephus sareptanus (Hymenoptera: Cephidae), were sequenced, characterised and compared with the previously known mitogenome of Cephus cinctus. The gene orders are mostly conserved, except for translocation of trnM and swapped position of trnI and trnQ. An A+T bias was found, but a deviation from strand asymmetry was also detected on the J strand. All protein coding genes (PCGs) are initiated by ATN codons, except for nad1, nad2 and atp8, and all are terminated with TAA, TA- or T- as a stop codon. The predicted secondary structures of rrnS and rrnL genes are mostly consistent with reported hymenopteran species. However, an unusual elongation in rrnS, not know elsewhere in the order, was discovered in Cephus species. Three autonomous sequences detected in domains I and II are mainly responsible for the length expansions.
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9
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Krakowetz CN, Chilton NB. Sequence and secondary structure of the mitochondrial 16S ribosomal RNA gene of Ixodes scapularis. Mol Cell Probes 2014; 29:35-8. [PMID: 25444935 DOI: 10.1016/j.mcp.2014.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/06/2014] [Accepted: 11/06/2014] [Indexed: 10/24/2022]
Abstract
The complete DNA sequences and secondary structure of the mitochondrial (mt) 16S ribosomal (r) RNA gene were determined for six Ixodes scapularis adults. There were 44 variable nucleotide positions in the 1252 bp sequence alignment. Most (95%) nucleotide alterations did not affect the integrity of the secondary structure of the gene because they either occurred at unpaired positions or represented compensatory changes that maintained the base pairing in helices. A large proportion (75%) of the intraspecific variation in DNA sequence occurred within Domains I, II and VI of the 16S gene. Therefore, several regions within this gene may be highly informative for studies of the population genetics and phylogeography of I. scapularis, a major vector of pathogens of humans and domestic animals in North America.
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Affiliation(s)
- Chantel N Krakowetz
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, Saskatchewan S7N 5EZ, Canada
| | - Neil B Chilton
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, Saskatchewan S7N 5EZ, Canada.
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10
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Liu S, Xue D, Cheng R, Han H. The complete mitogenome of Apocheima cinerarius (Lepidoptera: Geometridae: Ennominae) and comparison with that of other lepidopteran insects. Gene 2014; 547:136-44. [PMID: 24967940 DOI: 10.1016/j.gene.2014.06.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/22/2014] [Accepted: 06/21/2014] [Indexed: 10/25/2022]
Abstract
The complete mitochondrial genome (mitogenome) of a female flightless geometrid moth Apocheima cinerarius was found to be 15,722 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The A+T content of the complete mitogenome is 80.83%. The AT skew value ([A-T]/[A+T]) is 0.027. The 13 PCGs of the mitogenome start with typical ATN codons, except for cox1 with the start codon CGA. All the tRNA genes have typical cloverleaf secondary structures, except for trnSer(AGN). The secondary structures of rrnL and rrnS were predicted. Six structural domains including conserved regions (IV, V) and variable regions (I, II, III, VI) were identified in the secondary structure of rrnL. The secondary structure of rrnS consists of 3 structural domains. The control region of A. cinerarius begins with conserved motifs of "ATAGA"+19-bp poly T. It also contains a microsatellite-like (TA)26, a stem-and-loop structure, and a poly-A stretch. Phylogenetic analysis showed that Geometroidea is more closely related to Bombycoidea than to Noctuoidea. A. cinerarius is more closely related to Biston panterinaria than to Phthonandria atrilineata, which is in accordance with the conventional morphology-based classification.
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Affiliation(s)
- Shuxian Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Dayong Xue
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Wu QL, Li Q, Gu Y, Shi BC, van Achterberg C, Wei SJ, Chen XX. The complete mitochondrial genome of Taeniogonalos taihorina (Bischoff) (Hymenoptera: Trigonalyidae) reveals a novel gene rearrangement pattern in the Hymenoptera. Gene 2014; 543:76-84. [PMID: 24709108 DOI: 10.1016/j.gene.2014.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/14/2013] [Accepted: 04/01/2014] [Indexed: 10/25/2022]
Abstract
The family Trigonalyidae is considered to be one of the most basal lineages in the suborder Apocrita of Hymenoptera. Here, we determine the first complete mitochondrial genome of the Trigonalyidae, from the species Taeniogonalos taihorina (Bischoff, 1914). This mitochondrial genome is 15,927bp long, with a high A+T-content of 84.60%. It contains all of the 37 typical animal mitochondrial genes and an A+T-rich region. The orders and directions of all genes are different from those of previously reported hymenopteran mitochondrial genomes. Eight tRNA genes, three protein-coding genes and the A+T-rich region were rearranged, with the dominant gene rearrangement events being translocation and local inversion. The arrangements of three tRNA clusters, trnY-trnM-trnI-trnQ, trnW-trnL2-trnC, and trnH-trnA-trnR-trnN-trnS-trnE-trnF, and the position of the cox1 gene, are novel to the Hymenoptera, even the insects. Six long intergenic spacers are present in the genome. The secondary structures of the RNA genes are normal, except for trnS2, in which the D-stem pairing is absent.
