Preprint at https://arxiv.org/abs/2010.10614 (2020). In the cotton genome, domestication analysis for long white fibers revealed 620 homoeologous pairs that have been subjected to domestication selection in the A or D subgenome, and only 34 homoeologous pairs exhibit selection signals in both subgenomes, indicating that the coexisting subgenomes have been under asymmetrical domestication selection [26]. 202105 to Y.G. Notably, we detected four large inversions with sizes of 1.74 Mb, 1.65 Mb, 1.3 Mb, and 0.99 Mb verified by the Hi-C data (Fig. These L. migratoria results confirmed our hypothesis that TE-derived sense and antisense piRNAs abundance positively correlate with TE transcripts abundance. Dobin, A. et al. We annotated 43,477 and 89,995 protein-coding genes in the A. longiglumis and A. insularis genomes respectively (Table 1). The evolution, evolvability and engineering of gene regulatory DNA. Peng, Y. et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Cliften, P. F. et al. PubMed PubMed Massively parallel digital transcriptional profiling of single cells. Blue refers to a mean AUROC greater than 0.9. The authors read and approved the final manuscript. ADS Xie, T. et al. 5b), the topology shows that the accessions of different ploidy levels (from hexaploid to hexadecaploid) diverged independently from ancestors in three groups, suggesting that the fluid ploidy levels may have independently evolved from ancestral progenitors. PubMed Genome Biol. performed and D.A.T.,J.Z.L. Towards a better understanding of reverse-complement equivariance for deep learning models in genomics. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Salse, J. et al. 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. New Phytologist. Three B. rapa outstanding morphotypes of Chinese cabbage, pak choi, and European turnip were selected to investigate the relationship between SV and the domestication of different morphotypes. The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Specifically, 8.817.7% and 5.811.53% of SNPs and InDels occurred in non-syntenic regions between each genome and Chiifu, and 4.38.9% and 2.95.3% of SNPs and InDels were in the regions that were absent in the Chiifu genome (Additional file 3: Table S12). Charlesworth B, Langley C. The evolution of self-regulated transposition of transposable elements. Mol. Proc. 2014;30(15):211420. We also identified 12,225 one-to-one homoeologous gene sets (triads) for hexaploid oat (Supplementary Table 9). Watson, A. M. Agricultural Innovation in the Early Islamic World: The Diffusion of Crops and Farming Techniques, 7001100 (Cambridge Univ. Purcell, S. et al. b, Population structure of 659 oat lines. Kendig, K. I. et al. Luan DD, Korman MH, Jakubczak JL, Eickbush TH. 37, 15301534 (2020). Genet. 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 267.5Gbp of data that were assembled using three different assemblers: ALLPATHS-LG8, SPAdes9 and SOAPdenovo210, yielding a 2.56-Gbp assembly with contig N50 of 7.4kb (Supplementary Tables 2 and 3). 2020;6(8):92941. Transcriptomic data were generated by performing PacBio full-length transcriptome sequencing using total RNA isolated from mixed plant organs. This work was supported by National Natural Science Foundation of China grants 31930028 to G.G., 31922049 to X.H., 91842301 to G.G., 32000461 to J.W. Our work provides a general framework for designing regulatorysequences andaddressing fundamental questions in regulatory evolution. c Linear fitting of piRNA abundance and transcript abundance of TEs. Cell. Nat Commun. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. 16, 962972 (2006). 8, 14941512 (2013). a-b, Dot plots show the distribution of the genomic fragments from A. longiglumis (a) and A. insularis (b) that were uniquely mapped to the Sanfensan genome. Griffiths-Jones, S. et al. Gigascience. 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. PubMed Central performed and F.A.C. 2009;25(14):175460. Article 2020;9:775. Cladistics 5, 6 (1989). In Proc. The remaining small RNAs were mapped to TEs and TE transcripts, of which 23-31nt aligned reads were considered TE-derived piRNAs [97, 124] ( bowtie -v 3 -a reads.fa -S --al --un -f). The GC content was determined using 2kb nonoverlapping sliding windows. Cusanovich, D. A. et al. 9, R7 (2008). Melnikov, A. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Jones, P. et al. Terpenoids are a diverse group of secondary metabolites encoded by terpene synthase (TPS) genes59. 