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The complete mitochondrial genome of the Lutjanus ehrenbergii was sequenced by Sanger platform. The circular mitogenome of L. ehrenbergii (16,512 bp) encoded the typical 37 genes, and one non-coding regions. All of the protein-encoding genes were located on the H chain except ND6. The nucleotide composition was A (28.04%), T (24.84%), C (30.89%) and G (16.23%). Phylogenetic analysis based on the 13PCGs sequences showed that L. ehrenbergii was closely related to the sister species of Lutjanus russellii and Lutjanus carponotatus. These studies provided important mitochondrial genome data of L. ehrenbergii, phylogenetic tree analysis revealed the position of L. ehrenbergii in Lutjaniformes.

Abstract The barn swallow (Hirundo rustica) poses a number of fascinating scientific questions, including the taxonomic status of postulated subspecies. Here, we obtained and assessed the sequence variation of 411 complete mitogenomes, mainly from the European H. r. rustica, but other subspecies as well. In almost every case, we observed subspecies-specific haplogroups, which we employed together with estimated radiation times to postulate a model for the geographical and temporal worldwide spread of the species. The female barn swallow carrying the Hirundo rustica ancestral mitogenome left Africa (or its vicinity) around 280 thousand years ago (kya), and her descendants expanded first into Eurasia and then, at least 51 kya, into the Americas, from where a relatively recent (<20 kya) back migration to Asia took place. The exception to the haplogroup subspecies specificity is represented by the sedentary Levantine H. r. transitiva that extensively shares haplogroup A with the migratory European H. r. rustica and, to a lesser extent, haplogroup B with the Egyptian H. r. savignii. Our data indicate that rustica and transitiva most likely derive from a sedentary Levantine population source that split at the end of the Younger Dryas (YD) (11.7 kya). Since then, however, transitiva received genetic inputs from and admixed with both the closely related rustica and the adjacent savignii. Demographic analyses confirm this species’ strong link with climate fluctuations and human activities making it an excellent indicator for monitoring and assessing the impact of current global changes on wildlife.

Here, we report the complete mitochondrial (mt) genome of Antheraea pernyi Qing_6, an improved strain serving silk production and edible insect resource for 50 years in Northeast China. The circular mt genome spans 15,572 bp in length and contains 37 typical coding genes (13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes). Its A + T-rich region is 552 bp in size exhibiting identical sequence with the first modern improved strain Qinghuang_1. Comparison analysis identified only 12 variable sites (5 substitutions and 7 indels) between Qing_6 and Qinghuang_1. The phylogenetic analysis also clustered Qing_6 and Qinghuang_1 together first, which was in line with the breeding history of the two strains.

GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” approach, conducts de novo assembly, filters and disentangles the assembly graph, and produces all possible configurations of circular organelle genomes. For 50 published plant datasets, we are able to reassemble the circular plastomes from 47 datasets using GetOrganelle. GetOrganelle assemblies are more accurate than published and/or NOVOPlasty-reassembled plastomes as assessed by mapping. We also assemble complete mitochondrial genomes using GetOrganelle. GetOrganelle is freely released under a GPL-3 license ( https://github.com/Kinggerm/GetOrganelle ).

The complete mitochondrial genome of the New Zealand parasitic nematode Teladorsagia circumcincta field strain NZ_Teci_NP was sequenced and annotated. The 14,083 bp-long mitogenome contains 12 protein-coding genes (atp8 gene missing), two ribosomal RNAs (rRNAs), and 22 transfer RNAs (tRNAs). Phylogenetic analysis showed that T. circumcincta NZ_Teci_NP forms a monophyletic cluster with the remaining Haemonchidae species and further reinforces the high levels of diversity and gene flow observed among Trichostrongylidae.

