The spiral gingers (Costus L.) are a pantropical genus of herbaceous
perennial monocots; the Neotropical clade of Costus radiated rapidly in
the past few million years into over 60 species. The Neotropical spiral
gingers have a rich history of evolutionary and ecological research that
can motivate and inform modern genetic investigations. Here, we present
the first two chromosome-level genome assemblies in the genus, for C.
pulverulentus and C. lasius, and briefly compare their synteny. We
assembled the C. pulverulentus genome from a combination of short-read
data, Chicago and Dovetail Hi-C chromatin-proximity sequencing, and
alignment with a linkage map. We assembled the C. lasius genome with
Pacific Biosciences HiFi long reads and alignment to the C. pulverulentus
genome. These two assemblies are the first published genomes for
non-cultivated tropical plants. These genomes solidify the spiral gingers
as a model system and will facilitate research on the poorly understood
genetic basis of tropical plant diversification.
more »
« less
Genome assemblies and comparison of two Neotropical spiral gingers: Costus pulverulentus and C. lasius
The spiral gingers (Costus L.) are a pantropical genus of herbaceous perennial monocots; the Neotropical clade of Costus radiated rapidly in the past few million years into over 60 species. The Neotropical spiral gingers have a rich history of evolutionary and ecological research that can motivate and inform modern genetic investigations. Here, we present the first 2 chromosome-level genome assemblies in the genus, for C. pulverulentus and C. lasius, and briefly compare their synteny. We assembled the C. pulverulentus genome from a combination of short-read data, Chicago and Dovetail Hi-C chromatin-proximity sequencing, and alignment with a linkage map. We annotated the genome by mapping a C. pulverulentus transcriptome and querying mapped transcripts against a protein database. We assembled the C. lasius genome with Pacific Biosciences HiFi long reads and alignment to the C. pulverulentus genome. These 2 assemblies are the first published genomes for non-cultivated tropical plants. These genomes solidify the spiral gingers as a model system and will facilitate research on the poorly understood genetic basis of tropical plant diversification.
more » « less- NSF-PAR ID:
- 10413636
- Publisher / Repository:
- Oxford University Press
- 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 The slender anole, Anolis apletophallus, is a small arboreal lizard of the rainforest understory of central and eastern Panama. This species has been the subject of numerous ecological and evolutionary studies over the past 60 years as a result of attributes that make it especially amenable to field and laboratory science. Slender anoles are highly abundant, short-lived (nearly 100% annual turnover), easy to manipulate in both the lab and field, and are ubiquitous in the forests surrounding the Smithsonian Tropical Research Institute in Panama, where researchers have access to high-quality laboratory facilities. Here, we present a high-quality genome for the slender anole, which is an important new resource for studying this model species. We assembled and annotated the slender anole genome by combining 3 technologies: Oxford Nanopore, 10× Genomics Linked-Reads, and Dovetail Omni-C. We compared this genome with the recently published brown anole (Anolis sagrei) and the canonical green anole (Anolis carolinensis) genomes. Our genome is the first assembled for an Anolis lizard from mainland Central or South America, the regions that host the majority of diversity in the genus. This new reference genome is one of the most complete genomes of any anole assembled to date and should facilitate deeper studies of slender anole evolution, as well as broader scale comparative genomic studies of both mainland and island species. In turn, such studies will further our understanding of the well-known adaptive radiation of Anolis lizards.
-
more » « less
Abstract Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding interspecific genetic diversity and phylogenetic relationships. Here, we present single haplotype de novo genome assemblies for the gray wolf and coyote, generated by applying the trio-binning approach to long sequence reads generated from the genome of a female first-generation hybrid produced from a gray wolf and coyote mating. The assemblies were highly contiguous, with contig N50 sizes of 44.6 and 42.0 Mb for the wolf and coyote, respectively. Genome scaffolding and alignments between the two Canis assemblies and published dog reference genomes showed near complete collinearity, with one exception: a coyote-specific chromosome fission of chromosome 13 and fusion of the proximal portion of that chromosome with chromosome 8, retaining the Canis-typical haploid chromosome number of 2n = 78. We evaluated mapping quality for previous RADseq data from 334 canids and found nearly identical mapping quality and patterns among canid species and regional populations regardless of the genome used for alignment (dog, coyote, or gray wolf). These novel wolf and coyote genome reference assemblies will be important resources for proper and accurate inference of Canis demography, taxonomic evaluation, and conservation genetics.
-
more » « less
Societal Impact Statement Rafflesia is a genus of parasitic plants with the largest flowers in the world, unique to the threatened forest habitats of tropical Asia. Here, we report on genes that are active (the transcriptome) inRafflesia seeds as part of a larger effort to understandRafflesia .Rafflesia has never been grown successfully outside of its native range. Consequently, seed banking is not yet possible, precluding a critical management strategy for conservation. The study ofRafflesia seed biology is a critical step to improve its cultivation, which will educate the public about unique species and the importance of conserving their habitats.Summary Rafflesia is of great interest as one of the only two plants known to have completely lost its chloroplast genome.Rafflesia is a holoparasite and an endophyte that lives inside the tissues of its host, a tropical grape vine (Tetrastigma ), emerging only to bloom—with the largest flower of any plant. Here, we report the firstRafflesia seed transcriptome and compare it with those of other plants to deepen our understanding of its extraordinary life history.We assembled a transcriptome from RNA extracted from seeds of the Philippine endemic
Rafflesia speciosa and compared this with those of other plants, includingArabidopsis , parasitic plantsStriga andCuscuta , and the mycoheterotrophic orchidAnoectochilus .Genetic and metabolic seed pathways in
Rafflesia were generally similar to the other plant species. However, there were some notable exceptions. We found evidence of horizontal transfer of a gene potentially involved in circumventing host defenses. Moreover, we identified a possible convergence among parasitic plants becauseRafflesia ,Striga , andCuscuta shared important similarities. We were unable to find evidence of genes involved in mycorrhizal symbiosis, suggesting that mycoheterotrophy is unlikely to play a role inRafflesia parasitism.To date, ex situ propagation of
Rafflesia by seed has been mostly unsuccessful. Our research is a bold step forward in understanding the fundamentals ofRafflesia seed biology that will inform the continued propagation and seed‐banking efforts concerning this recalcitrant plant. We discuss our findings in the broader context of the conservation of a genus in peril. -
more » « less
Abstract Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score of 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus Pisaster. These novel genomic resources for P. helianthoides will underwrite population genomic, comparative genomic, and phylogenomic analyses—as well as their integration across scales—of SSW and environmental stressors.
