Universal DNA primers for amplification of complete mitochondrial protein-coding genes and ribosomal RNA genes from Crocodilia

Carabidae are one of the most species-rich families of beetles, comprising more than 40,000 described species worldwide. Forty-three complete or partial mitochondrial genomes (mitogenomes) from this family have been published in GenBank to date. In this study, we sequenced a nearly complete mitogenome of Amara aulica (Carabidae), using a next-generation sequencing method. This mitogenome was 16,646 bp in length, which encoded the typical 13 mitochondrial protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Combining with the published mitogenomes of Carabidae and five outgroup species from Trachypachidae, Gyrinidae and Dytiscidae, we performed phylogenetic estimates under maximum likelihood and Bayesian inference criteria to investigate the phylogenetic relationships of carabid beetles. The results showed that the family Carabidae was a non-monophyletic assemblage. The subfamilies Cicindelinae, Elaphrinae, Carabinae, Trechinae and Harpalinae were recovered as monophyletic groups. Moreover, the clade (Trechinae + (Brachininae + Harpalinae)) was consistently recovered in all analyses.

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Plastome Diversity and Phylogenomic Relationships in Asteraceae

Plants ◽

10.3390/plants10122699 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2699

Author(s):

Joan Pere Pascual-Díaz ◽

Sònia Garcia ◽

Daniel Vitales

Keyword(s):

Ribosomal Rna ◽

Evolutionary Rate ◽

Plastid Dna ◽

Single Copy ◽

Phylogenomic Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Plastid Genomes ◽

The Family ◽

Rna Genes

Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae—as well as in the sister family Calyceraceae—lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family’s phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

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Plastome Diversity and Phylogenomic Relationships in Asteraceae

10.20944/preprints202111.0167.v1 ◽

2021 ◽

Author(s):

Joan Pere Pascual-Díaz ◽

Sònia Garcia ◽

Daniel Vitales

Keyword(s):

Ribosomal Rna ◽

Evolutionary Rate ◽

Plastid Dna ◽

Single Copy ◽

Phylogenomic Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Plastid Genomes ◽

The Family ◽

Rna Genes

Plastid genomes are in general highly conserved given their slow evolutionary rate, thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridisation, both processes usually complicating systematic inferences. In this study, we have generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity, and repeat composition of these sequences. By comparing the whole plastome sequences obtained, we confirmed the double inversion located in the long single copy region, for most of the species analysed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also show that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae -as well as in the sister family Calyceraceae - are lacking the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, are overall consistent with the general consensus for the family’s phylogeny, while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.

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Halojulellaceae a new family of the order Pleosporales

Phytotaxa ◽

10.11646/phytotaxa.130.1.2 ◽

2013 ◽

Vol 130 (1) ◽

pp. 14 ◽

Cited By ~ 20

Author(s):

HIRAN A. ARIYAWANSA ◽

EVAN B.G. JONES ◽

SATINEE SUETRONG ◽

SITI A. ALIAS ◽

JI-CHUAN KANG ◽

...

Keyword(s):

Ribosomal Rna ◽

Marine Species ◽

Morphological Characters ◽

Molecular Data ◽

Marine Habitat ◽

Protein Coding ◽

Protein Coding Genes ◽

New Family ◽

Distinct Genus ◽

Rna Genes

Halojulellaceae fam. nov. and Halojullela gen. nov. are introduced to accommodate Julella avicenniae, a marine species in the suborder Pleosporineae, order Pleosporales, Dothideomycetes. Justification for the new family is based on combined gene analysis of the large and small subunits of the nuclear ribosomal RNA genes (LSU, SSU) and two protein coding genes RPB2 and TEF1, as well as morphological characters. Halojulellaceae and Halojulella are characterized by immersed to semi-immersed, clypeate ascomata, with short, papillate ostioles, cellular, hyphae-like, pseudoparaphyses, 8-spored, fissitunicate, clavate to cylindrical asci with a well-developed apical apparatus, a moderately long pedicel with a club-like base and hyaline or golden brown, ellipsoidal, muriform ascospores and is typified by Halojulella avicenniae. Halojullela differs from Julella, (type J. buxi) in its marine habitat and distinctly differing ascus with the apical apparatus being well-developed and moderately long club-like pedicel. Morphological characters and molecular data show that H. avicenniae belongs in the Pleosporales, outside any of the known families, and thus a new family is introduced to accommodate it. Julella is maintained as a distinct genus which is presently most likely polyphyletic with saprobic and lichenized elements and needs further study as no molecular data is presently available for any species.

