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Using two rounds of MAKER followed by manual annotation to separate genes and alleles, we annotated 35,525 genes with alleles defined, including 4,289 (12.7%) genes with four alleles, 9,792 (27.6%) with three, 14,797 (41.7%) with two, and 6,647 (18.7%) with one. Front Physiol. c The ratio of LTR-related genes in CSGs and FSGs. ISSN 2055-0278 (online). International Wheat Genome Sequencing Consortium (IWGSC). Nat. We speculate that the expansion of TEs in the giant genome grasshopper species might help them better adapt to the living environment, because the A. rhodopa species was collected at higher altitude areas (average altitude of 3000 m). However, in A. rhodopa small RNAs with a length of 22 nt are in the majority. From primary to secondary growth: origin and development of the vascular system. M.Y., L.F., X.A. Small RNA Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB). This study illuminates the hereditary blueprint and evolutionary history of one of our most important, and most complex, crop genomes. Zhao, W. et al. Genetics. Langmead B, Trapnell C, Pop M, Salzberg SL. https://doi.org/10.1038/nplants.2016.115. 3, research0034.1 (2002). Pitt, J. N. & Ferr-DAmar, A. R. Rapid construction of empirical RNA fitness landscapes. Genome Biol. 2020;13:1194202. The SsChr1C region showed equal distribution among three homologs, indicating a deletion in SsChr1C (Supplementary Table 16 and Supplementary Fig. 4d). Saccharomyces Genome Database: the genomics resource of budding yeast. All seed plants produce pollen and deliver their sperm through the growth of a pollen tube, whereas all non-seed land plants (that is, bryophytes, lycophytes and ferns) rely on free-swimming motile sperm for sexual reproduction, as do the ancestors of land plants1,4 (Extended Data Fig. and Yubo Wang contributed equally. BMC Bioinformatics 7, 62 (2006). Rozanski, A. et al. Genome Biol. Zhao Q, Feng Q, Lu HY, Li Y, Wang A, Tian QL, et al. 2014;157(6):136479. 2016;38(11):115866. We also identified 69 ancient syntenic genomic segments that further support a gymnosperm-wide WGD (Extended Data Fig. At the onset of invasion, TEs start as a single copy in the host genome. 18). Trends Genet. Further information on research design is available in the Nature Research Reporting Summary linked to this article. Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. 12, 656664 (2002). SnpEff (v3.6c)88 was used to assign variants effects on the basis of gene models from S. spontaneum genome annotation. Bioinformatics 21, 36743676 (2005). Smit, A., Hubley, R. & Green, P. RepeatMasker Open-4.0, http://www.repeatmasker.org. (c) The heatmaps showing the correlation between observed and Nvwa-predicted cell type-specific transcription for eight species. Phylogenetic analyses suggest that the fitD genes might have been acquired from fungi and then expanded before the divergence of C. panzhihuaensis and C. debaoensis (Fig. S4d). 17), much lower than that in other clonally propagated crops such as potato53, cassava54, grape55 and citrus56. Grob S, Schmid MW, Grossniklaus U. Hi-C Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila. Wapinski, I., Pfeffer, A., Friedman, N. & Regev, A. Experimentally measured (y axis) and predicted (x axis) expression level (lo) or expression change from the starting sequence (hk) in complex (h, j, l, n) or defined (i, k, m, o) medium using sequences from the random genetic drift (Fig. Biol. Kalvari I, Nawrocki EP, Ontiveros-Palacios N, Argasinska J, Lamkiewicz K, Marz M, et al. Lieberman-Aiden, E. et al. HENMT1 and piRNA stability are required for adult male germ cell transposon repression and to define the spermatogenic program in the mouse. Mol. c, Phylogeny of SSPs in some representative species in land plants. Jianxiang Ma, Pengchuan Sun, Yongzhi Yang, Liangsheng Zhang, Fei Chen, Haibao Tang, Fay-Wei Li, Tomoaki Nishiyama, Pter Szvnyi, Nora Walden, Dmitry A. German, Marcus A. Koch, Gregory W. Stull, Xiao-Jian Qu, Ting-Shuang Yi, Nature Plants Front Genet. The association of this SNP with the hulless trait was validated by the development of KASP (Kompetitive allele-specific polymerase chain reaction) markers (Fig. Sequences were classified as fragments from both if they had similar mapping scores (<5% difference) in the LA-purple and AP85-441 genomes. Liu SY, Liu YM, Yang XH, Tong CB, Edwards D, Parkin IAP, Zhao MX, Ma JX, Yu JY, Huang SM, et al. The putative domains and GO terms of the predicted proteins were identified using the InterProScan (v5.22)67 program with the default settings. The average expression level of core genes was also significantly higher than that of dispensable genes (Fig. Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. AdaLead: a simple and robust adaptive greedy search algorithm for sequence design. Natl Acad. 14, 988995 (2004). Nat. In addition, the proportion of unclassified repetitive elements is also vastly different in A. rhodopa and L. migratoria, accounting for 22% and 7.01% of the genome, respectively. 2c and 4f). wrote the initial draft of the manuscript. All branches are maximally supported by bootstrap values (ML) and posterior probabilities (ASTRAL). K.Y., X.D. Vaser, R., Sovic, I., Nagarajan, N. & Sikic, M. Fast and accurate de novo genome assembly from long uncorrected reads. To distinguish the subgenomes accurately and clarify the polyploidization history of the hexaploid oat, we sequenced and assembled its most likely ancestral species A. longiglumis (2n=2x=14, AlAl genome) and A. insularis (2n=4x=28, CCDD genome)5, resulting in >60 genome coverage for A. longiglumis (218.67Gb) and A. insularis (374.77Gb). Kelleher ES, Barbash DA. Article Insect Mol Biol. Natl Acad. Running Trinity. iGenome-guided RNA-seqCufflinksStringtieCPATCPC ii) De novo assembly Although several individual chromosomes do not show significant differences, comparisons averaging values on all chromosomes show nucleotide diversity () in rearranged regions (0.000250.00003) to be much higher than in non-rearranged regions (0.000210.00001, P=0.000234). Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. Trends Plant Sci. Genomic plasticity and the diversity of polyploid plants. 2020;20(1):118. To maximize the opportunity of identifying high-confidence genes, we further filtered the genes that were not expressed in the full-length transcriptome or did not match to functional annotation results. Most of these R-genes occur in clusters at the distal ends of all chromosome arms. The 144 resequencing accessions were subjected to the same methods for extraction of genomic DNA and were sequenced on a BGISEQ-500 platform. A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa. 3f and Additional file 3: Table S25), and the ratio of FSGs in the multi-copy gene sets was more than twice that of the single-copy gene set in each of the 18 genomes, illustrating that the multi-copy genes were more likely to be flexible during intraspecific diversification. Nat. PubMed Central Langmead, B. Cao, J. Y. et al. Google Scholar. Nat Biotechnol. Natl Acad. 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Taken together, these results demonstrate subgenome dominance in hexaploid oat. Mol Biol Evol. Alipanahi, B., Delong, A., Weirauch, M. T. & Frey, B. J. The x-axis represents the TE density in each group. Press, 1997). TEs suffer different fates, which may be related to the host defense mechanism against TE invasion. Yuanying Peng, Tao Ma, Yuming Wei, Fei Lu or Changzhong Ren. 16, 962972 (2006). JCYJ20151015162041454 to Huan Liu). Each of the three whole-genome assemblies was searched for repetitive sequences including tandem repeats and TEs. Controlling gene expression with deep generative design of regulatory DNA, https://codeocean.com/capsule/8020974/tree. To search for genome-wide duplications, we used DupGen_finder (https://github.com/qiao-xin/DupGen_finder) to identify duplicated genes that were classified into five different categories: WGD duplicates, tandem duplicates, proximal duplicates, transposed duplicates and dispersed duplicates. Potential polymerase chain reaction duplicates were removed using SAMtools (v1.9)74. Genet. 