Sugarcane Genome Hub

Sugarcane Genome Hub provides a reference monoploid sugarcane genome assembly and associated gene models to support genomic and comparative analyses of Saccharum spp.

Key Features:

• Reference monoploid assembly: A monoploid genome sequence assembled from a minimum tiling path of 4,660 BACs into a 382 megabase contiguous sequence representing gene-rich regions of sorghum.
• BAC selection and sequencing: The 4,660 BACs were selected based on whole-genome profiling and sequenced via BAC sequencing.
• Colinearity with sorghum: Assembly construction leveraged colinearity with sorghum to order and assemble sugarcane sequences.
• Gene models: Predictive models for approximately 25,316 protein-coding genes are provided for the assembly.
• Non-colinear genes: Approximately 17% of predicted genes lack colinearity with sorghum orthologs.
• Inter-species differences: Comparative analyses identify differences between S. officinarum and S. spontaneum driven by transposable element variation and several large chromosomal rearrangements affecting genome size and basic chromosome numbers.
• Polyploidization inference: Analyses support independent polyploidization events in S. officinarum and S. spontaneum after their divergence.

Scientific Applications:

• Genetic studies: Enable genetic studies of Saccharum spp., including gene discovery and characterization.
• Breeding programs: Inform breeding programs by supplying genome assembly and gene models that delineate species-specific genomic differences.
• Biotechnological applications: Support biotechnological applications for crop and bioenergy trait improvement through access to gene models and comparative genomic information.
• Comparative and evolutionary genomics: Facilitate comparative genomics with sorghum and other Poaceae to study colinearity, transposable elements, chromosomal rearrangements, and polyploidization.

Methodology:

Minimum tiling path of 4,660 BACs was selected by whole-genome profiling; BACs were sequenced and assembled into a 382 Mb contiguous monoploid sequence; assembly construction leveraged colinearity with sorghum; gene prediction produced ~25,316 protein-coding models; comparative analyses identified ~17% non-colinear genes and characterized transposable element variation and large chromosomal rearrangements supporting independent polyploidization.