scholarly journals Systematics of Vriesea (Bromeliaceae): phylogenetic relationships based on nuclear gene and partial plastome sequences

2019 ◽  
Vol 192 (4) ◽  
pp. 656-674 ◽  
Author(s):  
Talita Mota Machado ◽  
Oriane Loiseau ◽  
Margot Paris ◽  
Anna Weigand ◽  
Leonardo M Versieux ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Nuclear Gene ◽  
Evolutionary Relationships ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
A Genome ◽  
Genome Skimming

Abstract Vriesea is the second largest genus in Tillandsioideae, the most diverse subfamily of Bromeliaceae. Although recent studies focusing on Tillandsioideae have improved the systematics of Vriesea, no consensus has been reached regarding the circumscription of the genus. Here, we present a phylogenetic analysis of core Tillandsioideae using the nuclear gene phyC and plastid data obtained from genome skimming. We investigate evolutionary relationships at the intergeneric level in Vrieseeae and at the intrageneric level in Vriesea s.s. We sampled a comprehensive dataset, including 11 genera of Tillandsioideae and nearly 50% of all known Vriesea spp. Using a genome skimming approach, we obtained a 78 483-bp plastome alignment containing 35 complete and 55 partial protein-coding genes. Phylogenetic trees were reconstructed using maximum-likelihood based on three datasets: (1) the 78 483 bp plastome alignment; (2) the nuclear gene phyC and (3) a concatenated alignment of 18 subselected plastid genes + phyC. Additionally, a Bayesian inference was performed on the second and third datasets. These analyses revealed that Vriesea s.s. forms a well-supported clade encompassing most of the species of the genus. However, our results also identified several remaining issues in the systematics of Vriesea, including a few species nested in Tillandsia and Stigmatodon. Finally, we recognize some putative groups within Vriesea s.s., which we discuss in the light of their morphological and ecological characteristics.

scholarly journals Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yu Sun ◽  
Hua Huang ◽  
Yudong Liu ◽  
Shanshan Liu ◽  
Jun Xia ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Base Pairs ◽  
Rich Region ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Lepidopteran Insects

AbstractIn this study, we analyzed the complete mitochondrial genome (mitogenome) of Speiredonia retorta, which is a pest and a member of the Lepidoptera order. In total, the S. retorta mitogenome was found to contain 15,652 base pairs encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, as well as an adenine (A) + thymine (T)-rich region. These findings were consistent with the mitogenome composition of other lepidopterans, as we identified all 13 PCGs beginning at ATN codons. We also found that 11 PCGs terminated with canonical stop codons, whereas cox2 and nad4 exhibited incomplete termination codons. By analyzing the mitogenome of S. retorta using Bayesian inference (BI) and maximum likelihood (ML) models, we were able to further confirm that this species is a member of the Erebidae family.

scholarly journals Complete mitochondrial genome of the freshwater fish Onychostoma lepturum (Teleostei, Cyprinidae): genome characterization and phylogenetic analysis

ZooKeys ◽  
2020 ◽  
Vol 1005 ◽  
pp. 57-72
Author(s):  
I-Chen Wang ◽  
Hung-Du Lin ◽  
Chih-Ming Liang ◽  
Chi-Chun Huang ◽  
Rong-Da Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Genomic Variation ◽  
Rrna Genes ◽  
Valid Species ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes

The cyprinid genus Onychostoma Günther, 1896 consists of 24 valid species distributed in Southeast Asia, including Taiwan, Hainan, mainland China and the Indochina region. In the present study, we determined the complete mitochondrial genome of O. lepturum, which is 16,598 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a typical control region (D-loop). To verify the molecular phylogeny of the subfamily Acrossocheilinae, we provide new insights to better understand the taxonomic status of Acrossocheilus, Onychostoma and Folifer brevifilis. The phylogenetic trees presented three major clades based on the 13 protein-coding genes from 28 Acrossocheilinae species. Clades I and II represent the Onychostoma and Acrossocheilus groups, respectively. Species of Acrossocheilus, Onychostoma and F. brevifilis are included in Clade III, which is considered as an ancestral group. This work provides genomic variation information and improves our understanding of the Acrossocheilinae mitogenome, which will be most valuable in providing new insights for phylogenetic analysis and population genetics research.

scholarly journals Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae)

ZooKeys ◽  
2020 ◽  
Vol 969 ◽  
pp. 23-42
Author(s):  
Qiu Zhongying ◽  
Chang Huihui ◽  
Yuan Hao ◽  
Huang Yuan ◽  
Lu Huimeng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Bayesian Inference ◽  
Mitochondrial Genomes ◽  
Rich Region ◽  
Stem Loop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Relationship Of ◽  
Complete Mitochondrial Genomes