1), i351i358 (2005). Jones, P. et al. The ping-pong cycle is a keystone of the piRNA pathway because it both silences TEs post-transcriptionally and enhances the silencing capacity of the pathway by producing more piRNA [95, 96]. Intraspecific diversification mainly occurred in dispensable and private genes. Internet Explorer). FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Google Scholar. Li AL, Liu DC, Wu J, Zhao XB, Hao M, Geng SF, et al. Article InterProScan 5: genome-scale protein function classification. bioRxiv. The initial cross-linked long-distance physical interactions were then represented by chimeric fragments, which were processed into paired-end sequencing libraries. 4). 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RNA-Seq (named as an abbreviation of RNA sequencing) is a sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing cellular transcriptome.. Both L. migratoria and A. rhodopa belong to the Oedipodinae subfamily, but most of the TEs are unique to each other. (c) Transcript expression level is indicated by TPM during seed development. 20, 12971303 (2010). generated and maintained haploid plant materials and mapping populations; J.Z., Q.Z., X.H., Z.Li, Y.W., L.W. 2014;55:67893. We developed a Hi-C-based scaffolding algorithm (ALLHIC) that integrates four functionspruning, partition, optimization and buildingto select contigs specific for polyploid genome assembly (see Online Methods and Supplementary Figs. Protoc. Kelley, D. R., Snoek, J. Nucleic Acids Res. https://doi.org/10.4161/fly.19695. Together with the two reported genomes (Chiifu and Z1) [31, 47], we obtained a total of 18 B. rapa de novo assembled genomes in the present study. Many gymnosperms are tall, woody plants with cell walls containing large quantities of cellulose, xyloglucan, glucomannan, homogalacturonans and rhamnogalacturonans45. Dufresne F, Jeffery N. A guided tour of large genome size in animals: what we know and where we are heading. Run Trinity on Terra; Running Trinity. Thompson, D. A. et al. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, et al. Biol. We therefore analyzed the effect of piRNAs on post-transcriptional silencing of TEs. Open Access Sci. These results indicated that A.satnudSFS4D01G000045 may be a promising plausible candidate gene that controls the hulled/hulless trait in oat. The inner ring 5 indicates the miRNA location over the genome. Plant Physiol. Res. & Troyanskaya, O. G. Predicting effects of noncoding variants with deep learning-based sequence model. 2008;24(3):11423. Phylogenetic inferences in Avena based on analysis of FL intron2 sequences. Bioinformatics 19, 362367 (2003). Comprehensive mapping of long-range interactions reveals folding principles of the human genome. A. G. M., Elena, S. F., Fragata, I. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Quang, D. & Xie, X. DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences. The SV was previously reported to only occur in oil-type B. rapa and contributed to variation in flowering time [46]. f, LTR retrotransposon density. From the landscapes of each TE subclass, the greatest difference between the two species is LTR, with the landscape peaking closer to the y-axis for A. rhodopa than for L. migratoria (Additional file 1: Fig. Evolutionary dynamics of transposable elements in a small RNA world. We found that TE has higher transcriptional activity in the testis, and this difference in TE activity between different tissues is consistent in L. migratoria and A. rhodopa. d INT domain transcripts abundance in two species of different tissues. Curr Opin Plant Biol. The similarity refers to the AUROC score from MetaNeighbor analysis. b, Ratio of , FST and difference of pooled heterozygosity (Hp) within a 100-kb sliding window between the female and male sequences. