RT Journal Article
SR Electronic
T1 Genetic variation in a complex polyploid: unveiling the dynamic allelic features of sugarcane
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 361089
DO 10.1101/361089
A1 Danilo Augusto Sforça
A1 Sonia Vautrin
A1 Claudio Benicio Cardoso-Silva
A1 Melina Cristina Mancini
A1 María Victoria Romero da Cruz
A1 Guilherme da Silva Pereira
A1 Mônica Conte
A1 Arnaud Bellec
A1 Nair Dahmer
A1 Joelle Fourment
A1 Nathalie Rodde
A1 Marie-Anne Van Sluys
A1 Renato Vicentini
A1 Antônio Augusto Franco Garcia
A1 Eliana Regina Forni-Martins
A1 Monalisa Sampaio Carneiro
A1 Hermann Paulo Hoffmann
A1 Luciana Rossini Pinto
A1 Marcos Guimarães de Andrade Landell
A1 Michel Vincentz
A1 Helene Berges
A1 Anete Pereira Souza
YR 2018
UL http://biorxiv.org/content/early/2018/08/21/361089.abstract
AB Background Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (approximately 10 Gb) and a high content of repetitive regions. Gene expression mechanisms are poorly understood in these cultivars. An approach using genomic, transcriptomic and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane.Results The hypothetical HP600 and centromere protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behavior of this complex polyploid. The genomically side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog with all haplotypes of HP600 and CENP- C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing duplications of HP600 and CENP-C (paralogs). This duplication occurred before the Saccharum genus formation and after the separation of sorghum and sugarcane, resulting in a nonexpressed HP600 pseudogene and a recombined fusion version of CENP-C and orthologous gene Sobic.003G299500 with at least two chimerical gene haplotypes expressed. The genetic map construction supported the difficulty of mapping markers located in duplicated regions of complex polyploid genomes.Conclusion All these findings describe a low synteny region in sugarcane, formed by events occurring in all members of the Saccharum genus. Additionally, evidence of duplicated and truncate gene expression and the behavior of genetic markers in a duplicated region was found. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding the complex polyploid genome.ºCCelsius degreesBACsBacterial Artificial ChromosomesBESBAC ends sequencingBpbase pairsBRIXSoluble solid contentCDSCoding DNA sequenceCenH3histone H3CENP-CCentromere protein CCMAA3 ChromomycinDAPI4’,6-diamidino-2-phenylindoleDNADeoxyribonucleic acidESTExpressed Sequence TagFISHFluorescent in situ hybridizationGbGiga-base pairsGBSGenotyping by sequencingHMWHigh-molecular-weightKbKilo-base pairsQTLQuantitative Trait LociLTRLong Terminal RepeatMinMinutesMyaMillions Years AgoPCRPolymerase chain reactionPFGEPulsed Field Gel ElectrophoresisRNARibonucleic acidRNAseqRNA sequencingSecSecondsSNPSingle Nucleotide PolymorphismTEsTransposable Elements