PubMed Central Nuclei were isolated from the young leaf tissues of AP85-441 following the method described by Ming et al.57. To test whether genomic rearranged regions (RAR) have a genetic difference from non-rearranged regions (non-RAR), we compared the population genetic statistics π, SNP density, and Tajima’s D between rearranged and non-rearranged regions in each of four sets (A, B, C and D) of chromosomes 2, 5, 6 and 7. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. and L.L. Resistance genes are seven times more likely to locate in the four rearranged regions than in other chromosomes or regions (P < 2.2 × 1016, Fisher’s exact test; Supplementary Table 20). PCA was performed using the GCTA software on the filtered 4,476,608 variants. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. 0 Modern sugarcane cultivars are the product of complex and repeated hybridization between S. officinarum and S. spontaneum, resulting in complex hybrids with chromosome numbers and morphologies that differ from those of their progenitors. Natl. The program show-snps, implemented in the MUMmer package78, was used to identify SNPs and indels with parameters –Clr, which means only SNPs/indels from ambiguous mapping were reported. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Patrick, J. W., Botha, F. C. & Birch, R. G. Metabolic engineering of sugars and simple sugar derivatives in plants. The raw pair-end reads of 64 S. spontaneum accessions were trimmed to remove the adaptors and low-quality bases using Trimmomatic82 after quality control by FastQC83. Plant Physiol. The consensus transposable element (TE) sequences generated above were imported to RepeatMasker (version 4.05)61 to identify and cluster repetitive elements. In autopolyploid genomes, homologous genes at the same locus on homologous chromosomes are defined as alleles22. A genomic analysis of disease-resistance genes encoding nucleotide binding sites in Sorghum bicolor. What You Get. The hybrid assembled contigs and BAC contigs correspond with ~99.72% accuracy (Supplementary Table 6). analyzed P450 genes; Z.Z. Lieberman-Aiden, E. et al. But the ortholog of SsNADP-ME1 in maize, ZmNADP-ME (GRMZM2G122479), displayed non-C4-type expression35, suggesting that neofunctionalization of SsNADP-ME1 for C4 in sugarcane occurred after the divergence of maize and tribe Andropogoneae. Biol. Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity. Yearb. 18). Mist; What It Does. Pertea, M., Kim, D., Pertea, G. M., Leek, J. T. & Salzberg, S. L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. and G.Z. The genomic rearranged regions inferred by collinear dot plot and alleles phasing are shown Supplementary Table 21. BMC Bioinformatics 12, 323 (2011). The quality of Hi-C sequencing was evaluated using HiC-Pro18 (Supplementary Table 7 and Supplementary Fig. The short fragments that appear to be homologous between SbChr08 and SsChr5 and between SbChr05 and SsChr7 are remains of homeologous genes in sorghum stratum SSA formed 13.4 million years ago, well before sorghum and Saccharum diverged25. RNA-seq reads were trimmed by Trimmomatic and then mapped to the AP85-441 genome by HiSAT275. Google Scholar. 0000004209 00000 n and Xingtan Z. wrote the manuscript. a, Evolution of chromosome numbers in Poaceae, from n = 10 in sorghum to n = 8 in S. spontaneum. 5). Res. In sugarcane and sweet sorghum, the stems are the principal sink tissues that store very high concentrations of sugars within the parenchyma cells42,43,44. Chalhoub, B. et al. Telomeres and centromeres were identified based on the .dat output files above. J. U.S. Dep. Following chromosome fissions and translocations in a diploid ancestor, translocated fragments may have undergone little recombination. Genet. Genome Res. <<6968758CA214F842A6F23C5CD8A245A2>]>> After the introduction of sugarcane to the Old World around the eighth century1, its spread to Caribbean, South American, Indian Ocean and Pacific island nations drove large human migrations, including slave labor2. Google Scholar. oz. and Q.Y. The inversion events that occurred in chromosome segments are shown with red curved arrows, and the chromosomes recombined with inverted chromosome segments are marked with red plus signs. We used a 1,000-kb sliding window and a 500-kb step to calculate the values of each statistic. Dutch breeders in Java made interspecific crosses between S. officinarum and a wild relative, S. spontaneum, to obtain disease resistance and stress tolerance traits of S. spontaneum while backcrossing to S. officinarum to recover high biomass and high sugar content4. To get high-quality annotation of protein-coding genes, we carried out two rounds of MAKER running, following extensive and careful manual inspections in JBrowse68. The rings indicate (from outermost to innermost) (1) 32 pseudo-molecules in Mbp, (2) gene density, (3) TE density and (4) distribution of the regions that contributed to modern hybrid sugarcane genomes along AP85-441 chromosomes. Also, my naturals with low porosity hair tend to be protein sensitive. 