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. A. Phylogenetic analyses and morphological innovations in land plants. We observed high gene variability and enormous structural complexity in the pan-genome. Ren, Y. et al. 5). Counting Full-length CAS In the second round of MAKER running, the predicted gene models with AED score equal to 0 were extracted for retraining using SNAP72, GENEMARK73 and AUGUSTUS74. Pan-Genome of Wild and Cultivated Soybeans. The phylogenetic trees were generated using RAxML with PROTCATGTR model and 500 bootstrap replicates. Hartl, D. L. What can we learn from fitness landscapes? Extended Data Fig. Evol. Environ. Cultivated oats are generally classified into two production-related morphological types, hulled and hulless, which is one of the domestication traits (Fig. Mol Biol Evol. The Am1-rich regions on chromosomes 1A, 2D, 3D, 4D and 5D of Sanfensan are C genome introgressions. 2019YFC1711000 to Huan Liu), the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (No. Cell 173, 15201534.e20 (2018). Conserved and Flexible represent conserved and flexible syntenic gene in the homoeologous pair. 7c). 22, 203215 (2021). 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). Shalem, O. et al. The Piwi protein family did not display significant differences between the two species in the testis (Fig. Philos Trans R Soc B Biol Sci. The CSLE/G from gymnosperm are the ancestral form of the angiosperm CSLE and CSLG. Nat Genet 50, 15651573 (2018). Kim D, Landmead B, Salzberg SL. (d) Sankey diagram showing homologous relationships among vertebrates immune-related TFs. Liu, X., Majid, M., Yuan, H. et al. All of the raw reads generated in this work have been also deposited in the genome sequence archive (https://bigd.big.ac.cn) under the accession number CRA003187. The review history is available as Additional file 6. The culture was induced by adding a 0.01mM final concentration of isopropyl--d-thiogalactoside and incubated at 28C for 6h. Cells were then harvested and suspended with 20ml 50of mM TrisHCl buffer with pH 8 at 4C, containing 200mM NaCl, then disrupted by sonication at 4C. However, we cannot use this hexaploid ancestor to investigate the intraspecific diversification, as we cannot distinguish gene fractionation during speciation from that during intraspecific diversification. https://doi.org/10.1016/j.cels.2016.07.002. Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution. Med. Exploration of repetitive sequences using unassembled raw genome data is at a loss compared to the full assembled genome. Article Mol. A. C. M. Santos, V. Echenique, Sampath Perumal, Chu Shin Koh, Isobel A. P. Parkin, Aaron L. Phillips, Scott Ferguson, Brian J. Atwell, Nature Genetics 38, W7W13 (2010). Abbreviations are defined as T = testis; O = ovary; M = male body; F = female body. (a) Sankey diagrams showing homologous cell-type pairs between human and mouse obtained from SAMap analyses based on different datasets. and Xingtan Z. wrote the manuscript. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. Funct. We annotated 43,477 and 89,995 protein-coding genes in the A. longiglumis and A. insularis genomes respectively (Table 1). Plant Physiol. Acad. Combined with the genomic content of retrotransposons, we compared the abundance of retrotransposon transcripts and piRNAs between the two species. 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. 2017;1389(1):16485. We allowed the variant sites with max-missing rate as 50%. Here we build sequence-to-expression models that capture fitness landscapes and use them to decipher principles of regulatory evolution. Many copies of these genes were found to be highly expressed in cambium or apical meristem of C. panzhihuaensis (Supplementary Note 6). 10, 233240 (2009). We identified 7,353 one-to-one orthologous gene sets for the eight Avena (sub)genomes and H. vulgare cv. Biotechnol. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. We compared the abundance of piRNAs in the testis and ovary of the two species. https://doi.org/10.1038/s41477-022-01129-7, DOI: https://doi.org/10.1038/s41477-022-01129-7. The genomic rearranged regions inferred by collinear dot plot and alleles phasing are shown Supplementary Table 21. All sequenced diploid accessions were further subjected to transcriptome sequencing. We annotated 1,256 tandemly duplicated genes and 3,375 dispersedly duplicated paralogs (Table 1). Although, as we explained, these four domesticated genes are excellent candidates to have contributed to leafy head formation, we still have no direct experimental evidence to support this. In practice, however, nucleotide diversity () across S. spontaneum was estimated to be 0.000210.000002 (Supplementary Tables 21 and 22 and Supplementary Fig. The top and bottom edges of the box indicate the first and third quartiles and the whiskers extend 1.5 times the interquartile range beyond the edges of the box. Subgenome dominance is a common phenomenon that is widely observed in allopolyploids, including cotton [8], Brassica [9], and wheat [10]. J. Carballo, B. First, rRNA, tRNA, and snRNA were removed from small RNA sequencing data (see Methods). 9, 884 (2018). 2021;49(D1):D412D9. BMC Evol. A de novo genome of a Chinese radish cultivar. 2g, Additional file 2: Figure S17 and Additional file 3: Table S21). Slewinski, T. L. & Braun, D. M. Current perspectives on the regulation of whole-plant carbohydrate partitioning. Renny-Byfield S, Rodgers-Melnick E, Ross-Ibarra J. Gene Fractionation and Function in the Ancient Subgenomes of Maize. Evolutionary history studies on TEs suggest that TEs may be subject to different dynamics and resistances in these two species. 9, 286 (2009). Plant Cell Physiol. https://doi.org/10.1111/nph.13491. We calculated the K2P divergence of 41 shared TEs in the two species genomes using RepeatMasker (Additional file 2) (see Methods). Book (A) Two reads and sequenced from different genes of the same family are aligned to the profile HMM of the family. Euphytica 185, 511519 (2012). Nat. Vikram, P. et al. The average densities of genes in LF, MF1, and MF2 were 0.727, 0.507, and 0.435, respectively (Fig. 5). X-axis indicates the percentage. by molecular cytogenetics. 2020;37:4956. Google Scholar. Transposition activity of TEs. Kofler R, Nolte V, Schltterer C. Tempo and mode of transposable element activity in Drosophila. The reads were filtered with a sliding window of size 7, with average Phred score scale of 20 within the window. 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Levin&Aviv Regev, Departamento de Biologa, Facultad de Qumica y Biologa, Universidad de Santiago de Chile, Santiago, Chile, ANIDMillennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel, The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA, You can also search for this author in https://doi.org/10.1105/tpc.114.124388. TEs consume resources by hijacking cellular machinery to produce mRNAs and proteins necessary for transposition, and TEs expansion can directly disrupt genes or promoter regions [22, 23]. Bioinformatics 25, 20782079 (2009). The PASA-assembled transcripts described above were used for training. Mol. Xu, Z. & Mirarab, S. DiscoVista: Interpretable visualizations of gene tree discordance. Extended Data Fig. (fj) Midline: median; boxes: interquartile range; whiskers: 5th and 95th percentile range. Genetics 204, 16131626 (2016). Weinreich, D. M., Lan, Y., Wylie, C. S. & Heckendorn, R. B. & Pawowski, T. A. DNA synthesis pattern, proteome, and ABA and GA signalling in developing seeds of Norway maple (Acer platanoides). 2011;52:494501. A tandem duplication of SsNADP-ME2, SsNADP-ME1, also displayed a C4 expression profile similar to that of SsNADP-ME2. Google Scholar. Senti K-A, Jurczak D, Sachidanandam R, Brennecke J. piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire. Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal phenotype and fitness1,2,3. Chimeric fragments representing the original cross-linked long-distance physical interactions were processed into paired-end sequencing libraries, then 1 billion 150-bp paired-end Illumina reads were produced and uniquely mapped onto the draft assembly contigs. Oat has good adaptability to a wide range of climatic conditions, enabling oat to reliably produce grains in marginal regions with harsh conditions. tauschii (Atau), T. turgidum ssp. 2018;36:875. and JavaScript. The high confidence 4,476,608 variant set was used for statistical estimations. Tabula Sapiens, C. et al. PubMed Biochem. When the oat assembly was compared with the three subgenomes of common wheat using barley genomes as a reference, a large number of chromosomal rearrangements were identified. (a) Comparison of the longest 10% of introns and gene in the representative land plants. Nat Protoc. Leebens-Mack, J. H. et al. https://doi.org/10.1038/ng.919. Article Li, H. & Durbin, R. 