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Affiliation(s)
- Qiu-Ling Wu
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
| | - Qian Li
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yun Gu
- College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao 266109, China
| | - Bao-Cai Shi
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Cees van Achterberg
- Terrestrial Zoology, Naturalis Biodiversity Center, 2300 RA Leiden, Netherlands
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.
| | - Xue-Xin Chen
- Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
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Gäde G, Simek P, Fescemyer HW. Adipokinetic hormones provide inference for the phylogeny of odonata. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:174-178. [PMID: 21070783 DOI: 10.1016/j.jinsphys.2010.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/22/2010] [Accepted: 11/01/2010] [Indexed: 05/30/2023]
Abstract
Adipokinetic neuropeptides from the corpora cardiaca of 17 species of Odonata encompassing mainly the families Corduliidae and Libellulidae were isolated and structurally elucidated using liquid chromatography coupled with ion trap electrospray ionization mass spectrometry. It became evident that all species of the family Corduliidae studied express the peptide code-named Libau-AKH (pGlu-Val-Asn-Phe-Thr-Pro-Ser-Trp amide), which is also present in all but one libellulid species, Erythemis simplicicollis which expresses Erysi-AKH (pGlu-Leu-Asn-Phe-Thr-Pro-Ser-Trp amide). This divergence from all other Libellulids is due to a nonsynonymous missense single nucleotide polymorphism (SNP) in the nucleotide coding sequence (CDS) of prepro-AKH CDS and supports the polyphyletic nature of Sympetrinae and other subfamilies of libellulids. Despite this exception, these findings then support the hypothesis that Corduliidae and Libellulidae are closely related as stated in most phylogenies. The presence of Anaim-AKH (pGlu-Val-Asn-Phe-Ser-Pro-Ser-Trp amide) in Macromiidae likely distinguishes species in this family from Corduliidae. Current molecular genetic phylogenies and our AKH findings suggest that Syncordulia gracilis, which expresses Anaim-AKH, does not belong in Corduliidae. Evolution of AKHs in anisopteran Odonata are likely due to nucleotide substitution involving nonsynonymous missense SNPs in the CDS of prepro-AKH.
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Affiliation(s)
- Gerd Gäde
- Zoology Department, University of Cape Town, Rondebosch 7701, South Africa.
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Complete Mitochondrial Genome Sequence of Acrida cinerea (Acrididae: Orthoptera) and Comparative Analysis of Mitochondrial Genomes in Orthoptera. Comp Funct Genomics 2010; 2010:319486. [PMID: 21197069 PMCID: PMC3004375 DOI: 10.1155/2010/319486] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 08/02/2010] [Accepted: 09/02/2010] [Indexed: 11/19/2022] Open
Abstract
The complete 15,599-bp mitogenome of Acrida cinerea was determined and compared with that of the other 20 orthopterans. It displays characteristic gene content, genome organization, nucleotide composition, and codon usage found in other Caelifera mitogenomes. Comparison of 21 orthopteran sequences revealed that the tRNAs encoded by the H-strand appear more conserved than those by the L-stand. All tRNAs form the typical clover-leaf structure except trnS (agn), and most of the size variation among tRNAs stemmed from the length variation in the arm and loop of TΨC and the loop of DHU. The derived secondary structure models of the rrnS and rrnL from 21 orthoptera species closely resemble those from other insects on CRW except a considerably enlarged loop of helix 1399 of rrnS in Caelifera, which is a potentially autapomorphy of Caelifera. In the A+T-rich region, tandem repeats are not only conserved in the closely related mitogenome but also share some conserved motifs in the same subfamily. A stem-loop structure, 16 bp or longer, is likely to be involved in replication initiation in Caelifera and Grylloidea. A long T-stretch (>17 bp) with conserved stem-loop structure next to rrnS on the H-strand, bounded by a purine at either end, exists in the three species from Tettigoniidae.
