Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete mitochondrial genome of the Papilio paris (Lepidoptera: Papilionidae).

ABSTRACT: In the present study, the complete sequence of the mitochondrial genome (mitogenome) of Papilio paris (Lepidoptera: Papilionidae) is described. The mitogenome (15,347 bp) of P. paris encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and an adenine (A) + thymine (T)-rich region. Its gene complement and order is similar to that of other sequenced Lepidopterans. Phylogenetic analyses based on 13 PCGs using maximum-likelihood (ML) revealed that P. paris resides in the Papilionoidea family. This study provided the valuable evidence on phylogenetic relationship of the P. paris at the molecular level and essential resource for further research on this species.

SUBMITTER: Sun Y

PROVIDER: S-EPMC7748820 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete mitochondrial genome of the Papilio paris (Lepidoptera: Papilionidae).

Sun Yu Y Huang Hua H Zhang Xiaojuan X Xia Jun J Geng Jian J Zhang Kai K

Mitochondrial DNA. Part B, Resources 20200120 1

In the present study, the complete sequence of the mitochondrial genome (mitogenome) of Papilio paris (Lepidoptera: Papilionidae) is described. The mitogenome (15,347 bp) of P. paris encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and an adenine (A) + thymine (T)-rich region. Its gene complement and order is similar to that of other sequenced Lepidopterans. Phylogenetic analyses based on 13 PCGs using maximum-likelihood (ML) r ...[more]

PMID: 33366725

Similar Datasets

Complete Mitochondrial Genome of Papilio protenor (Lepidoptera, Papilionidae) and Implications for Papilionidae Taxonomy

Project description:Abstract The complete mitochondrial genome (mitogenome) of Papilio protenor (Lepidoptera: Papilionidae) was sequenced and annotated in this study. The mitogenome comprised a typical circular, double-stranded DNA molecule of 15,268 bp in length including 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA (tRNA) genes, and an A+T-rich region. The gene order and mitogenome orientation were similar to those of all known Papilionidae species. The nucleotide composition of the P. protenor mitogenome exhibits considerable A+T bias (80.5%) and the AT (?0.019) and GC (?0.231) skewness is slightly negative. All of the PCGs except for cytochrome c oxidase (COI) start with a canonical ATN start codon, whereas the COI gene is tentatively designated by the CGA codon. Of the 13 PCGs, 11 contain the complete stop codon TAA or TAG, whereas COI and COII were terminated with a single T nucleotide. All tRNAs exhibit the typical cloverleaf structure, except for tRNASer(AGN), which does not contain the dihydrouridine arm. The 458 bp A+T-rich region is comprised of nonrepetitive sequences including the motif ATAGA followed by a poly-T stretch and a microsatellite-like (AT)6 element preceded by the ATTTA motif. Phylogenetic analysis of the 13 PCGs data using Bayesian inference, maximum likelihood methods, and maximum parsimony support the view that the subfamily Parnassiinae is regarded as an independent subfamily within Papilionidae and that Zerynthiini should be treated as one of the two clades of the subfamily Parnassiinae along with Parnasiini. In addition, the analysis strongly supports the monophyly of the subfamily Parnassiinae.

| S-EPMC5710649 | biostudies-literature

The complete mitochondrial genome of Papilio xuthus (Lepidoptera: Papilionidae) and implications for Papilioninae taxonomy.

Project description:The complete mitochondrial genome of Papilio xuthus (Lepidoptera: Papilionidae) was determined in this study. The mitochondrial genome is a circular molecule of 15 359 and contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. The nucleotide composition of the A. chinensis mitogenome is strongly biased toward A + T nucleotides (80.45%). Nine protein-coding genes and 14 tRNA genes are encoded on the H strand, and the other four protein-coding genes and eight tRNA genes are encoded on the L strand. The gene order and the orientation of their mitogenomes were similar to all know Papilionidae species. Finally, the phylogenetic relationships of 11 Papilionidae species were reconstructed based on complete mitochondrial genome using the Bayesian inference (BI) and the maximum-likelihood (ML) method. These molecular-based phylogenies support the traditional morphologically based view of relationships within the Papilionidae.

| S-EPMC7800277 | biostudies-literature

Complete mitochondrial genomes of Papilio nephelus chaon and Papilio epycides (Lepidoptera: Papilionidae: Papilioninae) and phylogenetic analysis.

