Building the sugarcane genome for biotechnology and identifying evolutionary trends

Abstract

BackgroundSugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.ResultsThree hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.ConclusionThis release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-540) contains supplementary material, which is available to authorized users.

Revisiting Meiosis in Sugarcane: Chromosomal Irregularities and the Prevalence of Bivalent Configurations

“…Next, we used information extracted from the centromeric bacterial artificial chromosome (BAC) insert of a R570 cultivar genomic library annotated in Setta et al (2014). This BAC (SCHRBa029018; GenBank: KF184699) contains the centromeric sequence repeat (137 bp) belonging to the SCEN family described by Nagaki et al (1998), examining an Egyptian cultivar.…”

“…The unusual genome complexity and inter-relationships within Saccharum (with ploidy levels ranging from 5× to 16×) has inspired several molecular studies that have elucidated aspects of sugarcane genome constitution (Souza et al, 2011; Setta et al, 2014), architecture (Garcia et al, 2013), and cytogenetics, studied mainly by D’Hont et al (1993; 1996; 1998), D’Hont (2005) and Piperidis et al (2010). However, there is a critical shortage of information on chromosome behavior throughout meiosis.…”

Pemanfaatan bioinformatika dalam bidang pertanian dan kesehatan (The utilization of bioinformatics in the field of agriculture and health)

“…Penelitian terkait sekuensing genom tanaman telah dilakukan pada padi dan jagung sejak 19 tahun yang lalu (COE 1998;Goff et al, 2002). Beberapa contoh lain genom lengkap dari spesies tanaman yang sudah disekuens dalam kurun waktu 10 tahun terakhir adalah tanaman kentang, tomat, kacang kedelai, rumput, kelapa sawit, karet, kopi dan tebu (Haas et al, 2009;Schmutz et al, 2010;Vogel et al, 2010;Xu et al, 2011;Sato et al, 2012;Singh et al, 2013;Denoeud et al, 2014;de Setta et al, 2014;Lau et al, 2016;Tang et al, 2016). Sebagian basis data terkait genom tanaman tersebut bersifat publik atau disebut open access sehingga dapat digunakan dalam penelitian lanjutan oleh para peneliti di seluruh dunia.…”

Perspectives on the genomics research of important crops in the tribe Andropogoneae: Focusing on the Saccharum complex

“…When low copy BESs were compared to the sorghum genome, they cover about 200 mega base pairs (Mbps), consisting of the entire size of euchromatic regions of sorghum. Those BACs were specifically selected for the initial sequencing of hybrid sugarcane cultivars because of their high possibility of being in the euchromatic regions of hybrid sugarcane cultivars, and these results were published soon after (de Setta et al, 2014). With the advances of NGS technologies, the entire genome has been sequenced with various platforms at this point.…”

“…S. bicolor is also an important food crop in Africa and South Asia, which is the "fifth-most important cereal crop grown in the world" after maize, wheat, rice, and barley (http://www.fao.org/). Sugarcane is an important crop worldwide, producing about 80% of the world's raw sugar and is getting more attention as feedstock for the production of 1 st generation bioethanol (de Setta et al, 2014). The genus Miscanthus has also been considered attractive as feedstock for lignocellulosic biofuel (2 nd generation bioethanol) production because it produces high yields of biomass but with low-nutrient requirements, adapts well to marginal land with resistance to abiotic stress, and does not compete with use for food.…”