Assembly Of Mitochondrial Genomes Research Articles

The genome sequence of purple glasswort, Salicornia ramosissima Woods (Amaranthaceae)

We present a genome assembly from an individual Salicornia ramosissima (purple glasswort; Tracheophyta; Magnoliopsida; Caryophyllales; Chenopodiaceae). The genome sequence is 529.1 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 328.55 kilobases and 153.3 kilobases in length, respectively.

Comparative mitochondrial genomics of endemic Mexican vesper yellow bats genus Rhogeessa (Chiroptera: Vespertilionidae) and insights into internal relationships in the family Vespertilionidae

In the species-rich family Vespertilionidae, vesper yellow bats in the genus Rhogeessa include eleven species, three of them endemic to Mexico. These insectivorous bats provide important ecosystem services, including pest control. Even though some aspects of their biology are well- known, only a few genomic resources are available for these species, which limits our understanding of their biology. In this study, we assembled and annotated the mitochondrial genome of four species: R. aenea, R. genowaysi, R. mira, and R. parvula. We generated a phylomitogenomic hypothesis based on translated protein-coding genes for a total of 52 species in the family Vespertilionidae and examined the phylogenetic position of the genus Rhogeessa and species within the family. The AT-rich mitogenomes of R. aenea, R. genowaysi, R. mira, and R. parvula are 16,763, 16,781, 16,807, and 16,794 pb in length, respectively. Each studied mitogenome encodes 13 Protein Coding Genes (PCGs), 22 transfer RNA genes, and 2 rRNA genes, and contains a putative control region (CR). All tRNAs exhibit a ‘cloverleaf’ secondary structure, except tRNA-Serine-1 that lacked the DHU arm in all studied mitogenomes. Selective pressure analyses indicated that all protein-coding genes are exposed to purifying selection. The phylomitogenomic analysis supported the monophyletic status of the family Vespertilionidae, confirmed the placement of Rhogeessa within the tribe Antrozoini, and clarified phylogenetic relationships within and among subfamilies and tribes in this family. Our results indicate that phylomitogenomics are useful to explore the evolutionary history of vesper bats. The assembly and comprehensive analysis of mitochondrial genomes offer the potential to generate molecular references and resources beneficial for genetic analyses aimed at understanding the ecology and evolution of these remarkable bats.

The genome sequence of subterranean clover, Trifolium subterraneum L. (Fabaceae)

We present a genome assembly from an individual Trifolium subterraneum (subterranean clover; Tracheophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence is 483.8 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 309.28 kilobases and 144.76 kilobases in length, respectively.

The genome sequence of strawberry clover, Trifolium fragiferum L. (Fabaceae)

We present a genome assembly from an individual Trifolium fragiferum (strawberry clover; Tracheophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence is 512.0 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 298.57 kilobases and 139.15 kilobases in length, respectively.

The genome sequence of the Lesser Skullcap, Scutellaria minor Huds., 1762 (Lamiaceae)

We present a genome assembly from an individual Scutellaria minor (Tracheophyta; Magnoliopsida; Lamiales; Lamiaceae). The genome sequence is 341.8 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 376.64 kilobases and 152.59 kilobases in length, respectively.

The genome sequence of rosebay willowherb Chamaenerion angustifolium (L.) Scop., 1771 (syn. Epilobium angustifolium L., 1753) (Onagraceae).

We present a genome assembly from an individual Chamaenerion angustifolium (fireweed; Tracheophyta; Magnoliopsida; Myrtales; Onagraceae). The genome sequence is 655.9 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 495.18 kilobases and 160.41 kilobases in length, respectively.

Phylogenetic origin of an insect fauna at the boundary of the Palaearctic and Oriental realms: Evidence from ‘site‐based’ mitogenomics