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Molecular phylogeny inferred from the mitochondrial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae)

Scientific Reports ◽

10.1038/s41598-020-78082-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Meng-Yuan Zhao ◽

Qing-Bo Huo ◽

Yu-Zhou Du

Keyword(s):

Ribosomal Rna ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

The Other ◽

Mitochondrial Genomes ◽

Stem Loop ◽

Protein Coding ◽

Protein Coding Genes ◽

Noncoding Control Region ◽

Rna Genes

AbstractIn this study, the mitochondrial genome of the stonefly, Oyamia nigribasis Banks, 1920 (Plecoptera: Perlidae), was sequenced and compared with the mtDNA genomes of 38 other stoneflies and two Ephemerae. The O. nigribasis mitogenome is a circular 15,923 bp molecule that encodes a large, noncoding control region (CR) and 37 typical mtDNA genes; these include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), respectively. Most of the PCGs initiated with ATN and terminated with TAN. The dihydrouridine (DHU) arm of tRNASer (AGN) was missing, whereas the other 21 tRNAs all exhibited the typical cloverleaf secondary structure. Stem-loop (SL) structures and tandem repeats were identified in the CR. Phylogenetic analyses using Bayesian inference and maximum likelihood were undertaken to determine relationships between stoneflies. Results indicated that the Antarctoperlaria, which contains Gripopterygidae, was absolutely separated from Arctoperlaria; this finding agrees with morphology. Finally, the overall relationships could be summarized as follows ((((Notonemouridae + Nemouridae) + Leuctridae) + (Scopuridae + (Capniidae + Taeniopterygidae))) + (((Perlodidae + Chloroperlidae) + Perlidae) + (Pteronarcyidae + (Peltoperlidae + Styloperlidae))) + ((Diamphipnoidae + Eustheniidae) + Gripopterygidae)).

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Intraspecies Variation in Tetrahymena rostrata

Microorganisms ◽

10.3390/microorganisms9102100 ◽

2021 ◽

Vol 9 (10) ◽

pp. 2100

Author(s):

Anne Watt ◽

Neil Young ◽

Ruth Haites ◽

Kerry Dunse ◽

Derek Russell ◽

...

Keyword(s):

Ribosomal Rna ◽

Small Subunit ◽

Ribosomal Rna Genes ◽

Clonal Variation ◽

Trna Genes ◽

Protein Coding ◽

Intraspecies Variation ◽

Geographic Origins ◽

Facultative Parasite ◽

Rna Genes

Two distinct isolates of the facultative parasite, Tetrahymena rostrata were compared, identifying and utilising markers that are useful for studying clonal variation within the species were identified and utilised. The sequences of mitochondrial genomes and several nuclear genes were determined using Illumina short read sequencing. The two T. rostrata isolates had similar morphology. The linear mitogenomes had the gene content and organisation typical of the Tetrahymena genus, comprising 8 tRNA genes, 6 ribosomal RNA genes and 45 protein coding sequences (CDS), twenty-two of which had known function. The two isolates had nucleotide identity within common nuclear markers encoded within the histone H3 and H4 and small subunit ribosomal RNA genes and differed by only 2–4 nucleotides in a region of the characterised actin genes. Variation was observed in several mitochondrial genes and was used to determine intraspecies variation and may reflect the natural history of T. rostrata from different hosts or the geographic origins of the isolates.

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Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae)

10.20944/preprints201810.0638.v1 ◽

2018 ◽

Author(s):

Luoyun Wang ◽

Jing Wang ◽

Caiyun He ◽

Jianguo Zhang ◽

Yanfei Zeng

Keyword(s):

Chloroplast Genome ◽

Mutation Rate ◽

Ribosomal Rna ◽

Sympatric Species ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Protein ◽

Optimal Codons ◽

Chloroplast Genomes ◽

Rna Genes

Hippophae is a tree species with ecological, economic and social benefits. In this study, we assembled and annotated chloroplast genomes of sympatric Hippophae gyantsensis and H. rhamnoides subsp. yunnanensis. Their full-length are 155260 and 156415 bp, respectively. Each of them has 131 genes, comprising 85 protein-coding genes, 8 ribosomal RNA genes and 38 transfer RNA genes. After comparing the chloroplast genomes, we found 1302 base difference loci, and 63.29% are located in the intergenic region or intron sequences and 36.71% are located in the coding sequences. The SSC region has the highest mutation rate, followed by the LSC region; the IR regions have the lowest mutation rate. Among the protein-coding genes, three had a ratio of nonsynonymous to synonymous substitutions (Ka/Ks) >1 (but P values were non-significant) and 66 had Ka/Ks <1 (46 were significant). In general, the chloroplast protein-coding genes may be subject to purification selection. Among H. gyantsensis and H. rhamnoides subsp. yunnanensis chloroplast protein-coding genes, there are 20 and 16 optimal codons, respectively. Most of the optimal codons were ending with A or U, which indicates significant AT preference. It is an important reference for studies on the general characteristics and evolution of the Hippophae chloroplast genome.