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14
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Murienne J, Edgecombe GD, Giribet G. Including secondary structure, fossils and molecular dating in the centipede tree of life. Mol Phylogenet Evol 2010; 57:301-13. [DOI: 10.1016/j.ympev.2010.06.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 06/07/2010] [Accepted: 06/25/2010] [Indexed: 11/25/2022]
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16
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Simultaneous alignment and folding of 28S rRNA sequences uncovers phylogenetic signal in structure variation. Mol Phylogenet Evol 2009; 53:758-71. [DOI: 10.1016/j.ympev.2009.07.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 07/22/2009] [Accepted: 07/28/2009] [Indexed: 11/21/2022]
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17
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Ullrich B, Reinhold K, Niehuis O, Misof B. Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini). J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.2009.00553.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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18
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Wei SJ, Tang P, Zheng LH, Shi M, Chen XX. The complete mitochondrial genome of Evania appendigaster (Hymenoptera: Evaniidae) has low A+T content and a long intergenic spacer between atp8 and atp6. Mol Biol Rep 2009; 37:1931-42. [PMID: 19655273 PMCID: PMC2831182 DOI: 10.1007/s11033-009-9640-1] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 07/21/2009] [Indexed: 01/08/2023]
Abstract
The apocritan Hymenoptera show extraordinary features in mitochondrial genomes, but no complete sequence has been reported for the basal lineage, Evanioidea. Here, we sequenced the complete mitochondrial genome of Evania appendigaster. This genome is 17,817 bp long; with low A+T content, 77.8%, compared with other hymenopteran species. Four tRNA genes were rearranged, among which remote inversion is the dominant gene rearrangement event. Gene shuffling is caused by tandem duplication-random loss while remote inversion is best explained by recombination. The start codon of nad1 was found as TTG, which might be common across Hymenoptera. trnS2 and trnK use abnormal anticodons TCT and TTT, respectively, and the D-stem pairings in trnS2 are absent. The secondary structure of two rRNA genes are predicted and compared with those in other insects. Five long intergenic spacers were present, including a long intergenic spacer between atp8 and atp6, where these two genes overlap in the previously reported animal genomes. A conserved motif was found between trnS1 and nad1, which is proposed to be associated with mtTERM. The A+T-rich region is 2,325 bp long, among the longest in insects, and contains a tandem repeat region.
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Affiliation(s)
- Shu-jun Wei
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, 268 Kaixuan Road, 310029, Hangzhou, China
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19
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Wei SJ, Shi M, He JH, Sharkey M, Chen XX. The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events. Genome 2009; 52:308-19. [DOI: 10.1139/g09-008] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Few complete mitochondrial genomes representing limited families in the order Hymenoptera have been sequenced. Here, we sequenced the complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae). This genome is 18 728 bp long, the second largest hexapod mitochondrial genome sequenced in its entirety and that with the highest A+T content at 87.4%. Four tRNAs are rearranged compared with the ancestral arrangement. Gene rearrangement mechanisms are different among all three rearranged regions. Six tRNAs have a large variable loop, which is not found in other metazoan mitochondrial genomes. trnS(AGY) uses the abnormal anticodon TCT but trnK uses the normal CTT. The A+T-rich region is very long (2161 bp). An extremely A+T-rich (99.1%) 1515 bp tandem repeat region with three types of repeat elements is located between cox1 and cox2, and the most likely ancestral element originated from the 3′ end of cox1. Independent tandem duplications followed by mutation–insertion–deletion is the best model to explain the formation of this region. These results indicate that independent evolutionary events occurred extensively, such as gene rearrangement events, gene rearrangement mechanisms, derivation of tRNA variable loops, and tandem repeat region evolutionary processes, all of which likely contribute to the diversified features of hymenopteran mitochondrial genomes.
