The brown bear (Ursus arctos) is the second largest and most widespread extant terrestrial carnivore on Earth and has recently emerged as a medical model for human metabolic diseases. Here, we report a fully phased chromosome-level assembly of a male North American brown bear built by combining Pacific Biosciences (PacBio) HiFi data and publicly available Hi-C data. The final genome size is 2.47 Gigabases (Gb) with a scaffold and contig N50 length of 70.08 and 43.94 Megabases (Mb), respectively. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis revealed that 94.5% of single copy orthologs from Mammalia were present in the genome (the highest of any ursid genome to date). Repetitive elements accounted for 44.48% of the genome and a total of 20,480 protein coding genes were identified. Based on whole genome alignment to the polar bear, the brown bear is highly syntenic with the polar bear, and our phylogenetic analysis of 7,246 single-copy orthologs supports the currently proposed species tree for Ursidae. This highly contiguous genome assembly will support future research on both the evolutionary history of the bear family and the physiological mechanisms behind hibernation, the latter of which has broad medical implications.
- Award ID(s):
- 1754451
- NSF-PAR ID:
- 10232211
- Date Published:
- Journal Name:
- Journal of Heredity
- ISSN:
- 0022-1503
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract -
more » « less
Abstract The evolutionary direction of gonochorism and hermaphroditism is an intriguing mystery to be solved. The special transient hermaphroditic stage makes the little yellow croaker (
Larimichthys polyactis ) an appealing model for studying hermaphrodite formation. However, the origin and evolutionary relationship between ofL. polyactis andLarimichthys crocea , the most famous commercial fish species in East Asia, remain unclear. Here, we report the sequence of theL. polyactis genome, which we found is ~706 Mb long (contig N50 = 1.21 Mb and scaffold N50 = 4.52 Mb) and contains 25,233 protein‐coding genes. Phylogenomic analysis suggested thatL. polyactis diverged from the common ancestor,L. crocea , approximately 25.4 million years ago. Our high‐quality genome assembly enabled comparative genomic analysis, which revealed several within‐chromosome rearrangements and translocations, without major chromosome fission or fusion events between the two species. Thedmrt1 gene was identified as the male‐specific gene inL. polyactis . Transcriptome analysis showed that the expression ofdmrt1 and its upstream regulatory gene (rnf183 ) were both sexually dimorphic.Rnf183 , unlike its two paraloguesrnf223 andrnf225 , is only present inLarimichthys andLates but not in other teleost species, suggesting that it originated from lineage‐specific duplication or was lost in other teleosts. Phylogenetic analysis shows that the hermaphrodite stage in maleL. polyactis may be explained by the sequence evolution ofdmrt1 . Decoding theL. polyactis genome not only provides insight into the genetic underpinnings of hermaphrodite evolution, but also provides valuable information for enhancing fish aquaculture. -
more » « less
Abstract The cabbage looper,
Trichoplusia ni , is a globally distributed highly polyphagous herbivore and an important agricultural pest.T. ni has evolved resistance to various chemical insecticides, and is one of the only two insect species that have evolved resistance to the biopesticideBacillus thuringiensis (Bt) in agricultural systems and has been selected for resistance to baculovirus infections. We report a 333‐Mb high‐qualityT. ni genome assembly, which has N50 lengths of scaffolds and contigs of 4.6 Mb and 140 Kb, respectively, and contains 14,384 protein‐coding genes. High‐density genetic maps were constructed to anchor 305 Mb (91.7%) of the assembly to 31 chromosomes. Comparative genomic analysis ofT. ni withBombyx mori showed enrichment of tandemly duplicated genes inT. ni in families involved in detoxification and digestion, consistent with the broad host range ofT. ni . High levels of genome synteny were found betweenT. ni and other sequenced lepidopterans. However, genome synteny analysis ofT. ni and theT. ni derived cell line High Five (Hi5) indicated extensive genome rearrangements in the cell line. These results provided the first genomic evidence revealing the high instability of chromosomes in lepidopteran cell lines known from karyotypic observations. The high‐qualityT. ni genome sequence provides a valuable resource for research in a broad range of areas including fundamental insect biology, insect‐plant interactions and co‐evolution, mechanisms and evolution of insect resistance to chemical and biological pesticides, and technology development for insect pest management. -
The hagfishes (Myxiniformes) arose from agnathan (jawless vertebrate) lineages and they are one of only two extant cyclostome taxa, together with lampreys (Petromyzontiformes). Even though whole genome sequencing has been achieved for diverse vertebrate taxa, genome-wide sequence information has been highly limited for cyclostomes. Here we sequenced the genome of the inshore hagfish Eptatretus burgeri using DNA extracted from the testis, with a short-read sequencing platform, aiming to reconstruct a high-coverage protein-coding gene catalogue. The obtained genome assembly, scaffolded with mate-pair reads and paired RNA-seq reads, exhibited an N50 scaffold length of 293 Kbp, which allowed the genome-wide prediction of coding genes. This computation resulted in the gene models whose completeness was estimated at the complete coverage of more than 83 % and the partial coverage of more than 93 % by referring to evolutionarily conserved single-copy orthologs. The high contiguity of the assembly and completeness of the gene models promise a high utility in various comparative analyses including phylogenomics and phylome exploration.more » « less
-
null (Ed.)Abstract The diatom, Cyclotella cryptica, is a well-established model species for physiological studies and biotechnology applications of diatoms. To further facilitate its use as a model diatom, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/jhered/esab021