Project description:The complete mitochondrial genome (mitogenome) sequences of Papilio nephelus chaon and Papilio epycides were sequenced by Illumina and analyzed in this study. They are 15,287 bp and 15,012 bp in size, respectively, and contains 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs), and 1 AT-rich control region (CR). The phylogenetic relationships of 56 species in the Papilionidae were inferred based on concatenated nucleotide sequences by using Maximum Likelihood with the selected best-fit model GTR + F+R6. The phylogenetic analysis showed that P. nephelus chaon and P. epycides were located in the genus Papilio. This study provides a basis for further study on mitogenome and phylogenetics of the Papilionidae.

| S-EPMC9258057 | biostudies-literature

Complete mitochondrial genome of Parnassius glacialis (Lepidoptera: Papilionidae).

Project description:Parnassius glacialis is a butterfly species distributed in China, Korea, Japan. The complete P. glacialis mitochondrial genome was assembled using Illumina sequencing data. The mitogenome is 15,353 bp long and contains 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. A phylogenetic analysis of P. glacialis and 14 related Papilionidae species indicated that P. glacialis is clustered with other Parnassius species. This study generated useful genetic information for future studies on the taxonomy, phylogeny, and evolution of Papilionidae species.

| S-EPMC8928835 | biostudies-literature

Chromosome-Level Genome Assembly of Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae).

Project description:A rarely seen butterfly species, the large swallowtail butterfly Papilio elwesi Leech, 1889 (Lepidoptera: Papilionidae), endemic to the Chinese mainland, has been declared a state-protected animal in China since 2000, but its genome is not yet available. To obtain high-quality genome assembly and annotation, we sequenced the genome and transcriptome of P. elwesi using the PacBio and PromethION platforms, respectively. The final assembled genome was 358.51 Mb, of which 97.59% was anchored to chromosomes (30 autosomes and 1 Z sex chromosome), with a contig/scaffold N50 length of 6.79/12.32 Mb and 99.0% (n = 1367) BUSCO completeness. The genome annotation pointed to 36.82% (131.99 Mb) repetitive elements and 1296 non-coding RNAs in the genome, along with 13,681 protein-coding genes that cover 98.6% (1348) of the BUSCO genes. Among the 11,499 identified gene families, 104 underwent significantly rapid expansions or contractions, and these rapidly expanding families play roles in detoxification and metabolism. Additionally, strong synteny exists between the chromosomes of P. elwesi and P. machaon. The chromosome-level genome of P. elwesi could serve as an important genomic resource for furthering our understanding of butterfly evolution and for more in-depth genomic analyses.

| S-EPMC10058580 | biostudies-literature

The complete mitochondrial genome of Parnassius mercurius Grum-Grshimailo (Lepidoptera: Papilionidae: Parnassiinae).

Project description:The mitogenome of Parnassius mercurius Grum-Grshimailo is determined to be 15,372 bp in length, including 37 typical insect mitochondrial genes and an AT-rich region. All PCGs start with ATN, except for COI with CGA; 12 of 13 PCGs harbour the common stop codon TAA or TAG, whereas COII end with a single T. The lrRNA and srRNA genes are 1344 bp and 775 bp in length, respectively. The AT-rich region contains several features characteristic of the lepidopterans. Phylogenetic analysis shows that P. mercurius is the closest relative of P. epaphus and P. nomion lineage, rather than the P. jacquemontii.

| S-EPMC7748828 | biostudies-literature

The complete mitochondrial genome of Luehdorfia chinensis Leech (Lepidoptera: Papilionidae) from China.

Project description:The complete mitochondrial genome of Luehdorfia chinensis that is endemic to China is determined. The circular genome is 15 550 bp in length and comprises 13 protein-coding genes (PCGs), 22 tRNAs, two rRNA gene and a control region. Gene order is identical to that of the putative ancestral arrangement of insects. The nucleotide composition of heavy strand is A (40.3%), C (11.2%), T (41.1%) and G (7.3%). All PCGs start with a typical ATN codon except for the gene COI that uses AAC as the start codon. Bayesian analyses support the monophyly of genus Papilio and the sister relationship of Luehdorfia chinensis and L. taibai.

| S-EPMC7799615 | biostudies-literature

Genome-Wide Analysis of Odorant and Gustatory Receptors in Six Papilio Butterflies (Lepidoptera: Papilionidae).

