Abstract
Sugarcane is a major crop used for food and bioenergy production. Modern cultivars are hybrids derived from crosses between Saccharum officinarum and Saccharum spontaneum. Hybrid cultivars combine favorable characteristics from ancestral species and contain a genome that is highly polyploid and aneuploid, containing 100–130 chromosomes. These complex genomes represent a huge challenge for molecular studies and for the development of biotechnological tools that can facilitate sugarcane improvement. Here, we describe full-length enriched cDNA libraries for Saccharum officinarum, Saccharum spontaneum, and one hybrid genotype (SP803280) and analyze the set of open reading frames (ORFs) in their genomes (i.e., their ORFeomes). We found 38,195 (19%) sugarcane-specific transcripts that did not match transcripts from other databases. Less than 1.6% of all transcripts were ancestor-specific (i.e., not expressed in SP803280). We also found 78,008 putative new sugarcane transcripts that were absent in the largest sugarcane expressed sequence tag database (SUCEST). Functional annotation showed a high frequency of protein kinases and stress-related proteins. We also detected natural antisense transcript expression, which mapped to 94% of all plant KEGG pathways; however, each genotype showed different pathways enriched in antisense transcripts. Our data appeared to cover 53.2% (17,563 genes) and 46.8% (937 transcription factors) of all sugarcane full-length genes and transcription factors, respectively. This work represents a significant advancement in defining the sugarcane ORFeome and will be useful for protein characterization, single nucleotide polymorphism and splicing variant identification, evolutionary and comparative studies, and sugarcane genome assembly and annotation.
Highlights
Sugarcane (Saccharum spp.) is a C4 grass that stores large amounts of sucrose in its stems, which can account for as much as 40%–50% of the culm dry weight [1]
We present the development of a protocol to produce full-length cDNA libraries for cloning and generation sequencing (NGS), using a commercial hybrid (SP803280) and two ancestor genotypes (Saccharum officinarum and Saccharum spontaneum)
Functional activity scores Following the functional class scoring (FCS) approach [37], we developed an algorithm that integrated transcript expression profiles and metabolic pathways to estimate the activities of metabolic pathways using in-house scripts and R-statistics modules
Summary
Sugarcane (Saccharum spp.) is a C4 grass that stores large amounts of sucrose in its stems, which can account for as much as 40%–50% of the culm dry weight [1]. Biomass from sugarcane can be used for bioenergy production; the bagasse can be burned to generate electricity [2] and can be hydrolyzed to yield simple sugars from the complex plant cell wall, which can be fermented to produce bioethanol [3]. These features place sugarcane among the best feedstock options for future bioenergy production. Breeding programs used two main species for sugarcane improvement: Saccharum officinarum (2n = 80, basic chromosome number x = 10) and Saccharum spontaneum (2n = 36–128, basic chromosome number x = 8) [4]. Breeding efforts are aiming to increase energy content (GJ/ha) using Saccharum spontaneum genotypes to produce an Energycane, a higher yield cane, with increased fiber content and higher tolerance to drought
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