In this study, the whole mitochondrial genomes (mitogenomes) from four species were sequenced. The complete mitochondrial genomes of Sinopodisma pieli, S. houshana, S. qinlingensis, and S. wulingshanensis are 15,857 bp, 15,818 bp, 15,843 bp, and 15,872 bp in size, respectively. The 13 protein-coding genes (PCGs) begin with typical ATN codons, except for COXI in S. qinlingensis, which begins with ACC. The highest A+T content in all the sequenced orthopteran mitogenomes is 76.8% (S. qinlingensis), followed by 76.5% (S. wulingshanensis), 76.4% (S. pieli) and 76.4% (S. houshana) (measured on the major strand). The long polythymine stretches (T-stretch) in the A+T-rich region of the four species are not adjacent to the trnI locus but are inside the stem-loop sequences on the major strand. Moreover, several repeated elements are found in the A+T-rich region of the four species. Phylogenetic analysis based on 53 mitochondrial genomes using Bayesian Inference (BI) and Maximum Likelihood (ML) revealed that Melanoplinae (Podismini) was a monophyletic group; however, the monophyly of Sinopodisma was not supported. These data will provide important information for a better understanding of the phylogenetic relationship of Melanoplinae.

scholarly journals The complete mitochondrial genome of the Golden Birdwing butterfly Troides aeacus: insights into phylogeny and divergence times of the superfamily Papilionoidea

2019 ◽  
Author(s):  
Si-Yu Dong ◽  
Guo-Fang Jiang ◽  
Gang Liu ◽  
Fang Hong ◽  
Yu-Feng Hsu
Keyword(s):  
Bayesian Inference ◽  
Mitochondrial Genome ◽  
Phylogenetic Trees ◽  
Complete Mitochondrial Genome ◽  
Divergence Times ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
High Bootstrap ◽  
Molecular Dataset ◽  
Troides Aeacus

AbstractBackgroundThe Lepidoptera is one of the largest insect orders. Previous studies on the evolution of Lepidoptera did not confidently place butterflies, and many relationships among superfamilies in the megadiverse clade Ditrysia remain largely uncertain. Here, we generated a molecular dataset with 78 species of lepidopterian insects, including a new complete mitochondrial genome (mitogenome) sequences of the Golden Birdwing Butterfly, Troides aeacus, which was listed in appendix II of CITES.MethodsBased on the concatenated nucleotide sequences of 13 protein-coding genes, we constructed phylogenetic trees with Bayesian Inference (BI) and Maximum Likelihood (ML) methods, and calculated the divergence times of Lepidoptera.ResultsMonophyly of the Papilionoidea including skippers (Hesperiidae) is strongly supported by a high bootstrap value. Butterflies were placed sister to the remaining obtectomeran Lepidoptera, and the latter was grouped with high bootstrap supports. Additionally, Papilionidae probably diverged from the group (Hesperiidae + (Nymphalidae + Pieridae)) at 102.65 Mya, the Early Cretaceous. T. aeacus and the Golden kaiserihind Teinopalpus aureus diverged in the Cretaceous of 85.32 Mya. The age of Papilionoidea indicates that the primary break up of Gondwana may have an effect on the current distributions of butterflies.

scholarly journals Mitogenome and phylogenetic analysis of typhlocybine leafhoppers (Hemiptera: Cicadellidae)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jia Jiang ◽  
Xiaoxiao Chen ◽  
Can Li ◽  
Yuehua Song
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Study ◽  
Phylogenetic Trees ◽  
Tandem Repeats ◽  
Morphological Characters ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Tree Topologies ◽  
Complete Mitogenome

AbstractMitogenomes have been widely used to estimate phylogenetic relationships among insects and provide data useful for augmenting traditional morphological characters in delimiting species. Here, complete mitogenome sequences of two closely related typhlocybine leafhoppers, Cassianeuracassiae (Ahmed, 1970) and C. bimaculata Dworakowska, 1984, were obtained and found to be 15,423 bp and 14,597 bp in length, respectively. The gene order was found to be similar to other published leafhopper mitogenomes, but the control region of C.bimaculata is the shortest among known leafhoppers and lacks tandem repeats. Phylogenetic analysis of 13 protein-coding genes (PCGs), the first and second codons of 13 PCGs, 13 PCGs and two rRNAs formed three well-supported tree topologies. The topologies of phylogenetic trees inferred from three datasets were almost identical, which was consistent with previous molecular phylogenies of this group. Comparative morphological study of the ovipositors revealed several characters potentially useful for diagnosing genera and resolving their phylogenetic relationships. Phylogenetic analysis of these and other morphological characters yielded a tree that is mostly consistent with the tree obtained from analysis of mitogenome sequences. In both molecular and morphological phylogenenies, Typhlocybini and Zyginellini clustered into one clade, but neither was recovered as monophyletic.