21, 5654–5666 (2003). Protoc. Alignment to sorghum showed chromosome fissions in ancestral homologs of sorghum chromosomes 5 and 8, paleo-duplicated chromosome pairs A5 and A11 in grasses (Fig. Biotechnol. and M.S. SnpEff (v3.6c)88 was used to assign variants effects on the basis of gene models from S. spontaneum genome annotation. Based on gene expression and phylogenetic analysis, 8 genes—SsCA1, SsCA2, SsPEPC1, SsPEPC-k1, SsNADP-MDH2, SsNADP-ME2, SsPPDK1 and SsPPDK-RP2—were identified as C4-type genes (Supplementary Table 17). ), the US National Science Foundation Plant Genome Research Program (grant IOS-1025976 to D.M.B. 1 Adapted from Maas (1984).. 2 For some crops, the concentration given may exceed the overall salinity tolerance of that crop and cause some reduction in yield in addition to that caused by chloride ion toxicities.. 3 Values given are for the maximum concentration in the irrigation water. http://www.softberry.com/berry.phtml?topic=fgenesh&group=help&subgroup=gfind, http://tree.bio.ed.ac.uk/software/figtree/, http://www.repeatmasker.org/RepeatModeler/, http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, http://creativecommons.org/licenses/by/4.0/, https://doi.org/10.1038/s41588-018-0237-2, Evolutionary expansion and functional divergence of sugar transporters in The reduction of basic chromosomes from 10 to 8 in S. spontaneum is caused by chromosome fissions followed by translocations of two ancestral chromosomes homologous to sorghum chromosomes 5 and 8. Hardigan, M. A. et al. Chimeric fragments representing the original cross-linked long-distance physical interactions were then processed into paired-end sequencing libraries, and 1,001 million 150-bp paired-end reads were produced on the Illumina HiSeq X Ten platform. 2c, event 3), presumably occurred after the two rounds of WGD. ‘Noble’ S. officinarum cultivars, typically 2n = 8x = 80 (n is the haploid chromosome number in eukaryotic organisms and x is the monoploid chromosome number in polyploid organisms), accumulate sucrose in the stem reaching up to 50% of the dry weight but are vulnerable to biotic and abiotic stresses. 6) showed that among 21,661 gene families, 1,278 (6%) were unique to S. spontaneum. Abrusan, G., Grundmann, N., DeMester, L. & Makalowski, W. TEclass—a tool for automated classification of unknown eukaryotic transposable elements. Further information on research design is available in the Nature Research Reporting Summary linked to this article. Although the sequenced genome is haploid, each gamete contains four sets of homologous or hom(e)ologous chromosomes, representing two WGDs (that is, from one to two to four). The assembly allowed us to predict 28 potential centromeric regions along the 32 chromosomes, with length ranging from 0.25 to 11.85 Mbp (Supplementary Table 12). In unanchored sequences, 3,130 gene/alleles were annotated. CAS Population genomic analyses detected balancing selection in these rearranged regions, a mechanism to maintain genetic diversity. Humectants are perfect for low porosity hair because it attracts moisture from the outside elements. We resequenced 64 diverse S. spontaneum accessions from the world germplasm collection, identifying 4.48 million high-confidence variants that included 3,961,408 SNPs, 201,854 insertions and 291,346 deletions, averaging 1.52 variants per kb. Kortschak, H. P., Hartt, C. E. & Burr, G. O. Comparison with rice, sorghum, maize and Arabidopsis (Supplementary Fig. A high level of homologous gene retention was detected from sequencing multiple haplotypes in sugarcane, despite extreme autopolyploid redundancy21. The parameter standard errors were estimated using bootstrapping (bootstrap = 200) when doing the admixture analyses. Thank you for visiting nature.com. Chromosomal assembly was constructed based on proximity-guided assembly using our newly developed program, ALLHIC, which is designed for polyploid genome scaffolding (see Supplementary Note for details). Theor. Out of 1,440 conserved genes, 1,397 (97.1%) were re-annotated in the AP85-441 genome, among which 1,101 (76.5%) were complete and duplicated BUSCO genes. Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Acad. Zhang, J., Zhang, X., Tang, H. et al. Cladistics 5, 6 (1989). This variety is wonderful for evolving hybrid types especially to get disease and stress proof types. In addition, the GO enrichment analyses showed that the non-rearranged regions are enriched in GOs related to basic life cycles, primarily in photosynthesis, respiration and ATP synthesis (both FDR and P < 0.05, Fisher’s exact test; Supplementary Table 23), whereas the rearranged regions were enriched in many GOs related to secondary life processes, whole celluar process and intracellular anabolic and catabolic processes, transmembrane transport and ion binding (both FDR and P < 0.05, Fisher’s exact test; Supplementary Table 24). Brandes, E. W. & Sartoris, G. B. Sugarcane: its origin and improvement. AP85-441 contains 1,842 Mbp of repetitive sequences, accounting for 58.65% of the assembled genome (Supplementary Table 14). Opin. 102, 892–899 (2001). 