skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: The complete genome sequences of Erythroxylum coca and Erythroxylum novogranatense
The flowering plant genus Erythroxylum contains approximately 300 species, including the economically and socially consequential crops called coca. We present the genome sequences of Erythroxylum coca and E. novogranatense, two cultigens produced for medicinal and quotidian use in the Andes and Amazon regions of South America, as well as the international cocaine industry. Sequencing was performed on an Illumina X-Ten platform, and reads were assembled by a de novo method followed by finishing via comparison with several species from the same genus. The BioProject, raw and assembled data can be accessed in GenBank for E. coca (PRJNA676123; JAJMLV000000000) and E. novogranatense (PRJNA675212; JAJKBF000000000).  more » « less
Award ID(s):
2010821
PAR ID:
10399999
Author(s) / Creator(s):
; ; ;
Date Published:
Journal Name:
Biodiversity Genomes
ISSN:
2687-7945
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; (, Genome Biology and Evolution)
    O’Neill, Rachel (Ed.)
    Abstract Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly, we determined that the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. Ab initio and transcript-informed gene modeling and annotation identified 29,405 genes, including a conserved Hox cluster. E. sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared E. sp. EZ gene families and transcription factors associated with environmental stress response (“defensome”) with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in E. sp. EZ noncoding elements near genes involved in environmental response pathways as well as losses of transcription factors important for environmental response. These data provide key insights into the biology of E. sp. EZ as well as the diversification of Echinometra more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond. 
    more » « less
  2. ; ; ; (, Zootaxa)
    null (Ed.)
    The leafhopper genus Thaia Ghauri, 1962 and two related genera, Parathaia Kuoh, 1982 and Pseudothaia Kuoh, 1982, are revised. Nlunga Dworakowska, 1974, previously treated as a subgenus of Thaia, is elevated to the genus level, and Parathaia Kuoh, 1982, previously treated as a synonym of Thaia, is reinstated to valid status. The Oriental species lacking foveae on the pronotum are excluded from Nlunga and transferred to a new genus, Etmaria gen. n. Two species, Pseudothaia caudata Song & Li, 2013 and Thaia (Nlunga) leishanensis (Song & Li, 2007), are treated as Incertae sedis within Erythroneurini. Moreover, nine additional new species are described and illustrated: Nlunga parareeneni, Etmaria brevis, E. chaiyaphumica, E. dentata, E. indonesica, E. magna, E. triquetra, E. ulterior and Pseudothaia forcipis spp. nov. 
    more » « less
  3. ; ; ; (, Genome Biology and Evolution)
    Fraser, Bonnie (Ed.)
    Abstract Kangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semiarid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered in the United States. The precarious state of many Dipodomys populations, including those occupying extreme environments, make species of this genus valuable subjects for studying the impacts of habitat degradation and fragmentation on population genomic patterns and for characterizing the genomic bases of adaptation to harsh conditions. To facilitate exploration of such questions, we assembled and annotated a reference genome for the banner-tailed kangaroo rat (Dipodomys spectabilis) using PacBio HiFi sequencing reads, providing a more contiguous genomic resource than two previously assembled Dipodomys genomes. Using the HiFi data for D. spectabilis and publicly available sequencing data for two other Dipodomys species (Dipodomys ordii and Dipodomys stephensi), we demonstrate the utility of this new assembly for studies of congeners by conducting inference of historic effective population sizes (Ne) and linking these patterns to the species’ current extinction risk statuses. The genome assembly presented here will serve as a valuable resource for population and conservation genomic studies of Dipodomys species, comparative genomic research within mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes. 
    more » « less
  4. ; ; ; ; ; ; (, Phytotaxa)
    During the development of the taxonomic treatment of Ernestia we came across a taxonomic novelty and a species for which taxonomic verification was needed from Colombia. Herein, we propose Ernestia rheophytica a new species belonging to the sensu stricto clade of the genus, and clarify the identity of Acisanthera goudotii, now treated as E. goudotii. We also clarify the status of the original material of E. goudotii and propose the lectotypification of E. ovata and its synonymization under E. goudotii. Ernestia rheophytica, as the name indicates, is a rheophytic species, a rare habit in Melastomataceae, especially in Marcetieae. 
    more » « less
  5. ; ; ; ; ; ; ; ; ; ; et al (, Frontiers in Genetics)
    The parasitoid wasp Muscidifurax raptorellus (Hymenoptera: Pteromalidae) is a gregarious species that has received extensive attention for its potential in biological pest control against house fly, stable fly, and other filth flies. It has a high reproductive capacity and can be reared easily. However, genome assembly is not available for M. raptorellus or any other species in this genus. Previously, we assembled a complete circular mitochondrial genome with a length of 24,717 bp. Here, we assembled and annotated a high-quality nuclear genome of M. raptorellus , using a combination of long-read (104× genome coverage) and short-read (326× genome coverage) sequencing technologies. The assembled genome size is 314 Mbp in 226 contigs, with a 97.9% BUSCO completeness score and a contig N50 of 4.67 Mb, suggesting excellent continuity of this assembly. Our assembly builds the foundation for comparative and evolutionary genomic analysis in the genus of Muscidifurax and possible future biocontrol applications. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email