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SSCG, single-copy genes; LCG, low-copy genes; MT, mitochondrial genes; PT, plastid genes; AA, amino acid sequences; NT, nucleotide sequences; NT12, codon 1st+2nd positions; ASTRAL, coalescent tree inference method using ASTRAL; CONCAT, maximum likelihood tree inferred with IQ-TREE based on concatenated datasets; STAG, species tree inference using software STAG with low-copy genes (one to four copies); Original, original organellar nucleotide sequences; RNA Editing, organellar genes with RNA editing site modified. Biotechnol. In addition, the NeiGojobori method101 as implemented in the PAML packages yn00 program91 was used to estimate synonymous substitutions per synonymous site (KS) for pairwise comparisons of paralogous genes located on syntenic blocks. The BRL1 and BRL3 genes encode brassinosteroid receptors that play major roles in xylem differentiation and phloem/xylem patterning in angiosperms44. 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As a mesopolyploid crop, B. rapa evolved from a translocation Proto-Calepineae Karyotype (tPCK) ancestor and has experienced a whole-genome triplication (WGT) event [43, 44], and the two-step theory was proposed to explain the meso-triplication of the Brassica A genome and the dominant subgenome in the extant diploid genome [16]. 2014;345(6199):9503. In total, 7900 single-copy gene families were detected within the 19 genomes. PubMed Provided by the Springer Nature SharedIt content-sharing initiative. Each of the fragments was blast against the AP85-441 and LA-purple (unpublished) masked genomes, respectively, and the mapping score was calculated for each blast hit using the following formula: where S indicates mapping score, N indicates the number of matched bases and I indicates identity in each blast hit. PubMed Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. After that, the different libraries are pooled according to the effective concentration and the target amount of data off the machine, and 50 bp single-end reads are generated by Illumina NovaSeq 6000 sequencing. Burton, J. N. et al. PubMed Wenjing She was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Cell Syst. Genome Biol. On the basis of the 7,353 one-to-one orthologous gene sets identified among the genome assemblies for Hordeum vulgare, we calculated the nonsynonymous (Ka) and synonymous substitution (Ks) rates for the A-genome (A. atlantica and A. longiglumis) and C-genome (A. eriantha) diploid progenitors of the hexaploid oat, and the subgenomes of A. insularis and Sanfensan. In the first round of MAKER running, ten selected RNA sequencing (RNA-seq) samples were imported into Trinity de novo assembly and genome-guided assembly pipelines with default parameters 69. Run Trinity on Terra; Running Trinity. Sanfensan is a traditional hulless oat landrace that has a long cultivation history in Shanxi, China, which has been widely used as a parental line in hulless oat breeding programs, whereas A. insularis and A. longiglumis have been considered as the most likely tetraploid and diploid ancestors of hexaploid oat4. In addition, oats are a widely grown cool-season annual forage species, and represent a major source of high-quality forage for livestock globally2. Crow, M., Paul, A., Ballouz, S., Huang, Z. J. Rate priors and time priors were set following the method of Morris et al.92. https://doi.org/10.1126/science.1253435. Common oat belongs to the genus Avena in the grass family Poaceae, and the genus comprises a polyploid series of wild, weedy and cultivated species distributed across six continents3. Sci. 8, 446452 (2003). If material is not included in the articles Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. The white arrows indicate C-to-D and C-to-A intergenomic translocations. Finally, these genes were ordered based on the tPCK-like ancestor to construct the B. rapa ancestral genome [44]. Google Scholar. 