New Phytol. 0000004761 00000 n From a BAC library of AP85-441, 35,156 BAC clones were pooled into 712 libraries (mostly of 48 BACs; Supplementary Table 1), and individual BAC pools were sequenced independently by a Hiseq 2500 with PE250 (paired-end model and 250-bp read length), yielding 267.5 Gbp of data that were assembled using three different assemblers: ALLPATHS-LG8, SPAdes9 and SOAPdenovo210, yielding a 2.56-Gbp assembly with contig N50 of 7.4 kb (Supplementary Tables 2 and 3). Tissue-specific transcriptome analysis within the maturing sugarcane stalk reveals spatial regulation in the expression of cellulose synthase and sucrose transporter gene families. The sequence alignment/map format and SAMtools. PubMed  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. 18). Of 4,289 genes, on average, 37.6% displayed neutral expression and 62.4% displayed non-neutral expression, suggesting that the expression of alleles varied. Purcell, S. et al. Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) Insertions larger than 50 bp were identified on Assemblytics79, a Web-based SV analytics tool, and further inserted into the reference genome. 0000000016 00000 n U.S. Dep. The homologous genome expression levels of the four homologous genomes were similar in examined tissues (Supplementary Fig. 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. The ancestor of SbChr05 (A12) split into two major segments, C5S (A12S) and C5L (A12L)24, that translocated into ancestors of SbChr06 (A2) and SbChr07 (A5), respectively (Fig. Genes with significant improvement were replaced with the FGENESH annotation. Due to polyploidy, existing Hi-C scaffolding programs such as LACHESIS14 and SALSA17 link S. spontaneum allelic haplotypes together and are no longer suitable for this autopolyploid genome. 0000001851 00000 n Plant Biol. Chalhoub, B. et al. BMC Bioinformatics 7, 62 (2006). Nucleic Acids Res. To exploit the fact that paralogs are often located on all four of a set of hom(e)ologous chromosomes, we developed a framework to carry out a more sensitive study of gene pair similarities (Supplementary Note). We mapped the sequences back to the AP85-441 genome, and they were randomly and evenly distributed, not constituting a set or sets of chromosomes as expected (Fig. Li, B. Plants 1, 14001 (2015). Brown sugar (light and dark): Brown sugar retains some of the surface molasses syrup, which imparts a characteristic pleasurable flavor. Sequencing was performed using the Illumina HiSeq 2500 platform. The two crops also have different plant physiologies: Sugar cane is a C4 crop, while sugar beets are C3, and in sugar cane the sugar is stored in the stalk, while in beets it is stored in the roots. ), the Natural Science Foundation of China (31201260 to J.Z. Hoang, N. V. et al. Jisen Zhang or Chifumi Nagai or Ray Ming. BMC Bioinformatics 9, 18 (2008). 101, 103–111 (1966). The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement. Construction and characterization of a papaya BAC library as a foundation for molecular dissection of a tree-fruit genome. Article  Proc. Wang, L.-P. et al. The HaplotypeCaller was used to estimate the SNPs and indels for putative diploids using the default parameters. Sugarcane has been cultivated in Brazil since 1532 as sugar was one of the first commodities exported to Europe by the Portuguese settlers. 19, 141–147 (2003). 17, 66 (2016). You are using a browser version with limited support for CSS. Benson, G. Tandem repeats finder: a program to analyze DNA sequences. manually checked the gene allele annotation; S.R.D., D.M.B., S.E.H. 2c, event 5). 189, 629–642 (2011). Bioinformatics 23, 1061–1067 (2007). by molecular cytogenetics. USA 108, 1513–1518 (2011). 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. BUSCO20 version 3 was used for evaluation of annotation completeness. Genome Res. Fractions at approximately 100 kb were recovered and cloned into the pSMART BAC vector (Lucigen). The two sugar crops together take up slightly more than 2% of the cultivated croplands in the world. Indigenous and traditional foods of Sri Lanka inherit a long history and unique traditions continued from several thousands of years. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Plotree, D. & Plotgram, D. PHYLIP-phylogeny inference package (version 3.2). Cultivated sugarcanes (Saccharum spp., Poaceae) are unusual among leading crops in that they are polyploid interspecific hybrids, with singularly complex genomes. Gen. Genet. and JavaScript. Google Scholar. The lowest chromosome number recorded for natural Saccharum accession is a 2n = 5x = 40 S. spontaneum that no longer exists; however, exactly one haploid (1n = 4x = 32) S. spontaneum, AP85-441, generated from a culture of octoploid SES2086, provides a foundation for assembly of a prototypical version of the sugarcane chromosome set. In addition, the RNA-seq reads were mapped to the AP85-441 genome using HiSAT275 version 2.10 and reassembled using StringTie76 version 1.3.4, which is a reference-based RNA assembler. The longest pseudo-molecule was used as reference for each set of haplotypes, and the other three haplotypes were mapped against the reference for SNP/indel and SV calling using the nucmer78 program. Plant Physiol. generated and maintained haploid plant materials and mapping populations; J.Z., Q.Z., X.H., Z.Li, Y.W., L.W. These filtering strategies reduced the raw unfiltered set of variants (SNPs and indels) to the working set of 68,911 variants. 