AbstractAimKnowledge of taxonomy and species distributions in highly diverse lineages of invertebrates remains too incomplete for the study of biogeographical patterns at the global scale. This limits the understanding of processes leading to the formation and maintenance of boundaries between major biogeographical realms. Site‐based metagenomic approaches may provide an alternative source of data for inference of historical processes of in situ speciation and interchange among biogeographical regions. We applied the methodology to explore the historical biogeography of the Qinling Mountains at the boundary of the Oriental and Palaearctic regions.LocationThe focal area in the Qinling Mountains; sites in Borneo, Panama, and Spain, representing the Oriental, Neotropical and Palaearctic faunas.Time PeriodContemporary.Major Taxa StudiedChrysomelidae, a group of ~40,000 species with worldwide distribution.MethodsMass‐trapped insects were subjected to deep Illumina DNA sequencing and mitochondrial genome assembly, followed by phylogenetic analysis and historical biogeographical inference on a dated tree. The methodology produced 622 mitogenomes (304 newly sequenced) each representing a morphologically distinct species.ResultsAncestral area reconstruction revealed that the Qinling fauna is a composite of distinct clades that, respectively, have Oriental or Palaearctic ancient origins, while in situ speciation and local clade formation were limited. The global diversity of Chrysomelidae consists of regionalised deep clades at the level of the major zoogeographic realms, which remain recognisable where these realms abut in the Qinling mountains. Yet, the Qinling fauna is clearly distinct from the source areas although local lineage ages are generally <20 Ma.Main ConclusionsThe Qinling fauna is a composite of clades that have either Oriental or Palaearctic origin, indicating the important role of immigration at the realm boundary. Global site‐based phylogenetic analyses based on metagenomic sequencing can address previously intractable questions about the historical biogeography of poorly studied groups even without a fully developed taxonomy.

The genome sequence of spotted medick, Medicago arabica (L.) Huds. (Fabaceae)

We present a genome assembly from an individual Medicago arabica (the spotted medick; Tracheophyta; Magnoliopsida; Fabales; Fabaceae). The genome sequence is 515.5 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 324.47 kilobases and 125.07 kilobases in length, respectively.

The genome sequence of common knotgrass, Polygonum aviculare L. (Polygonaceae)

We present a genome assembly from an individual Polygonum aviculare (common knotgrass; Eudicot; Magnoliopsida; Caryophyllales; Polygonaceae). The genome sequence is 351.6 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 333.39 kilobases and 163.28 kilobases in length, respectively.

The genome sequence of great wood-rush, Luzula sylvatica (Huds) Gaudin

We present a genome assembly from an individual specimen of Luzula sylvatica (great wood-rush; Tracheophyta; Magnoliopsida; Poales; Juncaceae). The genome sequence is 444.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 633.36 kilobases and 201.32 kilobases in length, respectively.

The genome sequence of field madder, Sherardia arvensis L., 1753 (Rubiaceae)

We present a genome assembly from an individual Sherardia arvensis (field madder; Tracheophyta; Magnoliopsida; Gentianales; Rubiaceae). The genome sequence is 440.9 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies have lengths of 203.98 kilobases and 152.73 kilobases in length, respectively.

The overview of methods for assembling complex mitochondrial genomes in land plants.

The large size and complex structural rearrangements inherent in mitochondrial genomes of land plants pose challenges for their sequencing. Originally, the assembly of these genomes required the cloning of mitochondrial DNA fragments, followed by Sanger sequencing. Subsequently, the advent of next-generation sequencing significantly expedited the process. This review highlights instances of plant mitochondrial genome assembly employing various technologies, including 454 sequencing, Illumina short sequencing reads, and Pacific Biosciences or Oxford Nanopore Technology long sequencing reads. The combination of short and long reads in hybrid assembly has proven to be the most efficient approach for achieving reliable assemblies of land plant mitochondrial genomes.

Evaluating the efficacy of MEANGS for mitochondrial genome assembly of cartilaginous and ray-finned fish species.

The assembly of complete and circularized mitochondrial genomes (mitogenomes) is essential for population genetics, phylogenetics and evolution studies. Recently, Song etal. developed a seed-free tool called MEANGS for de novo mitochondrial assembly from whole genome sequencing (WGS) data in animals, achieving highly accurate and intact assemblies. However, the suitability of this tool for marine fish remains unexplored. Additionally, we have concerns regarding the overlap sequences in their original results, which may impact downstream analyses. In this Letter to the Editor, the effectiveness of MEANGS in assembling mitogenomes of cartilaginous and ray-finned fish species was assessed. Moreover, we also discussed the appropriate utilization of MEANGS in mitogenome assembly, including the implementation of the data-cut function and circular detection module. Our observations indicated that with the utilization of these modules, MEANGS efficiently assembled complete and circularized mitogenomes, even when handling large WGS datasets. Therefore, we strongly recommend users employ the data-cut function and circular detection module when using MEANGS, as the former significantly reduces runtime and the latter aids in the removal of overlapped sequences for improved circularization. Furthermore, our findings suggested that approximately 2× coverage of clean WGS data was sufficient for MEANGS to assemble mitogenomes in marine fish species. Moreover, due to its seed-free nature, MEANGS can be deemed one of the most efficient software tools for assembling mitogenomes from animal WGS data, particularly in studies with limited species or genetic background information.