Teinopalpus aureus Mell (Lepidoptera: Papilionidae) is distributed throughout China, Vietnam and Laos, and is listed as a Class I species in China. To identify whether the exuviae of larva is belonging to Teinopalpus aureus Mell, 1923 or not, and to compare the gene structure and genetic differences among the known populations, ten mitogenomes of T. aureus from the exuviae of larva collected in the Michelia maudiae were sequenced. This method of sequencing the mitogenomes of exuviae of larva can give us the chance to monitor the conservation of rare butterflies. Ten mitogenomes of T. aureus showed typical gene arrangements and contained 13 protein-coding genes (PCGs), two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). The two haplotypes with one base different in T. aureus were found. We also conducted phylogenetic analyses including all different populations of T. aureus to assess the phylogenetic relationship of T. aureus. The lengths of the 12S rRNA and 16S rRNA genes from both haplotypes were 776 base pairs (bp) and 1,334 bp, respectively. The genetic distance of the ten samples was calculated as 0-0.000065 on the basis of the whole mitogenomes. T. aureus found in Taishun, Zhejiang province, China had a close phylogenetic relationship with the clade of T. aureus found in Pingshan, Jiangxi province, China, which was supported by neighbour-joining analysis.

The complete mitochondrial genome of the New Zealand parasitic nematode Haemonchus contortus field strain NZ_Hco_NP was sequenced and annotated. The 14,001 bp-long mitogenome contains 12 protein-coding genes (atp8 gene missing), two ribosomal RNAs, 22 transfer RNAs, and a 583 bp non-coding region. Phylogenetic analysis showed that H. contortus NZ_Hco_NP forms a monophyletic cluster with the remaining three Haemonchidae species, and further illustrates the high levels of diversity and gene flow among Trichostrongylidae.

Background  PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more accurate and contiguous genomes. In eukaryotes the mitochondrial genome is sequenced alongside the nuclear genome often at very high coverage. A dedicated tool for mitochondrial genome assembly using HiFi reads is still missing. Results  MitoHiFi was developed within the Darwin Tree of Life Project to assemble mitochondrial genomes from the HiFi reads generated for target species. The input for MitoHiFi is either the raw reads or the assembled contigs, and the tool outputs a mitochondrial genome sequence fasta file along with annotation of protein and RNA genes. Variants arising from heteroplasmy are assembled independently, and nuclear insertions of mitochondrial sequences are identified and not used in organellar genome assembly. MitoHiFi has been used to assemble 374 mitochondrial genomes (368 Metazoa and 6 Fungi species) for the Darwin Tree of Life Project, the Vertebrate Genomes Project and the Aquatic Symbiosis Genome Project. Inspection of 60 mitochondrial genomes assembled with MitoHiFi for species that already have reference sequences in public databases showed the widespread presence of previously unreported repeats. Conclusions  MitoHiFi is able to assemble mitochondrial genomes from a wide phylogenetic range of taxa from Pacbio HiFi data. MitoHiFi is written in python and is freely available on GitHub ( https://github.com/marcelauliano/MitoHiFi ). MitoHiFi is available with its dependencies as a Docker container on GitHub (ghcr.io/marcelauliano/mitohifi:master).

We, the Editor, authors and Publisher of Mitochondrial DNA Part B: Resources, have retracted the following article: Qiang Li, Xin Jin, Zuqin Chen, Chuan Xiong, Ping Li & Wenli Huang (2019) 'Characterization of the complete mitochondrial genome of an important edible fungus Auricularia Polytricha' 4:1, 1107-1108, DOI https://doi.org/10.1080/23802359.2019.1586494 . This article has been retracted at the request of the authors as, subsequent to publication, it has been identified that the species reported in the article is incorrect. The species should be Suillus sp. and not Auricularia polytricha as reported. The article has therefore been retracted as the data reported in the article are inaccurate. We have been informed in our decision-making by our policy on publishing ethics and integrity and the COPE guidelines on retractions. The retracted article will remain online to maintain the scholarly record, but it will be digitally watermarked on each page as \"Retracted\".

In the present research, the mitochondrial genome of Ephemera serica was sequenced through next generation sequencing methods and its phylogenetic position in Ephemeroptera was analyzed. Total mitochondrial genome is 15,004 bp in length, and contains 13 protein coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Mitogenomic phylogeny trees were constructed including 45 species from 13 families. The results show that E. serica is closely related to E. rufomaculata.