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Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora
- Source :
- G3: Genes|Genomes|Genetics
- Publication Year :
- 2021
-
Abstract
- The angiosperm genus Silene is a model system for several traits of ecological and evolutionary significance in plants, including breeding system and sex chromosome evolution, host-pathogen interactions, invasive species biology, heavy metal tolerance, and cytonuclear interactions. Despite its importance, genomic resources for this large genus of approximately 850 species are scarce, with only one published whole-genome sequence (from the dioecious species Silene latifolia). Here, we provide genomic and transcriptomic resources for a hermaphroditic representative of this genus (S. noctiflora), including a PacBio Iso-Seq transcriptome, which uses long-read, single-molecule sequencing technology to analyze full-length mRNA transcripts. Using these data, we have assembled and annotated high-quality full-length cDNA sequences for approximately 14,126 S. noctiflora genes and 25,317 isoforms. We demonstrated the utility of these data to distinguish between recent and highly similar gene duplicates by identifying novel paralogous genes in an essential protease complex. Furthermore, we provide a draft assembly for the approximately 2.7-Gb genome of this species, which is near the upper range of genome-size values reported for diploids in this genus and threefold larger than the 0.9-Gb genome of Silene conica, another species in the same subgenus. Karyotyping confirmed that S. noctiflora is a diploid, indicating that its large genome size is not due to polyploidization. These resources should facilitate further study and development of this genus as a model in plant ecology and evolution.
- Subjects :
- 0106 biological sciences
AcademicSubjects/SCI01140
AcademicSubjects/SCI00010
Silene conica
Iso-Seq
Sequence assembly
AcademicSubjects/SCI01180
01 natural sciences
Genome
03 medical and health sciences
Magnoliopsida
Genome Size
Genetics
Silene latifolia
Silene
Molecular Biology
Genome size
Genetics (clinical)
Silene noctiflora
030304 developmental biology
PacBio
0303 health sciences
biology
Genomics
biology.organism_classification
Genome Report
karyotype
Evolutionary biology
genome assembly
AcademicSubjects/SCI00960
Subgenus
Transcriptome
010606 plant biology & botany
Subjects
Details
- ISSN :
- 21601836
- Volume :
- 11
- Issue :
- 8
- Database :
- OpenAIRE
- Journal :
- G3 (Bethesda, Md.)
- Accession number :
- edsair.doi.dedup.....97e1a4751c7add089e51d45358a5bf33