Metagenomic ecosystem monitoring of soft scale insects and mealybug communities

Soft scale insects and mealybugs are phloem-feeding Hemipterans that are considered major pests in agriculture and horticulture throughout the world. However, correct taxonomic identification in the field can be difficult, making it hard for growers to implement control strategies. In viticulture, soft scale insects are a major issue due to their ability to secrete honeydew, which facilitates the development of sooty mould, and their propensity for being transmission vectors of several viral diseases of grapevine. To facilitate the rapid identification and quantification of vineyard-associated insects a metagenomic-based bioinformatic pipeline (MitoMonitor) was developed for generalised ecosystem monitoring, which automated the assembly and classification of insect mitochondrial genomes from shotgun sequencing data using the Barcode of Life Database API. The proof-of-concept application of MitoMonitor on metagenomic data obtained from eight samples from South Australian vineyards led to the identification of Parthenolecanium corni (European fruit scale)—which was thought to be absent in Australian vineyards—as the dominant coccoid species across the samples, with less frequent, and also lower abundance of Pseudococcus viburni (obscure mealybug) and Pseudo. longispinus (long-tailed mealybug). In addition, parisitoidism by Coccophagus scutellaris (Aphelinidae) wasps was also detected. The discovery of Parth. corni as a member of scale communities in these samples has significant implications for the development of effective control strategies for this important group of pests in affected areas.

Complete Mitochondrial Genome Assembly of an Upland Wild Rice Species, Oryza granulata and Comparative Mitochondrial Genomic Analyses of the Genus Oryza.

Wild upland rice species, including Oryza granulata, possess unique characteristics that distinguish them from other Oryza species. For instance, O. granulata characteristically has a GG genome and is accordingly classified as a basal lineage of the genus Oryza. Here, we deployed a versatile hybrid approach by integrating Illumina and PacBio sequencing data to generate a high-quality mitochondrial genome (mitogenome) assembly for O. granulata. The mitogenome of O. granulata was 509,311 base pairs (bp) with sixty-seven genes comprising two circular chromosomes, five ribosomal RNA (rRNA) coding genes, twenty-five transfer RNA (tRNA) coding genes, and thirty-seven genes coding for proteins. We identified a total of 378 simple sequence repeats (SSRs). The genome also contained 643 pairs of dispersed repeats comprising 340 palindromic and 303 forward. In the O. granulata mitogenome, the length of 57 homologous fragments in the chloroplast genome occupied 5.96% of the mitogenome length. Collinearity analysis of three Oryza mitogenomes revealed high structural variability and frequent rearrangements. Phylogenetic analysis showed that, compared to other related genera, O. granulata had the closest genetic relationship with mitogenomes reported for all members of Oryza, and occupies a position at the base of the Oryza phylogeny. Comparative analysis of complete mitochondrial genome assemblies for Oryza species revealed high levels of mitogenomic diversity, providing a foundation for future conservation and utilization of wild rice biodiversity.

Assembly and phylogeographical analysis of novel Taenia solium mitochondrial genomes suggest stratification within the African-American genotype

BackgroundTaenia solium is a parasite of public health concern, causing human taeniasis and cysticercosis. Two main genotypes have been identified: Asian and African-American. Although characterizing T. solium genotypes is crucial to understanding the genetic epidemiology of its diseases, not much is known about the differences between T. solium mitochondrial genomes from different genotypes. Also, little is known about whether genotypes are further subdivided. Therefore, this study aimed to identify a set of point mutations distributed throughout the T. solium mitochondrial genome that differentiate the African-American from the Asian genotype. Another objective was to identify whether T. solium main genotypes are further stratified.MethodsOne Mexican and two Peruvian T. solium mitochondrial genomes were assembled using reads available in the NCBI Sequence Read Archive and the reference genome from China as a template. Mutations with respect to the Chinese reference were identified by multiple genome alignment. Jensen–Shannon and Grantham scores were computed for mutations in protein-coding genes to evaluate whether they affected protein function. Phylogenies by Bayesian inference and haplotype networks were constructed using cytochrome c oxidase subunit 1 and cytochrome b from these genomes and other isolates to infer phylogeographical relationships.ResultsA set of 31 novel non-synonymous point mutations present in all genomes of the African-American genotype were identified. These mutations were distributed across the mitochondrial genome, differentiating the African-American from the Asian genotype. All occurred in non-conserved protein positions. Furthermore, the analysis suggested a stratification of the African-American genotypes into an East African and a West African sublineage.ConclusionsA novel set of 31 non-synonymous mutations differentiating the main T. solium genotypes was identified. None of these seem to be causing differences in mitochondrial protein function between parasites of the two genotypes. Furthermore, two sublineages within the African-American genotype are proposed for the first time. The presence of the East African sublineage in the Americas suggests an underestimated connection between East African and Latin American countries that might have arisen in the major slave trade between Portuguese Mozambique and the Americas. The results obtained here help to complete the molecular epidemiology of the parasite.Graphical

