The complete mitogenome of Lamproptera curia (Lepidoptera: Papilionidae) and phylogenetic analyses of Lepidoptera

Abstract Mitochondrial genome rearrangements have been used for defining historical relationships, but there have been incidences of convergences at different taxonomic levels. Here, we sequenced complete mitogenome of Aleurodicus rugioperculatus (Aleyrodidae: Aleurodicinae) to examine gene rearrangements and phylogenetic relationships within the family Aleyrodidae. We identified five gene blocks (I-V) in the whitefly ancestor that are shared plesiomorphies retained in different whitefly lineages. Gene block I is conserved in all whiteflies except three species (Tetraleurodes acaciae and two Bemisia species). Conversely, we detected 83 derived gene boundaries within the family. Mapping these gene boundaries onto a phylogenetic tree revealed that 16 were symplesiomorphies for two subfamilies; 9 were synapomorphies at different taxonomic levels, and 28 autapomorphies for individual species. Bayesian Inference (BI) and Maximum Likelihood (ML) phylogenetic analyses yielded similar topologies supporting the monophyly of Aleyrodinae and Aleurodicinae. Exclusion of PCG third codon positions from phylogenetic analyses improved both node support and consistency with prior analyses. To understand the significance of gene order convergence on phylogeny of the whiteflies, more species-level data is required.

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Genomic Skimming and Nanopore Sequencing Uncover Cryptic Hybridization in One of World's Most Threatened Primates

10.1101/2021.04.16.440058 ◽

2021 ◽

Author(s):

Joanna Malukiewicz ◽

Reed Austin Cartwright ◽

Jorge A Dergam ◽

Claudia S Igayara ◽

Patricia A Nicola ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Genomic Data ◽

Nanopore Sequencing ◽

Model Species ◽

Direct Dna Sequencing ◽

Technical Requirements ◽

Exotic Invasive ◽

Complete Mitogenome ◽

Diversity Estimates ◽

Callithrix Aurita

The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world's most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.

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Phylogenetic analyses of the harvest mouse, Micromys minutus (Rodentia: Muridae) based on the complete mitogenome sequences

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2015.08.004 ◽

2015 ◽

Vol 62 ◽

pp. 121-127 ◽

Cited By ~ 3

Author(s):

Jie Jing ◽

Xuhao Song ◽

Chaochao Yan ◽

Ting Lu ◽

Xiuyue Zhang ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Complete Mitogenome ◽

Harvest Mouse ◽

Micromys Minutus

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Complete mitogenome of endemic Plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis

10.1101/2020.10.09.332866 ◽

2020 ◽

Author(s):

Prateek Dey ◽

Sanjeev Kumar Sharma ◽

Indrani Sarkar ◽

Swapna Devi Ray ◽

Padmnabhan Pramod ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Purifying Selection ◽

Mitochondrial Control Region ◽

Scientific Basis ◽

Illegal Trade ◽

Protein Coding ◽

Complete Mitogenome ◽

Usage Analysis ◽

Phylogenetic Revision

AbstractPsittacula cyanocephala is a parakeet endemic to the Indian sub-continent, widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting further studies to resolve such issues. Since the mitochondrial genome provides useful information about a species concerning its evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species, scientific basis for phylogenetic revision of genus Psittacula.

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Complete Mitogenome of Endangered and Endemic Nicobar Treeshrew (Tupaia Nicobarica) and Comparison with Other Scandentians

10.21203/rs.3.rs-880056/v1 ◽

2021 ◽

Author(s):

Shantanu Kundu ◽

Avas Pakrashi ◽

Manokaran Kamalakannan ◽

Devkant Singha ◽

Kaomud Tyagi ◽

...

Keyword(s):

Mitochondrial Genome ◽

Biomedical Research ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Andaman Sea ◽

Nicobar Island ◽

Taxonomic Rank ◽

Strong Negative Selection ◽

Complete Mitogenome

Abstract The Nicobar treeshrew (Tupaia nicobarica) is an endangered smaller mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate evolutionary relationship. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (ML and BA) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (11.4 to 18.8 MYR) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. The present study suggests the assembly of whole-genome to improve the understanding of evolutionary relationships of treeshrews and its implication in biomedical research.

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The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora

PeerJ ◽

10.7717/peerj.8603 ◽

2020 ◽

Vol 8 ◽

pp. e8603

Author(s):

Özgül Doğan ◽

Michael Schrödl ◽

Zeyuan Chen

Keyword(s):

Phylogenetic Analyses ◽

Divergence Time ◽

Invasive Pest ◽

Sister Group Relationship ◽

Trna Genes ◽

Agricultural Pests ◽

Protein Coding ◽

Atp Production ◽

Arion Vulgaris ◽

Complete Mitogenome

Stylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Arion vulgaris Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of A. vulgaris measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for COX1, ND5 and ATP8 and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for trnC and trnS1 (AGN). Phylogenetic analyses confirmed the position of A. vulgaris within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of A. vulgaris and Arion rufus (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth’s most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (ATP8, COX1, COX3, ND3, ND4 and ND6) detected by the branch-specific aBSREL approach and three genes (ATP8, CYTB and ND4L) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of trnW-trnY and of trnE-trnQ-rrnS-trnM-trnL2-ATP8-trnN-ATP6-trnR clusters for the genus Arion. Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes.