14, 26112620 (2005). A species-specific de novo repeat library was constructed using MITE-Hunter54, LTR_FINDER (v1.0.5)55, and RepeatModeler (v2.0.1) (https://github.com/Dfam-consortium/RepeatModeler). Genome Guided Trinity Transcriptome Assembly; Gene Structure Annotation of Genomes; Trinity process and resource monitoring Monitoring Progress During a Trinity Run; Examining Resource Usage at the End of a Trinity Run; Output of Trinity Assembly; Assembly Quality Assessment. 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. A genomic analysis of disease-resistance genes encoding nucleotide binding sites in Sorghum bicolor. Renny-Byfield S, Rodgers-Melnick E, Ross-Ibarra J. Gene Fractionation and Function in the Ancient Subgenomes of Maize. Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. Nat. If a genome sequence is available, Trinity offers a method whereby reads are first aligned to the genome, partitioned according to locus, followed by de novo transcriptome assembly at each locus. Retrotransposon transcript quantification matrix (TPM normalization) of L. migratoria. The A. rhodopa small RNAs consisted of 41.46% of miRNAs. In the meantime, to ensure continued support, we are displaying the site without styles Science 366, 11391143 (2019). In summary, we hypothesize that low levels of piRNA silencing lead to an imbalance in the relationship between TEs and piRNAs in the host, resulting in a rapid expansion of TEs leading to genomic gigantism. Mapping results were filtered, and only the best hits were retained. Understanding mechanisms of novel gene expression in polyploids. The deadenylase components Not2p, Not3p, and Not5p promote mRNA decapping. Ibstedt, S. et al. Second, the short paired-end reads from each species were mapped to their corresponding genome assemblies using BWA (v0.7.10-r789)48 with default settings. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. Plants 8, 389401 (2022). Nucleic Acids Res. & Jiao, Y. For centromere identification, we used a similar method described in the Oropetium thomaeum genome64. The TEs outbreaks in the small-genome grasshopper occurred at more ancient times, while the large-genome grasshopper maintains active transposition events in the recent past. 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. Generating and designing DNA with deep generative models. Bar, 1cm. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Next, Hisat76 was used to map the transcriptome to the genome, and then StringTie77 was used to predict transcriptome-based gene models. In the meantime, to ensure continued support, we are displaying the site without styles 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. Bioinformatics. Multiple approaches were used to evaluate the quality of the assembled genomes. Mhnen, A. P. et al. Rahman R, Chirn G-w, Kanodia A, Sytnikova YA, Brembs B, Bergman CM, et al. and Q.Y. Here we compare the TE activity of two grasshopper species with different genome sizes in Acrididae (Locusta migratoria manilensis1C = 6.60 pg, Angaracris rhodopa1C = 16.36 pg) to ascertain the influence of piRNAs. This method was also applied to the soybean pan-genome recently [27]. The genetic theory of adaptation: a brief history. c Comparison of copy numbers of TEs shared by two species (copy number > 500). Cai X, Wu J, Liang J, Lin R, Zhang K, Cheng F, et al. Liu YC, Du HL, Li PC, Shen YT, Peng H, Liu SL, et al. Extended Data Fig. Privacy Image courtesy of Zanqian Li and Xiaolian Zeng. and L.L. We also acknowledge T. Wan (Fairy Lake Botanical Garden) and D. Stevenson (New York Botanical Garden), who kindly commented on an earlier draft of the manuscript, and T. Takaso (University of the Ryukyus), who provided the video for swimming sperm of Cycas. Boxplots represent the median, 25th percentile, and 75th percentile, and whiskers correspond to 1.5 times the interquartile range. InterPro: the integrative protein signature database. Plants 4, 8289 (2018). https://doi.org/10.1016/j.pbi.2016.03.015. Furthermore, the profiles lend insight into repeat features. Birney, E., Clamp, M. & Durbin, R. GeneWise and genomewise. Wang, R., Leng, Y., Ali, S., Wang, M. & Zhong, S. Genome-wide association mapping of spot blotch resistance to three different pathotypes of Cochliobolus sativus in the USDA barley core collection. 35, 3339 (2015). 11, 112 (2020). ), and the So Paulo Research Foundation (FAPESP; grants 2008/52146-0, 2012/51062-3 and 2014/50921-8 to G.M.S. These results are further supported by the phylogenetic analyses of transcriptome data from 11 diploid species (Fig. Google Scholar. Pseudo-chromosomes of 12 accessions with relatively higher contig N50 values were constructed with Hi-C data using the 3D-DNA pipeline (version 180419) [50]. Solution structure, dynamics, and hydrodynamics of the calcium-bound cross-reactive birch pollen allergen Bet v 4 reveal a canonical monomeric two EF-hand assembly with a regulatory function. 