The genome sequence of the tree of heaven, Ailanthus altissima (Mill.) Swingle, 1916.

We present a genome assembly from an individual Ailanthus altissima (tree of heaven; Streptophyta; Magnoliopsida; Sapindales; Simaroubaceae). The genome sequence is 939 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules. The mitochondrial and plastid genome assemblies are 661.1 kilobases and 161.1 kilobases long, respectively.

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads.

PacBio high fidelity (HiFi) sequencing reads are both long (15-20kb) 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. 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. 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).

Assembly and phylogenomic analysis of cotton mitochondrial genomes provide insights into the history of cotton evolution

Cotton is a major crop that provides the most important renewable textile fibers in the world. Studies of the taxonomy and evolution of cotton species have received wide attentions, not only due to cotton’s economic value but also due to the fact that Gossypium is an ideal model system to study the origin, evolution, and cultivation of polyploid species. Previous studies suggested the involvement of mitochondrial genome editing sites and copy number as well as mitochondrial functions in cotton fiber elongation. Whereas, with only a few mitogenomes assembled in the cotton genus Gossypium, our knowledge about their roles in cotton evolution and speciation is still scarce. To close this gap, here we assembled 20 mitogenomes from 15 cotton species spanning all the cotton clades (A–G, K, and AD genomes) and 5 cotton relatives using short and long sequencing reads. Systematic analyses uncovered a high level of mitochondrial gene sequence conservation, abundant sequence repeats and many insertions of foreign sequences, as well as extensive structural variations in cotton mitogenomes. The sequence repeats and foreign sequences caused significant mitogenome size inflation in Gossypium and its close relative Kokia in general, while there is no significant difference between the lint and fuzz cotton mitogenomes in terms of gene content, RNA editing, and gene expression level. Interestingly, we further revealed the specific presence and expression of two novel mitochondrial open reading frames (ORFs) in lint-fiber cotton species. Finally, these structural features and novel ORFs help us gain valuable insights into the history of cotton evolution and polyploidization and the origin of species producing long lint fibers from a mitogenomic perspective.

Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds.

Indian cattle breeds (Bos indicus) are known for their remarkable adaptability to hot and humid climates, higher nutritious quality of milk, better disease tolerance, and greater ability to perform in poor feed compared to taurine cattle (Bos taurus). Distinct phenotypic differences are observed among the B. indicus breeds; however, the whole genome sequences were unavailable for these indigenous breeds. We aimed to perform whole genome sequencing to construct the draft genome assemblies of four B. indicus breeds; Ongole, Kasargod Dwarf, Kasargod Kapila, and Vechur (the smallest cattle of the world). We sequenced the whole genomes using Illumina short-read technology, and constructed de novo and reference-based genome assemblies of these native B. indicus breeds for the first time. The draft de novo genome assemblies of B. indicus breeds ranged from 1.98 to 3.42 Gbp. We also constructed the mitochondrial genome assemblies (~ 16.3 Kbp), and yet unavailable 18S rRNA marker gene sequences of these B. indicus breeds. The genome assemblies helped to identify the bovine genes related to distinct phenotypic characteristics and other biological processes for this species compared to B. taurus, which are plausibly responsible for providing better adaptive traits. We also identified the genes that showed sequence variation in dwarf and non-dwarf breeds of B. indicus compared to B. taurus. The genome assemblies of these Indian cattle breeds, the 18S rRNA marker genes, and identification of the distinct genes in B. indicus breeds compared to B. taurus will help in future studies on these cattle species.