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Genomic skimming and nanopore sequencing uncover cryptic hybridization in one of world’s most threatened primates

Scientific Reports ◽

10.1038/s41598-021-96404-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Joanna Malukiewicz ◽

Reed A. Cartwright ◽

Jorge A. Dergam ◽

Claudia S. Igayara ◽

Patricia A. Nicola ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Genomic Data ◽

Nanopore Sequencing ◽

Model Species ◽

Direct Dna Sequencing ◽

Technical Requirements ◽

Exotic Invasive ◽

Complete Mitogenome ◽

Diversity Estimates ◽

Callithrix Aurita

AbstractThe Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available for C. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified as C. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with a C. aurita phenotype and C. penicillata mitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates for C. aurita and three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such as C. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies of C. aurita and other marmosets.

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Sarcopeltis gen. nov. (Gigartinaceae, Rhodophyta), with S. skottsbergii comb. nov. from southern South America and S. antarctica sp. nov. from the Antarctic Peninsula

Phytotaxa ◽

10.11646/phytotaxa.468.1.4 ◽

2020 ◽

Vol 468 (1) ◽

pp. 75-88

Author(s):

JEFFERY R. HUGHEY ◽

GEOFFREY L. LEISTER ◽

PAUL W. GABRIELSON ◽

MAX H. HOMMERSAND

Keyword(s):

South America ◽

Antarctic Peninsula ◽

Dna Sequences ◽

Phylogenetic Analyses ◽

New Genus And Species ◽

Southern South America ◽

Complete Mitogenome ◽

Next Generation Sequencing Ngs ◽

The Antarctic ◽

Generation Sequencing

Gigartina skottsbergii is the currently accepted name for the large, peltate species of Gigartinaceae distributed in Argentina, Chile, and along the Antarctic Peninsula. However, phylogenetic analyses of DNA sequences for more than twenty years indicate that two species are passing under the name G. skottsbergii, and both DNA sequences and morpho-anatomy indicate that the species are assignable to an undescribed genus. To formally validate the new genus and species, we performed next generation sequencing (NGS) on the lectotype material of G. skottsbergii to document its genetic identity and obtained its complete mitogenome and partial plastid genome. Phylogenetic analysis of rbcL and cox1 sequences of the lectotype along with recent collections of G. skottsbergii from southern South America and Antarctica, confirmed the generic distinction and the presence of two morphologically similar taxa. We propose Sarcopeltis gen. nov., containing the generitype S. skottsbergii comb. nov. from southern South America, and S. antarctica sp. nov. from the Antarctic Peninsula. Sarcopeltis is characterized by the following suite of features: 1) peg-like secondary haptera that adhere to the substratum, 2) absence of an envelope surrounding each cystocarp, 3) presence of extensive, terminal, tubular gonimoblast filaments that fuse with surrounding vegetative cells, and 4) tetrasporangia formed from secondary filaments entirely in the medulla. This study demonstrates that genetic analysis of type material, together with recently obtained DNA sequences from field collected specimens, can provide clear and objective taxonomic conclusions.

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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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Unique Duplication of trnN in Odontoptilum angulatum (Lepidoptera: Pyrginae) and Phylogeny within Hesperiidae

Insects ◽

10.3390/insects12040348 ◽

2021 ◽

Vol 12 (4) ◽

pp. 348

Author(s):

Jiaqi Liu ◽

Jintian Xiao ◽

Xiangyu Hao ◽

Xiangqun Yuan

Keyword(s):

Phylogenetic Analysis ◽

Gene Rearrangement ◽

Tandem Duplication ◽

Sequence Similarity ◽

Phylogenetic Signal ◽

Phylogenetic Analyses ◽

Taxon Sampling ◽

Coding Region ◽

Rich Region ◽

Complete Mitogenome

To explore the variation and relationship between gene rearrangement and phylogenetic effectiveness of mitogenomes among lineages of the diversification of the tribe Tagiadini in the subfamily Pyrginae, we sequenced the complete mitogenome of Odontoptilum angulatum. The genome is 15,361 bp with the typical 37 genes, a large AT-rich region and an additional trnN (trnN2), which is completely identical to trnN (sequence similarity: 100%). The gene order differs from the typical Lepidoptera-specific arrangement and is unique to Hesperiidae. The presence of a “pseudo-trnS1” in the non-coding region between trnN1 and trnN2 supports the hypothesis that the presence of an extra trnN can be explained by the tandem duplication-random loss (TDRL) model. Regarding the phylogenetic analyses, we found that the dataset comprising all 37 genes produced the highest node support, as well as a monophyly of Pyrginae, indicating that the inclusion of RNAs improves the phylogenetic signal. Relationships among the subfamilies in Hesperiidae were also in general agreement with the results of previous studies. The monophyly of Tagiadini is strongly supported. Our study provides a new orientation for application of compositional and mutational biases of mitogenomes in phylogenetic analysis of Tagiadini and even all Hesperiidae based on larger taxon sampling in the future.

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