6) showed that among 21,661 gene families, 1,278 (6%) were unique to S. spontaneum. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Trends Genet. Zhang, J. et al. 58, 1442–1460 (2017). 5a,c; for other K-values, see Supplementary Fig. J. Comput. 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. definition of - senses, usage, synonyms, thesaurus. Whereas there are 3 TST genes in the sorghum genome47, the family has expanded in the S. spontaneum genome, which has 4 genes consisting of 13 homologs. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. Consequently, modern sugarcane cultivars are interspecific hybrids with approximately 80% chromosomes from S. officinarum, 10–15% chromosomes from S. spontaneum, and 5–10% recombinant chromosomes5. Bioinformatics 21, 1859–1875 (2005). 18a,b) that were also supported by phylogenetic relationships among the 64 accessions inferred by bootstrapping and geographic origins (Supplementary Table 23), with group 1 originating from China, the Philippines, Indonesia and Papua New Guinea and groups 2 and 3 originating from India, Pakistan and Iran. Said, J. I. et al. Domesticated in New Guinea ~10,000 years ago, ‘reeds that produce honey without bees’ were considered a luxury and an expensive spice from the sixth to fourth centuries bc. Identification of alleles in the AP85-441 genome was based on two strategies: (1) synteny-based and (2) coordinate-based approaches. In practice, however, nucleotide diversity (π) across S. spontaneum was estimated to be 0.00021 ± 0.000002 (Supplementary Tables 21 and 22 and Supplementary Fig. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. 81, 559–575 (2007). Res. Agric. We identified 361 sequences putatively encoding nucleotide-binding site (NBS) proteins, including 22 N-type, 169 NL-type, 68 CN-type and 102 CNL-type. Two inversions involving single chromosomes, ancestral SbChr05L (A12L) (homologous chromosome C of SsChr6) (Fig. 3 and Supplementary Table 15). The predicted LTRs were further classified into intact and non-intact LTRs, and the insertion time was estimated as T = K/2μ (K is the divergence rate, and μ is the neutral mutation rate; the default is 1.38 × 10−8 in LTR_retriever) using the scripts implemented in the LTR_retriever package65. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Article  2c, event 3) and the bottom of SsChr5C (Fig. Tonoplast sugar transporters (TSTs) have been characterized as sucrose transporters highly associated with vacuolar sucrose accumulation from sugar beet taproot45, sugarcane46 and sweet sorghum stems47 and watermelon fruit48. The leaves of the plant grow from the nodes of the stem, arranged in two rows on either side of the stem. Thank you for visiting nature.com. To provide a scaffold for contig assembly, four Hi-C libraries were constructed from young leaves of AP85-441. The corrected reads, along with BAC-assembled contigs, were imported to the assembly step. BMC Plant Biol. Price, A. L., Jones, N. C. & Pevzner, P. A. Extensive manual inspection of the annotation identified that 28,306 gene models had a significant difference in protein length or sequence similarity compared with other reported protein sequences in the NCBI NR database. We estimated the rate of uniquely mapped reads outputted from both BWA86 and Bowtie284. 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). A tonoplast sugar transporter underlies a sugar accumulation QTL in watermelon. Nat. Ren, Y. et al. Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily. Xu, Z. 1). Plant Cell Physiol. The rearranged regions in S. spontaneum with high levels of genomic diversity (π value) might result from a preponderance of adaptive genes related to habitat or stress adaptation, such as responses to various abiotic stresses (drought, salinity, alkaline, metal ions and so on), which are controlled by genes of whole celluar process and intracellular anabolic and catabolic processes, transmembrane transport and ion binding, as detected in these regions. 7), including Ty1/copia and Ty3/gypsy superfamilies that occurred between 0.72 and 2.9 million years ago. Wang, Y. et al. Internet Explorer). Two fissions in ancestral homologs of sorghum chromosomes SbChr05 and SbChr08 that resulted in translocations to a set of two chromosomes each occurred before the two rounds of WGDs in Saccharum and after the divergence of Saccharum and Miscanthus (Fig. and A.S. isolated BAC DNA; S.Chen, L.H., W.Zhang, Yanhong M., Z.Y., F.D. 