scholarly journals Exploring the relationship of Homalosilpha and Mimosilpha (Blattodea, Blattidae, Blattinae) from a morphological and molecular perspective, including a description of four new species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10618
Author(s):  
Shuran Liao ◽  
Yishu Wang ◽  
Duting Jin ◽  
Rong Chen ◽  
Zongqing Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Close Relationship ◽  
Relationship Of ◽  
The Relationship ◽  
Six Genes

This study utilized six genes (12S, 16S, 18S, 28S, COII and H3) from a total of 40 samples to construct maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees in order to infer the relationships between the morphologically similar genera Homalosilpha Stål, 1874 and Mimosilpha Bey-Bienko, 1957. The phylogenetic analysis showed the two genera have a close relationship and were recovered as sister groups based on ML and BI analyses. Four new species are described among these samples, i.e., Homalosilpha obtusangula sp. nov., Homalosilpha recta sp. nov., Homalosilpha alba sp. nov. and Homalosilpha clavellata sp. nov. based on morphological and COI data. A key to the worldwide Homalosilpha is provided.

Two new mitogenomes of Pellorneidae (Aves : Passeriformes) and a phylogeny of the superfamily Sylvioidea

2018 ◽  
Vol 66 (3) ◽  
pp. 167 ◽  
Author(s):  
Zuhao Huang ◽  
Feiyun Tu ◽  
Shan Tang
Keyword(s):  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Family Level ◽  
Partitioned Data ◽  
Control Regions

The superfamily Sylvioidea contains the most diversified species within the Passerida. The grey-cheeked fulvetta (Alcippe morrisonia) and the eyebrowed wren-babbler (Napothera epilepidota) are birds with a weak flight that live in lightly wooded or scrubland environments. In the present study, two new mitogenomes of A. morrisonia (KX376475) and N. epilepidota (KX831093) within the superfamily Sylvioidea were sequenced and their total lengths were 17788bp and 17913bp, respectively. Both mitogenomes comprised 13 protein-coding genes, 22 tRNAs, 2 rRNAs and two control regions (CR and CCR). Similar to most metazoans, both mitogenomes and their protein-coding genes encoded on the H-strand displayed typical positive AT skews and negative GC skews. Bayesian inference and maximum-likelihood phylogenetic analyses were conducted on the basis of partitioned data of mitogenomes and two identical topologies were observed. The family-level phylogenetic relationships ((((Pellorneidae, Leiothrichidae) Timaliidae) Zosteropidae) Sylviidae) among the superfamily Sylvioidea were strongly supported. Within the family Pellorneidae, A. morrisonia clustered with N. epilepidota. Within Leiothrichidae, we further demonstrated that Babax lanceolatus is sister to Garrulax perspicillatus, and Spizixos semitorques was nested within the genus Pycnonotus according to the mitogenomic data and we propose that the generic placement of Spizixos should be reconsidered.

scholarly journals Complete mitochondrial genome of Prismognathus prossi (Coleoptera: Lucanidae) with phylogenetic implications

2019 ◽  
Vol 30 (2) ◽  
pp. 90-96 ◽  
Author(s):  
Y. Cao ◽  
J. Liu ◽  
S. Zhou ◽  
Y. Chen ◽  
X. Wan
Keyword(s):  
Next Generation Sequencing ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Nucleotide Composition ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenetic Implications ◽  
Generation Sequencing

The complete mitochondrial genome of a Chinese stag beetle, Prismognathus prossi, was generated using the Illumina next-generation sequencing. The mitogenome sequence is 15,984 bp in length, the nucleotide composition isA 36.6%, C17.5%, T34.3% andG11.6%with theAT-content of 70.9%. The sequence has similar features with other reported insectmitogenomes, consisting of 13 proteincoding genes (PCGs), 22 transferRNAgenes, tworibosomalRNAsand a control region. All of the protein-coding genes start with the typicalATNinitiation codon except for COI. Maximum Likelihood (ML) and Bayesian Inference (BI) indicated that P. prossi share an affinity with Lucanus mazama, Lucanus fortunei and Cyclommatus vitalisi.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals The genome sequence of the European peacock butterfly, Aglais io (Linnaeus, 1758)

2021 ◽  
Vol 6 ◽  
pp. 258
Author(s):  
Konrad Lohse ◽  
Alexander Mackintosh ◽  
Roger Vila ◽  
◽  
◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Sex Chromosome ◽  
Gene Annotation ◽  
Protein Coding ◽  
Individual Male ◽  
Protein Coding Genes ◽  
A Genome ◽  
Inachis Io

We present a genome assembly from an individual male Aglais io (also known as Inachis io and Nymphalis io) (the European peacock; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 384 megabases in span. The majority (99.91%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Gene annotation of this assembly on Ensembl has identified 11,420 protein coding genes.

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