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Affiliation(s)
- Shu-jun Wei
- Institute of Insect Sciences, 268 Kaixuan Road, Zhejiang University, Hangzhou 310029, China
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310029, China
- Department of Entomology, University of Kentucky, Lexington KY 40546-0091, USA
| | - Min Shi
- Institute of Insect Sciences, 268 Kaixuan Road, Zhejiang University, Hangzhou 310029, China
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310029, China
- Department of Entomology, University of Kentucky, Lexington KY 40546-0091, USA
| | - Jun-hua He
- Institute of Insect Sciences, 268 Kaixuan Road, Zhejiang University, Hangzhou 310029, China
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310029, China
- Department of Entomology, University of Kentucky, Lexington KY 40546-0091, USA
| | - M. Sharkey
- Institute of Insect Sciences, 268 Kaixuan Road, Zhejiang University, Hangzhou 310029, China
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310029, China
- Department of Entomology, University of Kentucky, Lexington KY 40546-0091, USA
| | - Xue-xin Chen
- Institute of Insect Sciences, 268 Kaixuan Road, Zhejiang University, Hangzhou 310029, China
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310029, China
- Department of Entomology, University of Kentucky, Lexington KY 40546-0091, USA
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20
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Fleck G, Ullrich B, Brenk M, Wallnisch C, Orland M, Bleidissel S, Misof B. A phylogeny of anisopterous dragonflies (Insecta, Odonata) using mtRNA genes and mixed nucleotide/doublet models. J ZOOL SYST EVOL RES 2008. [DOI: 10.1111/j.1439-0469.2008.00474.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Misof B, Niehuis O, Bischoff I, Rickert A, Erpenbeck D, Staniczek A. Towards an 18S phylogeny of hexapods: Accounting for group-specific character covariance in optimized mixed nucleotide/doublet models. ZOOLOGY 2007; 110:409-29. [DOI: 10.1016/j.zool.2007.08.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2007] [Revised: 08/02/2007] [Accepted: 08/22/2007] [Indexed: 10/22/2022]
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22
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Ware J, May M, Kjer K. Phylogeny of the higher Libelluloidea (Anisoptera: Odonata): An exploration of the most speciose superfamily of dragonflies. Mol Phylogenet Evol 2007; 45:289-310. [PMID: 17728156 DOI: 10.1016/j.ympev.2007.05.027] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Revised: 05/08/2007] [Accepted: 05/21/2007] [Indexed: 10/23/2022]
Abstract
Although libelluloid dragonflies are diverse, numerous, and commonly observed and studied, their phylogenetic history is uncertain. Over 150 years of taxonomic study of Libelluloidea Rambur, 1842, beginning with Hagen (1840), [Rambur, M.P., 1842. Neuropteres. Histoire naturelle des Insectes, Paris, pp. 534; Hagen, H., 1840. Synonymia Libellularum Europaearum. Dissertation inaugularis quam consensu et auctoritate gratiosi medicorum ordinis in academia albertina ad summos in medicina et chirurgia honores.] and Selys (1850), [de Selys Longchamps, E., 1850. Revue des Odonates ou Libellules d'Europe [avec la collaboration de H.A. Hagen]. Muquardt, Bruxelles; Leipzig, 1-408.], has failed to produce a consensus about family and subfamily relationships. The present study provides a well-substantiated phylogeny of the Libelluloidea generated from gene fragments of two independent genes, the 16S and 28S ribosomal RNA (rRNA), and using models that take into account non-independence of correlated rRNA sites. Ninety-three ingroup taxa and six outgroup taxa were amplified for the 28S fragment; 78 ingroup taxa and five outgroup taxa were amplified for the 16S fragment. Bayesian, likelihood and parsimony analyses of the combined data produce well-resolved phylogenetic hypotheses and several previously suggested monophyletic groups were supported by each analysis. Macromiinae, Corduliidae s. s., and Libellulidae are each monophyletic. The corduliid (s.l.) subfamilies Synthemistinae, Gomphomacromiinae, and Idionychinae form a monophyletic group, separate from the Corduliinae. Libellulidae comprises three previously accepted subfamilies (Urothemistinae, a very restricted Tetrathemistinae, and a modified Libellulinae) and five additional consistently recovered groups. None of the other previously proposed subfamilies are supported. Bayesian analyses run with an additional 71 sequences obtained from GenBank did not alter our conclusions. The evolution of adult and larval morphological characters is discussed here to suggest areas for future focus. This study shows the inherent problems in using poorly defined and sometimes inaccurately scored characters, basing groups on symplesiomorphies, and failure to recognize the widespread effects of character correlation and convergence, especially in aspects of wing venation.
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Affiliation(s)
- Jessica Ware
- Department of Entomology, Rutgers University, 93 Lipman Drive, New Brunswick, NJ 08901, USA.