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. PubMed Central  Sticky ends were biotinylated and proximity-ligated to form chimeric junctions that were enriched for and then physically sheared to a size of 500–700 bp. 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. Figtree v.1.4 (see URLs) was used to visualize the trees. Nat. Watson, A. M. Agricultural Innovation in the Early Islamic World: The Diffusion of Crops and Farming Techniques, 700–1100 (Cambridge Univ. A new carboxylation reaction and the pathway of sugar formation. The top three principal components were used for assigning the 64 accessions and downstream population structure analysis. Biotechnol. Cladistics 5, 6 (1989). Average yields are around 90-100 tons/ha for the first planting, and between 40 and 60 tons/ha Telomeres and centromeres were identified based on the .dat output files above. Langmead, B. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. FPKM was calculated on the basis of unique mapping reads using the StringTie package76. 14, 206–216 (1972). RSEM was used to calculate transcript abundance70. For PacBio assembly, Canu v1.511 was used, as it is capable of avoiding collapsed repetitive regions and haplotypes. Nat. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. 11, 142–156 (2013). Genet. Analysis of the integrated S. spontaneum fraction in 15 resequenced hybrid genomes also yielded random distribution throughout the genome (Supplementary Fig. Curr. Plant Physiol. Both principal component analysis (PCA) and admixture-based analyses clustered the 64 S. spontaneum accessions into three distinct groups (Fig. In the modern hybrid sugarcane SP80-3280, approximately 12.25% of sequences are contributed by S. spontaneum. This project was supported by a startup fund from Fujian Agriculture and Forestry University to R.M., the International Consortium for Sugarcane Biotechnology (project #35, R.M. 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. The authors declare no competing interests. and Xingtan Z. wrote the manuscript. Fly 6, 80–92 (2012). Servant, N. et al. ‘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. RNA-seq reads were trimmed by Trimmomatic and then mapped to the AP85-441 genome by HiSAT275. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Then, the functional annotation and GO enrichment analyses of gene models were conducted in Blast2Go v4.1 software97. Crop Sci. De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana. Finally, a monoploid genome, containing eight representative pseudomolecules and 785 Mbp of sequence, was generated for further analysis (Fig. Google Scholar. & Braun, D. M. Tonoplast sugar transporters (SbTSTs) putatively control sucrose accumulation in sweet sorghum stems. The rings indicate (from outermost to innermost) monoploid genome in Mbp (a), SNP density among haplotypes (b), gene density (c), expression (d) and nucleotide diversity (e). Mol. However, inversions in ancestral SbChr08S and SbChr08L in two pairs, SsChr2AB and SsChr7AB, indicate that these occurred after the first WGD but before the second (Fig. Williams, L. E., Lemoine, R. & Sauer, N. Sugar transporters in higher plants—a diversity of roles and complex regulation. Hence, it is reasonable to hypothesize that TSTs are the most promising players to sequester sucrose into the vacuoles of the sugarcane stem46,47,49. Am. The high-molecular-weight DNA embedded in agarose was partially digested using HindIII. 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). Ecol. Methods 9, 357–359 (2012). Bioinformatics 26, 841–842 (2010). Plant Physiol. 11 and 12). Nature 554, 311–316 (2018). Biol. Chromosomes are represented with color codes to illuminate the evolution of segments from a common ancestor with 5 chromosomes. S. spontaneum contributed disease resistance genes to modern sugarcane hybrid cultivars. 0000004837 00000 n Bioinformatics 25, 1754–1760 (2009). Sugar cane is a Gramineae, tribe Andropogenae which contains 6 species. Bioinformatics 21, 3674–3676 (2005). Wu, G. A. et al. Protoc. a, Evolution of chromosome numbers in Poaceae, from n = 10 in sorghum to n = 8 in S. spontaneum. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Then ab initio gene predictors, including SNAP72, GENEMARK73 and AUGUSTUS74, were each trained with those selected proteins. Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato. S. spontaneum is a recent autopolyploid, and homologous genomes are fluid and changing after each meiosis. Bioinformatics 30, 2114–2120 (2014). We thank L. McHale for reviewing and commenting on the section on disease resistance genes. assembled and annotated the genome; J.B., R.M., Q.Z., Xingtan Z. J.Z. Four Hi-C libraries were created from tender leaves of AP85-441 at BioMarker Technologies Company as described previously58. We further analyzed the variations in gene number among tissues; the numbers of both neutral and non-neutral genes were similar among the examined tissues. 1), i351–i358 (2005).
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