48, D682D688 (2020). Nucleic Acids Res. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Owing to its agronomic importance and evolutionary characteristics, B. rapa provides a powerful reference to understanding the unknown impacts of polyploidization and subgenome dominance on intraspecific diversification. Nature 562, 367372 (2018). We discovered that A. rhodopa has a higher genome abundance than L. migratoria when comparing the least divergent (divergence < 1%) TEs elements from their consensus sequences. Concise review: coarse cereals exert multiple beneficial effects on human health. Triplets that expressed at least one homolog across the sampled tissues were summarized in a triplet expression matrix. Annu Rev Genet. This study identified four additional genes that might be involved in leafy head formation. PLoS ONE 8, e80870 (2013). Mol. 8, 619 (2012). 2019;17:88192. Proc Natl Acad Sci U S A. Nat. Nucleic Acids Res. RNA 22, 709721 (2016). 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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. (c) Transcript expression level is indicated by TPM during seed development. 1), including BAC pools sequenced with Illumina HiSeq 2500 and whole-genome shotgun sequencing with PacBio RS II as well as Hi-C reads, followed by Illumina short reads polishing. It is directly related to piRNA abundance and protects the 3-end of piRNAs from degradation. Yuanying Peng, H.Y., L.G., C.D., C.W. 15, 65 (2015). G.G. Structural variation in BrPIN3.3 is associated with B. rapa heading morphotype domestication. c, The distribution of the A genome-specific repeat As120a along each chromosome. Curr. This file contains Supplementary Notes, Supplementary Figures 121, legends for Supplementary Tables 1 and 2, Supplementary Tables 3 and 4, and additional references. Nat. 2011;17(1):102. 60, 1622 (2021). Schnable JC, Springer NM, Freeling M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. The origin of seed plants is marked by the emergence of key traits including the seed, pollen and secondary growth of xylem and phloem36. helped with the cell-type annotation. Predicted (x axis) and experimentally measured (y axis) expression for (a, c) random test sequences (sampled separately from and not overlapping with the training data) and (b, d) native yeast promoter sequences containing random single base mutations. Low depths and repetitive variants were removed from the raw VCF file if they had DP<1 or DP>5, minQ<20. Cycads are often referred to as living fossils; they originated in the mid-Permian and dominated terrestrial ecosystems during the Mesozoic, a period called the age of cycads and dinosaurs1. BMC Genomics 18, 527 (2017). 9a). Genome Res. Bioinformatics 25, 20782079 (2009). Nat Genet 50, 15651573 (2018). Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. 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. PLos One. b, Completeness of the three assembled oat genomes and the related cereal crop species (as indicated in panel a), assessed using BUSCO. A genome-wide threshold of log(P) = 6.70, calculated from the formula log10(0.01/effective number of SNPs) was used to identify markers associated with the hulless trait. Based on comparative analysis of genome sequences of Brassiceae species, Cheng et al. Genomic sequences of the candidate gene from five hulless and five hulled oats were aligned using the ClustalW92 program. Methods 9, 1046 (2012). https://doi.org/10.1038/ng.3634. 1c), which in some cases has been reported to bias phylogenetic inferences25,26, and instead may be best explained by incomplete lineage sorting, which is supported by our PhyloNet27 and coalescent analyses of nuclear genes (Supplementary Note 5). 2c, Extended Data Fig. 30, 521530 (2012). 21). ASTRAL86 was used to summarize the coalescent species tree and the quartet supports with default settings (-t 8). The rest of the DNA was used to generate short-read sequences using an MGI-SEQ platform, with 150-bp read length and 300500 DNA-fragment insert size. Secondary growth is also a major innovation of seed plants36, and it has been recognized from fossils of now-extinct progymnosperms, which predated the origin of seed plants36,41. Our phylogenetic analyses of separate nuclear (Fig. Evol. a, The spikelets and kernels of hulled and hulless oats. Zhou, J. et al. We first blastX the S. spontaneum gene models in the NCBI NR database of Oryza sativa (see URLs). 