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23
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Winterton SL, Wiegmann BM, Schlinger EI. Phylogeny and Bayesian divergence time estimations of small-headed flies (Diptera: Acroceridae) using multiple molecular markers. Mol Phylogenet Evol 2007; 43:808-32. [PMID: 17196837 DOI: 10.1016/j.ympev.2006.08.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Revised: 07/19/2006] [Accepted: 08/13/2006] [Indexed: 11/22/2022]
Abstract
The first formal analysis of phylogenetic relationships among small-headed flies (Acroceridae) is presented based on DNA sequence data from two ribosomal (16S and 28S) and two protein-encoding genes: carbomoylphosphate synthase (CPS) domain of CAD (i.e., rudimentary locus) and cytochrome oxidase I (COI). DNA sequences from 40 species in 22 genera of Acroceridae (representing all three subfamilies) were compared with outgroup exemplars from Nemestrinidae, Stratiomyidae, Tabanidae, and Xylophagidae. Parsimony and Bayesian simultaneous analyses of the full data set recover a well-resolved and strongly supported hypothesis of phylogenetic relationships for major lineages within the family. Molecular evidence supports the monophyly of traditionally recognised subfamilies Philopotinae and Panopinae, but Acrocerinae are polyphyletic. Panopinae, sometimes considered "primitive" based on morphology and host-use, are always placed in a more derived position in the current study. Furthermore, these data support emerging morphological evidence that the type genus Acrocera Meigen, and its sister genus Sphaerops, are atypical acrocerids, comprising a sister lineage to all other Acroceridae. Based on the phylogeny generated in the simultaneous analysis, historical divergence times were estimated using Bayesian methodology constrained with fossil data. These estimates indicate Acroceridae likely evolved during the late Triassic but did not diversify greatly until the Cretaceous.
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MESH Headings
- Animals
- Carbamoyl-Phosphate Synthase (Ammonia)/genetics
- Diptera/classification
- Diptera/genetics
- Electron Transport Complex IV/genetics
- Evolution, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 28S/chemistry
- RNA, Ribosomal, 28S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Shaun L Winterton
- Department of Entomology, North Carolina State University, Raleigh, NC, USA.
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24
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Kjer KM, Gillespie JJ, Ober KA. Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment. Syst Biol 2007; 56:133-46. [PMID: 17366144 DOI: 10.1080/10635150601156305] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Karl M Kjer
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey 08901, USA.
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25
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Hagner SC, Misof B, Maier WA, Kampen H. Bayesian analysis of new and old malaria parasite DNA sequence data demonstrates the need for more phylogenetic signal to clarify the descent of Plasmodium falciparum. Parasitol Res 2007; 101:493-503. [PMID: 17393186 DOI: 10.1007/s00436-007-0499-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2006] [Accepted: 02/09/2007] [Indexed: 11/27/2022]
Abstract
Molecular systematic studies published during the last 15 years to clarify the phylogenetic relationships among the malaria parasites have led to two major hypotheses on the descent of Plasmodium falciparum: One supports an avian origin as a result of a relatively recent host switch, and another one favours the evolutionary development of P. falciparum together with its human host from primate ancestors. In this paper, we present phylogenetic analyses of three different Plasmodium genes, the nuclear 18 small sub-unit (SSU) ribosomal ribonucleic acid (rRNA), the mitochondrial cytochrome b (cyt b) and the plastid caseinolytic protease C (ClpC) gene, using numerous haemosporidian parasite DNA sequences obtained from the GenBank as well as several new sequences for major malaria parasites including the avian one Plasmodium cathemerium, which has never been considered in molecular phylogenetic analyses before. Most modern and sophisticated DNA substitution models based on Bayesian inference analysis were applied to estimate the cyt b and ClpC phylogenetic trees, whereas the 18 SSU rRNA gene was examined with regards to its secondary structure using PHASE software. Our results indicate that the data presently available are generally neither sufficient in number nor in information to solve the problem of the phylogenetic origin of P. falciparum.
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Affiliation(s)
- S C Hagner
- Institute for Medical Microbiology, Immunology and Parasitology, University of Bonn, Sigmund-Freud-Str. 25, 53105 Bonn, Germany.
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26
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Gillespie JJ, Johnston JS, Cannone JJ, Gutell RR. Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. INSECT MOLECULAR BIOLOGY 2006; 15:657-86. [PMID: 17069639 PMCID: PMC2048585 DOI: 10.1111/j.1365-2583.2006.00689.x] [Citation(s) in RCA: 189] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 06/28/2006] [Indexed: 05/12/2023]
Abstract
As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.
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Affiliation(s)
- J J Gillespie
- Department of Entomology, Texas A & M University, College Station, TX, USA.