11, e1117721 (2016). Andrews, S. FastQC, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (Babraham Bioinformatics, 2010). Finally, a total of 37,617 SNPs were selected for the constructed tree using SNPhylo software. We used the T-test and Mann-Whitney U test with the one-tailed hypothesis to compare the differences of statistics (π, SNP density and Tajima’s D) between RAR and non-RAR. Bioinformatics 25, 1329–1330 (2009). and J.X. To identify tandem repeats within the genome, the Tandem Repeat Finder (TRF) package (version 4.07)63 was used with the modified parameters of ‘1 1 2 80 5 200 2,000 –d –h’ to find high-order repeats. Said, J. I. et al. Watson, A. M. Agricultural Innovation in the Early Islamic World: The Diffusion of Crops and Farming Techniques, 700–1100 (Cambridge Univ. ), the Natural Science Foundation of China (31201260 to J.Z. Fragments were further classified as sequences from AP85-441 and sequences from LA-purple if they had a best mapping score in the corresponding category. c, The genome duplications and rearrangements in S. spontaneum, Miscanthus (genetic map), and sorghum are shown. Plant Physiol. 11, 1650–1667 (2016). Plant. Cultivated sugarcanes (Saccharum spp., Poaceae) are unusual among leading crops in that they are polyploid interspecific hybrids, with singularly complex genomes. This is indirect evidence that S. spontaneum is autopolyploid, and it reinforces the importance of allele-specific annotation for mining effective alleles of resistance genes in hybrid cultivars. Wu, T. D. & Watanabe, C. K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. 161, 341–370 (2004). 0000001284 00000 n Transcripts with FPKM (fragments per kilobase of exon per million fragments mapped) < 1 and iso-percentage < 3% were removed from further analysis. Mascher, M. et al. The reads mapped to each of four homologous haploid sets (A, B, C and D) of the AP85-441 genome were retrieved for each of 64 accessions using SAMtools85 and Bedtools96. ), the Program for New Century Excellent Talents in Fujian Province (J.Z. Nature 554, 311–316 (2018). Unknown TEs were further classified using TEclass (version 2.1.3)62. This reference genome offers substantial new knowledge and unprecedented genomic resources for sugarcane breeders and researchers to mine disease resistance and other alleles in rearranged chromosomes from historic hybrid cultivars, and to track them in breeding populations to shorten the 13-year breeding cycle. a, Principal components (PCs) of accession variation. The genome size of AP85-441 was estimated at 3.36 Gbp by flow cytometry7. The sugarcane AP85-441 contig-level assembly incorporated sequencing data from a mixture of sequencing technologies (Supplementary Fig. The distribution of calling depths (DP) of each raw variant was estimated as a criterion for variants filtering. Dark brown sugar has a deeper color and stronger molasses flavor than light brown sugar. The four haplotypes (A, B, C and D) were split into four sub-genomes, each containing eight pseudo-molecules. BMC Plant Biol. Variants with more than 15% missing data were removed. For breeding polyploid crops such as sugarcane, the segregation of alleles with different expression levels may contribute to the segregation of traits in a breeding population. Most of the genetic diversity found within S. spontaneum has not been introgressed into commercial sugarcane, and in principle, this germplasm represents a rich source of desirable agronomic traits related to stress tolerance and biomass accumulation51. Maximum likelihood trees were constructed using the maximum likelihood method by running DNAML programs in the PHYLIP package92. Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum … The concept of the monoploid genome is aimed at retaining consensus sequences among four haplotypes and covering as many genetic materials as possible. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. We estimated the rate of uniquely mapped reads outputted from both BWA86 and Bowtie284. The variants were called from a cohort of 256 BAM files generated from the previous step for each of the eight chromosomes. Genome Res. Two inversions involving single chromosomes, ancestral SbChr05L (A12L) (homologous chromosome C of SsChr6) (Fig. startxref 0000006862 00000 n Meanwhile, published full-length transcripts based on IsoSeq in sugarcane were also recruited for annotation77. Genet. The Tajima’s D in rearranged regions (−0.659 ± 0.052) is much higher than in non-rearranged regions (−0.720 ± 0.011, P = 0.005013). Analysis of the integrated S. spontaneum fraction in 15 resequenced hybrid genomes also yielded random distribution throughout the genome (Supplementary Fig. Bioinformatics 25, 1754–1760 (2009). MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Natl. ( Genom. Sugarcane, Saccharum officinarum is the fruit which prevent decaying of tooth, relieves sore throat and flu, cure jaundice and antioxidant activity . For centromere identification, we used a similar method described in the Oropetium thomaeum genome64. PubMed Press, 2008). Reset, Restyle and Refresh has never been easier. Each BAC pool was independently assembled using ALLPATHS-LG8, SPAdes9 and SOAPdenovo210, and best results were retained. and L.-Q.C. BMC Bioinformatics 9, 18 (2008). Gen. Genet. 5, R12 (2004). 0000004464 00000 n 14). The variants sites were annotated as the SNPs and Indels, as well as intergenic and genic regions (including the synonymous, nonsynonymous, intronic, upstream and downstream variants). Both principal component analysis (PCA) and admixture-based analyses clustered the 64 S. spontaneum accessions into three distinct groups (Fig.
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