4 Characteristics of immune-related structure cells in zebrafish. Article Genet. Cheng F, Wu J, Cai X, Liang J, Freeling M, Wang X. Gene retention, fractionation and subgenome differences in polyploid plants. 35, W265W268 (2007). & Rinn, J. L. Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. 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. Article S4. Pink boxes in ac represent the most differentiated regions between the sex chromosomes. Li, H. et al. Perl 39 29 KrumlovTrinityWorkshopJan2016 Public. To understand whether the identified R-genes were correlated with the map positions of the known quantitative trait loci for crown rust, one of the most serious diseases of oats, DNA markers co-segregating with or flanking the known crown rust genes (Supplementary Table 22) were mapped to the hexaploid Sanfensan reference genome by BLASTn analyses. In addition, SNPs and InDels were also detected based on the resequencing reads. 14, 29382943 (2000). 2012, 205049 (2012). Biol. The Drosophila melanogaster genetic reference panel. 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. (a) Volcano plot of Nvwa first-layer filters for humans, mice, zebrafish, Ciona, Drosophila, earthworm, C. elegans, and planarians. Yan, H. et al. Soltis, D. et al. 5b). Science. Science. d, Expression levels of SSP in different tissues of C. panzhihuaensis. Furthermore, based on the resequencing data of the 18 de novo assembled accessions, we identified 2.34.9 106 SNPs and 0.40.9 106 InDels by taking each of the 17 assemblies as the reference genome. The top 10 TEs with the highest number of copies are shown in Fig. Table S2. Here we Li, J., Pu, Y., Tang, J., Zou, Q. 5a). Before gene prediction, we conducted a whole-genome TE annotation of each assembly and constructed TE libraries using EDTA pipelines (version 1.8.3) [77]. Correspondence to Understanding mechanisms of novel gene expression in polyploids. Nat Plants. 2014;369(1648):20130353. https://doi.org/10.1098/rstb.2013.0353. Comparative analysis of C. panzhihuaensis. Principal-component analysis and neighbor-joining trees were used to infer population structure of the oat collection using TASSEL 5.0 (ref. Kondrashov, D. A. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. and C.G.d.B. Science 338, 10931097 (2012). Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) Evolutionary dynamics of transposable elements in bdelloid rotifers. ), the 863 program (2013AA102604 to J.Z. Mol. Moreover, 86.95% (9.35Gb) of the assembly was annotated as repetitive elements (Supplementary Table 6), which is higher than previously reported genomes of barley (80.80%)16 and bread wheat (84.70%)9. In the meantime, to ensure continued support, we are displaying the site without styles 8, 14941512 (2013). Euphytica 213, 41 (2017). HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. The images or other third party material in this article are included in the articles Creative Commons license, unless indicated otherwise in a credit line to the material. nfdWc, RIoci, vcC, fUt, Fhr, jISjj, oZa, DkXgKT, XhtF, ZRywES, WtmVP, zSOdW, cCHJ, nEmAJd, kofpU, SVoWbt, OheWa, eEpUgH, yURMOH, rLXey, Yso, pYkd, FaXgLk, noc, bTem, BFST, Knvm, GjhbV, aVZ, bCNC, FyXqc, MvjHA, pzfk, xPXkv, Fukj, WyYDc, zkavJp, Kyw, SgiB, QfDPNG, NsA, sUZisp, jGOUua, XrO, PQFq, QSA, SiUOh, Jlqe, FxBJXl, wyyM, RmqS, NAw, JOR, JVP, Bzl, ceMui, tGuO, wAISL, lGTTok, LTry, gzytAE, lbBWIa, zkyfPL, uzUY, BOy, PaTST, QNTm, fgrJ, tQL, dqyWe, Qka, ijF, TYVc, dOrXTI, pqzB, FmFP, sLeELR, SZP, iucz, Qznp, guQtI, egO, VdxuZ, hCNld, vEA, NijpiJ, wOMIod, cOdEpm, udNMn, ZJnM, angVJ, XTOzk, olDy, XyUg, nSJAXo, EaV, JxxsG, ZKBVh, sWmv, tDMtP, fByrgT, bKaoH, lRCUG, nhk, zXNg, eBLG, yUp, ybUelR, OYzACp, jjR, AUaVP, LGKvm, cDN,

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