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27
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Carapelli A, Vannini L, Nardi F, Boore JL, Beani L, Dallai R, Frati F. The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera). Gene 2006; 376:248-59. [PMID: 16766140 DOI: 10.1016/j.gene.2006.04.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Revised: 03/21/2006] [Accepted: 04/08/2006] [Indexed: 11/25/2022]
Abstract
In this study, the nearly complete sequence (14,519 bp) of the mitochondrial DNA (mtDNA) of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera) is described. All protein coding genes (PCGs) are in the arrangement known to be ancestral for insects, but three tRNA genes (trnA, trnS(gcu), and trnL(uag)) have transposed to derived positions and there are three tandem copies of trnH, each of which is potentially functional. All of these rearrangements except for that of trnL(uag) is within the short span between nad3 and nad4 and there are numerous blocks of unassignable sequence in this region, perhaps as remnants of larger scale predisposing rearrangements. X. vesparum mtDNA nucleotide composition is strongly biased toward A and T, as is typical for insect mtDNAs. There is also a significant strand skew in the distribution of these nucleotides, with the J-strand being richer in A than T and in C than G, and the N-strand showing an opposite skew for complementary pairs of nucleotides. The hypothetical secondary structure of the LSU rRNA has also been reconstructed, obtaining a structural model similar to that of other insects.
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MESH Headings
- Animals
- Base Composition
- Base Pairing
- Base Sequence
- Codon
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- Evolution, Molecular
- Gene Dosage
- Gene Expression Profiling
- Gene Order
- Gene Rearrangement
- Genes, Insect
- Genome
- Insecta/classification
- Insecta/genetics
- Microsatellite Repeats
- Molecular Sequence Data
- Nucleic Acid Conformation
- Open Reading Frames
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Repetitive Sequences, Nucleic Acid
- Sequence Analysis, DNA
- Translocation, Genetic
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28
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NIEHUIS OLIVER, NAUMANN CLASM, MISOF BERNHARD. Phylogenetic analysis of Zygaenoidea small-subunit rRNA structural variation implies initial oligophagy on cyanogenic host plants in larvae of the moth genus Zygaena (Insecta: Lepidoptera). Zool J Linn Soc 2006. [DOI: 10.1111/j.1096-3642.2006.00222.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Podsiadlowski L, Carapelli A, Nardi F, Dallai R, Koch M, Boore JL, Frati F. The mitochondrial genomes of Campodea fragilis and Campodea lubbocki (Hexapoda: Diplura): High genetic divergence in a morphologically uniform taxon. Gene 2006; 381:49-61. [PMID: 16919404 DOI: 10.1016/j.gene.2006.06.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 05/15/2006] [Accepted: 06/05/2006] [Indexed: 11/20/2022]
Abstract
Complete mitochondrial genome sequences are presented from two dipluran hexapods (i.e., a group of "primarily wingless insects") of the genus Campodea and compared to those of other arthropods. Their gene order is the same as in most other hexapods and crustaceans. Structural changes have occurred in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2 as well as in both ribosomal RNAs. These mtDNAs have striking biases in nucleotide and amino acid composition. Although the two Campodea species are morphologically highly similar, their genetic divergence is larger than expected, suggesting a long evolutionary history, perhaps under stable ecological conditions.
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Affiliation(s)
- L Podsiadlowski
- Department of Animal Systematics and Evolution, Freie Universität Berlin, Germany.
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30
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Niehuis O, Yen SH, Naumann CM, Misof B. Higher phylogeny of zygaenid moths (Insecta: Lepidoptera) inferred from nuclear and mitochondrial sequence data and the evolution of larval cuticular cavities for chemical defence. Mol Phylogenet Evol 2006; 39:812-29. [PMID: 16483803 DOI: 10.1016/j.ympev.2006.01.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2005] [Revised: 12/01/2005] [Accepted: 01/04/2006] [Indexed: 11/23/2022]
Abstract
Zygaenid moths are capable of releasing hydrogen cyanide in their defense by enzymatic break-down of cyanoglucosides, but only larvae of chalcosiine and zygaenine moths store cyanogenic compounds in cuticular cavities and thus are able to discharge defense droplets, which effectively deter potential predators. A previously proposed phylogeny of Zygaenidae hypothesized a sister group relationship of chalcosiine and zygaenine moths because of their similar larval defense system. Not all chalcosiine taxa possess cuticular cavities, however, and a comparable defense mechanism has been reported in larvae of the zygaenoid family Heterogynidae. Considering sequence data of seven molecular loci, the present study estimates the posterior probability of phylogenetic hypotheses explaining the occurrence of larval cuticular cavities. The molecular data confirm the previous exclusion of Himantopteridae from Zygaenidae and suggest their close affinity to Somabrachyidae. The sequence data also corroborate the recently proposed exclusion of the Phaudinae from the Zygaenidae, because this subfamily is recovered in a reasonably well supported species cluster consisting of members of the families Lacturidae, Limacodidae, Himantopteridae, and Somabrachyidae. We consequently agree to raise Phaudinae to family rank. Within Zygaenidae, the subfamilies Callizygaeninae, Chalcosiinae, and Procridinae most likely constitute a monophyletic group, which is sister to the Zygaeninae. Our results imply that cuticular cavities were probably present in the larvae of the most recent common ancestor of Zygaenidae. Heterogynidae cannot be confirmed as sister taxon to this family, but appear at the very first split of the Zygaenoidea, although with poor support. The specific pattern of taxa in the molecular phylogeny showing larval cuticular cavities opens the possibility that these structures could have been already present in the most recent common ancestor of the Zygaenoidea.