Project description:The chemical interactions of insects and host plants are shaping the evolution of chemosensory receptor gene families. However, the correlation between host range and chemoreceptor gene repertoire sizes is still elusive in Papilionidae. Here, we addressed the issue of whether host plant diversities are correlated with the expansions of odorant (ORs) or gustatory (GRs) receptors in six Papilio butterflies. By combining genomics, transcriptomics and bioinformatics approaches, 381 ORs and 328 GRs were annotated in the genomes of a generalist P. glaucus and five specialists, P. xuthus, P. polytes, P. memnon, P. machaon and P. dardanus. Orthologous ORs or GRs in Papilio had highly conserved gene structure. Five Papilio specialists exhibited a similar frequency of intron lengths for ORs or GRs, but which was different from those in the generalist. Phylogenetic analysis revealed 60 orthologous OR groups, 45 of which shared one-to-one relationships. Such a single gene in each butterfly also occurred in 26 GR groups. Intriguingly, bitter GRs had fewer introns than other GRs and clustered into a large clade. Focusing on the two chemoreceptor gene families in P. xuthus, most PxutORs (52/58) were expressed in antennae and 31 genes in reproductive tissues. Eleven out of 28 foretarsus-expressed PxutGRs were female-biased genes, as strong candidates for sensing oviposition stimulants. These results indicate that the host range may not shape the large-scale expansions of ORs and GRs in Papilio butterflies and identify important molecular targets involved in olfaction, oviposition or reproduction in P. xuthus.

| S-EPMC9500883 | biostudies-literature

Ooencyrtus pitosina (Hymenoptera: Encyrtidae)-A natural enemy of Samoan swallowtail butterfly Papilio godeffroyi (Lepidoptera: Papilionidae).

Project description:A new species of encyrtid wasp, Ooencyrtus pitosina Polaszek, Noyes & Fusu sp. n., (Hymenoptera: Encyrtidae: Encyrtinae) is described as a gregarious parasitoid in the eggs of the endemic Samoan swallowtail butterfly Papilio godeffroyi (Lepidoptera: Papilionidae) in the Samoan archipelago. It is described here because it is an important natural enemy of this butterfly, and to facilitate identification for future work with this parasitoid and its host.

| S-EPMC10411748 | biostudies-literature

Comparative analysis on visual and olfactory signals of Papilio xuthus (Lepidoptera: Papilionidae) during foraging and courtship.

Project description:This study examined the roles of visual and olfactory responses during foraging and courtship in butterfly Papilio xuthus. P. xuthus showed obvious orientation to color in the range of 350-500 nm. Visits of P. xuthus females and males to blue, purple, and red artificial cloth flowers were ♀ 54.90% and ♂ 39.22%, ♀ 19.61% and ♂ 35.29%, and ♀ 9.80% and ♂ 19.61%, respectively. Application of 10% honey on these artificial flowers resulted in an increase of 3.41 and 3.26 fold in flower visits by the butterfly compared to controls. When 10% honey water was sprayed on flower branches without colorful flowers, branch visiting was very low, only seven times for females and two times for males, indicating that colors might be more critical than odor for foraging even though visual and olfactory perceptions both play important roles during foraging. During courtship, four types of chasing were observed in a natural population of P. Xuthus; the four types are males chasing females (49%), males chasing males (25%), females chasing males (13%), and females chasing females (10%). However, when odorless artificial models of butterflies were used, no significant differences were observed among these types of chasing, indicating that olfactory perception was crucial for the butterfly during courtship. Profiling volatile organic chemicals (VOCs) and individual bioassays revealed that VOCs contents of butterflies were not related to recognizing sex partners; by contrast, some level of α-farnesene, increased the frequency of male chasing female. This could be due to that α-farnesene is easy to be detected by butterflies because of its volatility and higher content in female.

| S-EPMC9242464 | biostudies-literature