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The first complete mitochondrial genome of marigold pest thrips,Neohydatothrips samayunkur(Sericothripinae) and comparative analysis

10.1101/361402 ◽

2018 ◽

Author(s):

Vikas Kumar ◽

Kaomud Tyagi ◽

Shantanu Kundu ◽

Rajasree Chakraborty ◽

Devkant Singha ◽

...

Keyword(s):

Mitochondrial Genome ◽

Ribosomal Rna ◽

Complete Mitochondrial Genome ◽

Hierarchical Level ◽

Evolutionary Relationships ◽

Protein Coding ◽

Intergenic Spacers ◽

Protein Coding Genes ◽

Scirtothrips Dorsalis ◽

Rna Genes

AbstractThe complete mitogenomes in order Thysanoptera is limited to subfamily Thripinae heretofore. In the present study, we sequenced the first mitochondrial genome ofNeohydatothrips samayunkur(15,295 bp), a member of subfamily Sericothripinae. The genome was characterized by 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three control regions (CRs). This mitogenome had two overlapping regions of 4 bp and twenty four intergenic spacers accounting for 165 bp. All the tRNA had typical cloverleaf secondary structures, except fortrnV and trnSwhich lacked DHU stem and loop. The mitogenomes ofN. samayunkurwas highly rearranged with many unique features as compared to other thrips mitogenomes,atp6andnad1were terminated with TAG and TGA stop codons respectively; location oftrnL2,trnA,trnC, andtrnVwas rearranged; and the first control region (CR1) was upstream ofnad6.The phylogenetic analysis of 13 PCGs implementing maximum likelihood and Bayesian inference showed the clustering ofN. samayunkurwithScirtothrips dorsalissupporting theScirtothripsgenus-group and Sericothripinae morphology based relationships. Generation of more mitogenomes from different hierarchical level in the order Thysanoptera is required to understand the gene rearrangements, phylogeny and evolutionary relationships.

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Complete mitogenome of Parum colligata (Lepidoptera: Sphingidae) and its phylogenetic position within the Sphingidae

Zootaxa ◽

10.11646/zootaxa.4652.1.6 ◽

2019 ◽

Vol 4652 (1) ◽

pp. 126-134 ◽

Cited By ~ 2

Author(s):

JUN LI ◽

KUNJIE HU ◽

YAQI ZHAO ◽

RUIRUI LIN ◽

YAOYAO ZHANG ◽

...

Keyword(s):

Mitochondrial Dna ◽

Ribosomal Rna ◽

Phylogenetic Analyses ◽

Transfer Rna ◽

Phylogenetic Position ◽

Rich Region ◽

Protein Coding ◽

Protein Coding Genes ◽

Complete Mitogenome ◽

Rna Genes

In this study, the complete mitochondrial DNA sequence of Parum colligata (Lepidoptera: Sphingidae: Smerinthinae) was sequenced firstly. The mitogenome is 15,288 bp in size, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and an A+T-rich region. In the mitogenome, Ile, Leu2, and Phe are the most frequently used codon families, while codons GCG, TGC, GGC, CTG, AGG, and ACG are absent. The A+T-rich region is 358 bp in length including a motif ‘ATAGA’, an 18 bp poly-T stretch, three copies of a 12 bp ‘TATATATATATA’, and a short poly-A element. The nucleotides sequence of A+T-rich region is closer to Sphinginae than Macroglossinae. Phylogenetic analyses, based on the PCGs by using Maximum Likelihood (ML) and Bayesian Inference (BI) methods, generated consistent results that Smerinthinae was clustered together with Sphinginae to be the sister groups rather than Macroglossinae.

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The complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) and its phylogenetic position in Decapoda

10.1101/2021.08.04.455109 ◽

2021 ◽

Author(s):

Longqiang Zhu ◽

Zhihuang Zhu ◽

Leiyu Zhu ◽

Dingquan Wang ◽

Jianxin Wang ◽

...

Keyword(s):

Ribosomal Rna ◽

Stop Codon ◽

Nucleotide Composition ◽

Start Codon ◽

Phylogenetic Position ◽

Base Pairs ◽

Protein Coding ◽

Protein Coding Genes ◽

Complete Mitogenome ◽

Rna Genes

In this study, the complete mitogenome of Lysmata vittata (Crustacea: Decapoda: Hippolytidae) has been determined. The genome sequence was 22003 base pairs (bp) and it included thirteen protein-coding genes (PCGs), twenty-two transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three putative control regions (CRs). The nucleotide composition of AT was 71.50%, with a slightly negative AT skewness (-0.04). Usually the standard start codon of the PCGs was ATN, while cox1, nad4L and cox3 began with TTG, TTG and GTG. The canonical termination codon was TAA, while nad5 and nad4 ended with incomplete stop codon T, and cox1 ended with TAG. We compared the order of genes of Decapoda ancestor and found that the positions of the two tRNAs genes ( trnA and trnR ) of the L. vittata were translocated. The phylogenetic tree showed that L. vittata was an independent clade, namely Hippolytidae.

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