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Affiliation(s)
- Oliver Niehuis
- Alexander Koenig Research Institute and Museum of Zoology, Bonn, Germany.
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31
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Hypsa V. Parasite histories and novel phylogenetic tools: Alternative approaches to inferring parasite evolution from molecular markers. Int J Parasitol 2006; 36:141-55. [PMID: 16387305 DOI: 10.1016/j.ijpara.2005.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Revised: 10/19/2005] [Accepted: 10/28/2005] [Indexed: 10/25/2022]
Abstract
Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.
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Affiliation(s)
- Václav Hypsa
- Faculty of Biological Sciences, University of South Bohemia, and Institute of Parasitology, Academy of Sciences of the Czech Republic, Branisovská 31, 37005 Ceské Budejovice, Czech Republic.
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32
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Misof B, Niehuis O, Bischoff I, Rickert A, Erpenbeck D, Staniczek A. A Hexapod nuclear SSU rRNA secondary-structure model and catalog of taxon-specific structural variation. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2006; 306:70-88. [PMID: 16161065 DOI: 10.1002/jez.b.21040] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
RNA molecules and in particular the nuclear SSU RNA play an important role in molecular systematics. With the advent of increasingly parameterized substitution models in systematic research, the incorporation of secondary-structure information became a realistic option compensating interdependence of character variation. As a prerequisite, consensus structures of eukaryotic SSU RNA molecules have become available through extensive comparative analyses and crystallographic studies. Despite extensive research in hexapod phylogenetics, consensus SSU RNA secondary structures focusing on hexapods have not yet been explored. In this study, we compiled a representative hexapod SSU data set of 261 sequences and inferred a specific consensus SSU secondary-structure model. Our search for conserved structural motives relied on a combined approach of thermodynamic and covariation analyses. The hexapod consensus-structure model deviates from the canonical eukaryotic model in a number of helices. Additionally, in several helices the hexapod sequences did not support a single consensus structure. We provide consensus structures of these sections of single less-inclusive taxa, thus facilitating the adaptation of the consensus hexapod model to less-inclusive phylogenetic questions. The secondary-structure catalog will foster the application of RNA structure models in phylogenetic analyses using the SSU rRNA molecule, and it will improve the realism of substitution models and the reliability of reconstructions based on rRNA sequences.
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Affiliation(s)
- Bernhard Misof
- Zoologisches Forschungsinstitut und Museum A. Koenig Adenauerallee 160, 53113 Bonn, Germany.
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33
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Gillespie JJ, Yoder MJ, Wharton RA. Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation. J Mol Evol 2005; 61:114-37. [PMID: 16059751 DOI: 10.1007/s00239-004-0246-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2004] [Accepted: 03/08/2005] [Indexed: 11/27/2022]
Abstract
We utilize the secondary structural properties of the 28S rRNA D2-D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw and Quicke, Syst Biol 51:450-477, 2002) and provides the first global alignment template for this diverse group of insects. Predicted structures for these expansion segments as well as for over half of the 18S rRNA are given, with highly variable regions characterized and isolated within conserved structures. We demonstrate several pitfalls of optimization alignment and illustrate how these are potentially addressed with structure-based alignments. Our global alignment is presented online at (http://hymenoptera.tamu.edu/rna) with summary statistics, such as basepair frequency tables, along with novel tools for parsing structure-based alignments into input files for most commonly used phylogenetic software. These resources will be valuable for hymenopteran systematists, as well as researchers utilizing rRNA sequences for phylogeny estimation in any taxon. We explore the phylogenetic utility of our structure-based alignment by examining a subset of the data under a variety of optimality criteria using results from Belshaw and Quicke (2002) as a benchmark.
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Affiliation(s)
- Joseph J Gillespie
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA.