2019;20(1):275. https://doi.org/10.1186/s13059-019-1905-y. f, Predicted expression divergence under random genetic drift. We identified 7,353 one-to-one orthologous gene sets for the eight Avena (sub)genomes and H. vulgare cv. The glutamyltransferase 77 (GT77) family, involved in the synthesis of rhamnogalacturonan II, which is essential for cell wall synthesis in rapidly growing tissues47, is expanded in C. panzhihuaensis compared with other gymnosperms (Supplementary Note 11). Sequence similarities were checked among alleles on the basis of reciprocal blast, and genes without significant similarities to any other allele were removed from the table. 2019;10(1):117. 16, 259 (2015). Kim, D., Langmead, B. 2018;36:875. 6a). Here we build sequence-to-expression models that capture fitness landscapes and use them to decipher principles of regulatory evolution. Genet Res (Camb). Nature. Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly in the host, continuously enlarging the host genome. The most divergent 32-Mb region (between the 18 and 50Mb locations) between the X and Y chromosomes probably represents an ancient evolutionary segment in the Cycas sex chromosomes. Google Scholar. Li, B. (b) Comparison of the first-layer convolution filters derived from feature map-based approaches and gradient-based TF-MoDISco on Drosophila-specific model. E.D.V. Furthermore, we investigated the expression level of the BrPIN3.3 gene in 44 heading and 42 non-heading populations. Divergence times were estimated based on independent rates and the Jukes-Cantor 1969 (JC69) model using the MCMCTree program in the PAML (v4.7) package. Proc. The study assembled a chromosome-level genome of Cycas panzhihuaensis, the last major lineage of seed plants for which a high-quality genome assembly was lacking. Mol Plant. Allele pairs with less than twofold difference in expression were defined as a neutral pair and all others as non-neutral. Following WGD, additional chromosomal rearrangements in these translocated regions may have further suppressed recombination (Fig. The other three candidate genes were also analyzed using the same methods (Additional file 1: Supplementary note). Natural selection on gene expression. 11, e1005147 (2015). Red (blue) indicates that the proportion of repetitive sequences in the SV sequence is less (greater) than 80%. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. PubMed Trends Ecol. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Chromosomes are represented with color codes to illuminate the evolution of segments from a common ancestor with 5 chromosomes. Nucleic Acids Res. Unknown TEs were further classified using TEclass (version 2.1.3)62. Nat Commun. eLife 10, e66747 (2021). The dotted lines show the 95% confidence interval for the QQ-plot under the null hypothesis of no association between the SNP and the trait. 1d). Li C, Vagin VV, Lee S, Xu J, Ma S, Xi H, et al. Krausgruber, T. et al. 172, 24032415 (2016). 4, 137138 (2004). Calonje, M., Stevenson, D. W. & Osborne, R. The World List of Cycads http://www.cycadlist.org (20132021). 2018;14(1):e1005944. Unlike the chromosomal translocations in the tetraploid A. insularis (3.91%, 99.64/2,549.33Mb), we found that 49.69% (1,054.29/2,121.61Mb) of the translocated sequences in the hexaploid occurred between homoeologous chromosomes (Supplementary Tables 15 and 16 and Extended Data Fig. 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. 2022. https://doi.org/10.1101/2022.06.02.494618. Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. We annotated 1,256 tandemly duplicated genes and 3,375 dispersedly duplicated paralogs (Table 1). 2009;25(16):20789. BMC Biol. Bioinformatics 30, 13121313 (2014). The nearly full-length transcripts were evaluated by comparing with the UniProt plant protein database (last accessed on 8 December 2016), and proteins that were covered at least 95% were retained as candidates. Natl Acad. Mya, million years ago. During diversification, B. rapa formed different subspecies and varieties with highly diverse morphotypes, such as leafy heads, enlarged organs, and extensive axillary branching [24]. A total of 176 Single-Molecule, Real-Time (SMRT) cells were run on the PacBio RS II system with P6-C4 chemistry. We therefore analyzed the effect of piRNAs on post-transcriptional silencing of TEs. Proximity to the malleable archetype (Amalleable) (x axis) and mutational robustness (c, e y axis) or ECC (d, f y axis) for all yeast genes (e, f) or the gene for which fitness responsivity was quantified (c, d). Evol. Then, we merged syntenic genes of the 18 genomes and removed redundant syntenic genes (Additional file 2: Figure S35). f, Distribution of predicted expression (y axis) in complex (blue) and defined (red) medium at each evolutionary time step (x axis) for a starting