De Novo Long-Read Genome Assembly and Annotation of the Luna Moth (Actias luna) Fully Resolves Repeat-Rich Silk Genes.

We present the first long-read de novo assembly and annotation of the luna moth (Actias luna) and provide the full characterization of heavy chain fibroin (h-fibroin), a long and highly repetitive gene (>20 kb) essential in silk fiber production. There are >160,000 described species of moths and butterflies (Lepidoptera), but only within the last 5 years have we begun to recover high-quality annotated whole genomes across the order that capture h-fibroin. Using PacBio HiFi reads, we produce the first high-quality long-read reference genome for this species.

The Complete Genome Sequence of (Saturniidae, Lepidoptera), the luna moth.

, the luna moth, is a Nearctic species in the family Saturniidae, the giant silk moths. Known for its large size, bright green wings and elongated tails, it is found in Eastern North America, from east of the Great Plains in the United States, and from Saskatchewan eastward through central Quebec to Nova Scotia in Canada. We present the complete genome sequence of this species.

The Complete Genome Sequences of 9 Species of Swallowtail Butterflies (Papilionidae, Lepidoptera).

We present the complete genome sequences of 9 species of Papilionidae from 3 genera (Graphium, Ornithoptera, Papilio). Illumina sequencing was performed on genetic material from individual wild-caught specimens. The reads were assembled using a de novo method followed by a finishing step.

Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes.

The integration of mitochondrial genome fragments into the nuclear genome is well documented, and the transfer of these mitochondrial nuclear pseudogenes (numts) is thought to be an ongoing evolutionary process. With the increasing number of eukaryotic genomes available, genome-wide distributions of numts are often surveyed. However, inconsistencies in genome quality can reduce the accuracy of numt estimates, and methods used for identification can be complicated by the diverse sizes and ages of numts.

Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses.

We report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies.

Rapid Shifts in Mitochondrial tRNA Import in a Plant Lineage with Extensive Mitochondrial tRNA Gene Loss.

In most eukaryotes, transfer RNAs (tRNAs) are one of the very few classes of genes remaining in the mitochondrial genome, but some mitochondria have lost these vestiges of their prokaryotic ancestry. Sequencing of mitogenomes from the flowering plant genus Silene previously revealed a large range in tRNA gene content, suggesting rapid and ongoing gene loss/replacement. Here, we use this system to test longstanding hypotheses about how mitochondrial tRNA genes are replaced by importing nuclear-encoded tRNAs.

MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database.

MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org).

Bovine Genome Database: new annotation tools for a new reference genome.

The Bovine Genome Database (BGD) (http://bovinegenome.org) has been the key community bovine genomics database for more than a decade. To accommodate the increasing amount and complexity of bovine genomics data, BGD continues to advance its practices in data acquisition, curation, integration and efficient data retrieval.

Lepidoptera genomes: current knowledge, gaps and future directions.

Butterflies and moths (Lepidoptera) are one of the most ecologically diverse and speciose insect orders. With recent advances in genomics, new Lepidoptera genomes are regularly being sequenced, and many of them are playing principal roles in genomics studies, particularly in the fields of phylo-genomics and functional genomics. Thus far, assembled genomes are only available for <10 of the 43 Lepidoptera superfamilies.

Positive Selection in Rapidly Evolving Plastid-Nuclear Enzyme Complexes.

Rates of sequence evolution in plastid genomes are generally low, but numerous angiosperm lineages exhibit accelerated evolutionary rates in similar subsets of plastid genes. These genes include clpP1 and accD, which encode components of the caseinolytic protease (CLP) and acetyl-coA carboxylase (ACCase) complexes, respectively. Whether these extreme and repeated accelerations in rates of plastid genome evolution result from adaptive change in proteins (i.

Most partial domains in proteins are alignment and annotation artifacts.

Background: Protein domains are commonly used to assess the functional roles and evolutionary relationships of proteins and protein families. Here, we use the Pfam protein family database to examine a set of candidate partial domains. Pfam protein domains are often thought of as evolutionarily indivisible, structurally compact, units from which larger functional proteins are assembled; however, almost 4% of Pfam27 PfamA domains are shorter than 50% of their family model length, suggesting that more than half of the domain is missing at those locations.

A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae).

In flowering plants, plastid genomes are generally conserved, exhibiting slower rates of sequence evolution than the nucleus and little or no change in structural organization. However, accelerated plastid genome evolution has occurred in scattered angiosperm lineages. For example, some species within the genus Silene have experienced a suite of recent changes to their plastid genomes, including inversions, shifts in inverted repeat boundaries, large indels, intron losses, and rapid rates of amino acid sequence evolution in a subset of protein genes, with the most extreme divergence occurring in the protease gene clpP.

Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes.

Many mitochondrial and plastid protein complexes contain subunits that are encoded in different genomes. In animals, nuclear-encoded mitochondrial proteins often exhibit rapid sequence evolution, which has been hypothesized to result from selection for mutations that compensate for changes in interacting subunits encoded in mutation-prone animal mitochondrial DNA. To test this hypothesis, we analyzed nuclear genes encoding cytosolic and organelle ribosomal proteins in flowering plants.

Simultaneous extraction of high-quality RNA and DNA from small tissue samples.

Purification of high-quality DNA and RNA from a single sample is becoming increasingly important for studies seeking both genomic and transcriptomic data. We compare different methods for isolating DNA and RNA from fish embryos (Gulf killifish; Fundulus grandis) and describe an optimal technique to extract high-quality DNA and RNA from a single embryo. The optimal method utilizes a chaotropic buffer and spin column technology.

Extensive mitochondrial DNA transfer in a rapidly evolving rodent has been mediated by independent insertion events and by duplications.

Mitochondrial DNA translocations to the nucleus (numt pseudogenes) are pervasive among eukaryotes, but copy number within the nuclear genome varies widely among taxa. As an increasing number of genomes are sequenced in their entirety, the origins, transfer mechanisms and insertion sites of numts are slowly being characterized. We investigated mitochondrial transfers within a genetically diverse rodent lineage and here report 15 numts totaling 21.

Molecular analyses of mitochondrial pseudogenes within the nuclear genome of arvicoline rodents.

Nuclear sequences of mitochondrial origin (numts) are common among animals and plants. The mechanism(s) by which numts transfer from the mitochondrion to the nucleus is uncertain, but their insertions may be mediated in part by chromosomal repair mechanisms. If so, then lineages where chromosomal rearrangements are common should be good models for the study of numt evolution.

Accelerated molecular evolution in Microtus (Rodentia) as assessed via complete mitochondrial genome sequences.

Microtus is one of the most taxonomically diverse mammalian genera, including over 60 extant species. These rodents have evolved rapidly, as the genus originated less than 2 million years ago. If these numbers are taken at face value, then an average of 30 microtine speciation events have occurred every million years.