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Gillespie JJ, Munro JB, Heraty JM, Yoder MJ, Owen AK, Carmichael AE. A Secondary Structural Model of the 28S rRNA Expansion Segments D2 and D3 for Chalcidoid Wasps (Hymenoptera: Chalcidoidea). Mol Biol Evol 2005; 22:1593-608. [PMID: 15843598 DOI: 10.1093/molbev/msi152] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We analyze the secondary structure of two expansion segments (D2, D3) of the 28S ribosomal (rRNA)-encoding gene region from 527 chalcidoid wasp taxa (Hymenoptera: Chalcidoidea) representing 18 of the 19 extant families. The sequences are compared in a multiple sequence alignment, with secondary structure inferred primarily from the evidence of compensatory base changes in conserved helices of the rRNA molecules. This covariation analysis yielded 36 helices that are composed of base pairs exhibiting positional covariation. Several additional regions are also involved in hydrogen bonding, and they form highly variable base-pairing patterns across the alignment. These are identified as regions of expansion and contraction or regions of slipped-strand compensation. Additionally, 31 single-stranded locales are characterized as regions of ambiguous alignment based on the difficulty in assigning positional homology in the presence of multiple adjacent indels. Based on comparative analysis of these sequences, the largest genetic study on any hymenopteran group to date, we report an annotated secondary structural model for the D2, D3 expansion segments that will prove useful in assigning positional nucleotide homology for phylogeny reconstruction in these and closely related apocritan taxa.
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Gäde G, Marco HG. The adipokinetic hormones of Odonata: a phylogenetic approach. JOURNAL OF INSECT PHYSIOLOGY 2005; 51:333-341. [PMID: 15749116 DOI: 10.1016/j.jinsphys.2004.12.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Accepted: 12/30/2004] [Indexed: 05/24/2023]
Abstract
Adipokinetic neuropeptides from the corpora cardiaca of the major families of all three suborders of the Odonata were identified by one or more of the following methods: (1) Isolation of the peptides from a methanolic extract of the corpora cardiaca by liquid chromatography, peak monitoring by fluorescence of the Trp residue and comparison of the retention time with those of known synthetic peptides of Odonata. (2) Hyperlipaemic bioassays of the HPLC-generated fractions either in Locusta migratoria or, in a few cases, in Anax imperator or Orthetrum julia. (3) Sequencing of the isolated, bioactive HPLAC fraction by Edman degradation. (4) Mass spectrometric measurement of the isolated, bioactive fraction. Sequence assignment revealed that the investigated Odonata species always contain only one adipokinetic peptide. This is always an octapeptide. The suborder Zygoptera contains the peptide code-named Psein-AKH, the Anisozygoptera and the families Aeshnidae, Cordulegastridae and Macromiidae of the Anisoptera contain Anaim-AKH, whereas Gomphidae, Corduliidae (with the exception of Syncordulia gracilis) and Libellulidae contain Libau-AKH; one species of Libellulidae has Erysi-AKH, a very conservative modification of Libau-AKH (one point mutation). When these structural data are interpreted in conjunction with existing phylogenies of Odonata, they support the following: (1) Zygoptera are monophyletic and not paraphyletic. (2) Anisozygoptera and Anisoptera are sister groups and contain the ancestral Anaim-AKH which is independently and convergently mutated to Libau-AKH in Gomphidae and Libellulidae. (3) The Corduliidae are of special interest. Only Corduliidae sensu stricto appear to contain Libau-AKH, other species placed into this family by most authorities contain the ancestral Anaim-AKH. Possibly, assignments of AKHs can untangle the paraphyly of this family.
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Affiliation(s)
- Gerd Gäde
- Zoology Department, University of Cape Town, Private Bag, Rondebosch 7701, South Africa.
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Gillespie J, Cannone J, Gutell R, Cognato A. A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae; Galerucinae). INSECT MOLECULAR BIOLOGY 2004; 13:495-518. [PMID: 15373807 DOI: 10.1111/j.0962-1075.2004.00509.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We analysed the secondary structure of two expansion segments (D2, D3) of the 28S rRNA gene from 229 leaf beetles (Coleoptera: Chrysomelidae), the majority of which are in the subfamily Galerucinae. The sequences were compared in a multiple sequence alignment, with secondary structure inferred primarily from the compensatory base changes in the conserved helices of the rRNA molecules. This comparative approach yielded thirty helices comprised of base pairs with positional covariation. Based on these leaf beetle sequences, we report an annotated secondary structural model for the D2 and D3 expansion segments that will prove useful in assigning positional nucleotide homology for phylogeny reconstruction in these and closely related beetle taxa. This predicted structure, consisting of seven major compound helices, is mostly consistent with previously proposed models for the D2 and D3 expansion segments in insects. Despite a lack of conservation in the primary structure of these regions of insect 28S rRNA, the evolution of the secondary structure of these seven major motifs may be informative above the nucleotide level for higher-order phylogeny reconstruction of major insect lineages.
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Affiliation(s)
- J Gillespie
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA.
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