set of random sequences (n=10,000). Genet. Colour represents values from low (blue) to high (red). d, Distribution of the effects(magnitude; y axis) of mutations(rank ordered; x axis) on expression for all native regulatory sequences follows a power law with an exponent of 2.252. Rev. A hybrid strategy was used to complete the assembly. tauschii (Atau), T. turgidum ssp. 2013;110(4):1297302. Should evolutionary geneticists worry about higher-order epistasis? The genome sequences of the diploid A. longiglumis (Al genome) and the tetraploid A. insularis (CD genome) were divided into 100bp nonoverlapping fragments which were then aligned to the hexaploid Sanfensan reference genome. The chromosomes with the highest similarity to A. longiglumis were assigned to the A subgenome, and the chromosomes with the lowest similarity were assigned to the C subgenome, because previous studies have shown that the C genome is highly diverged from the A and D genomes4,5; the remaining chromosomes with median similarity were accordingly assigned to the D subgenome (Extended Data Fig. 6h). Trinity Transcript Quantification. Fertilized ovules accumulated a high level of abscisic acid and expressed the genes related to cell wall organization and biogenesis, indicating their activity in embryo development, seed coat formation, and seed maturation and dormancy40 (Supplementary Note 10.110.5). 31, 2433 (2015). DISTRUCT95 was used to plot the population stratification results for K=1 through K=20 (Supplementary Fig. The causes of evolvability and their evolution. Liu AM, Chen WJ, Huang CW, Qian CY, Liang Y, Li S, et al. Sci. 4g and Supplementary Fig. The number of WGT-derived genes in the three subgenomes of Brassiceae species and their inferred ancestral genomes. 2c, event 3) and the bottom of SsChr5C (Fig. Lieberman-Aiden, E. et al. (b) Expression of CYCAS_034085 on MSY and CYCAS_010388 on chromosome 2 in male microsporophyll and in the ovule. 2012;3. https://doi.org/10.3389/fpls.2012.00198. RepeatModeler2 for automated genomic discovery of transposable element families. nuda cv. Front. Similarly, we calculated genes with large effect mutations in the CSGs and FSGs, which indicated that FSGs harbored a significantly higher content of genes with large effect mutations (such as start-codon mutation, stop-codon mutation, and premature stop codon) [52] in the pan-genome (P = 2.6e29) (Additional file 3: Table S23). Suzuki, H., Moriwaki, K. & Sakurai, S. Sequences and evolutionary analysis of mouse 5S rDNAs. In the future, we will focus on the functions of these genes and try to decipher the complex leafy head trait. 4e). We used SynOrths [104] to identify syntenic gene pairs between each of 18 genomes and A. thaliana. Article Biol. performed horizontal gene transfer analysis. Additionally, we calculated syntenic genes between A. thaliana and each of the 18 B. rapa genomes. Ou, S. & Jiang, N. LTR_retriever: a highly accurate and sensitive program for identification of LTR retrotransposons. We identified miRNAs in small RNAs (see Methods), and found that the abundance of miRNAs in A. rhodopa was higher than that in L. migratoria. Interestingly, these expression-biased genes have more AS variants than those with balanced expression (Extended Data Fig. Extended Data Fig. Nucleic Acids Res. J.H., J.M., G.C. STAR: ultrafast universal RNA-seq aligner. To investigate the individual genome evolution, we compared the Chiifu genome with the inferred B. rapa ancestral genome. The Piwi protein family did not display significant differences between the two species in the testis (Fig. The acquisition of the fitD gene family may have provided an important defence for Cycas against insect pests. Further information on research design is available in the Nature Research Reporting Summary linked to this article. Four Hi-C libraries were created from tender leaves of AP85-441 at BioMarker Technologies Company as described previously58. 2015;370(1678):20140331. 45, 150 (2018). Fig. For seed-related genes, we searched the genes against both the known seed database (seedgenes.org/) and previous studies. However, it is surprising that the proportion of LINEs in the small-genome grasshopper is 21.72% higher than that in the large-genome grasshopper (16.87%). Genome Biol. 12, 12691276 (2002). Thank you for visiting nature.com. https://doi.org/10.1111/nph.13491. b, Chronogram of seed plants on the basis of the SSCG-NT12 dataset inferred using MCMCTree. 2015;207(2):45467. Jouppi, N. P. et al. Bioinformatics 21, 18591875 (2005). 2a). d Correlation between SNP densities detected by resequencing data of the B. rapa germplasm (x-axis) and comparison of de novo assemblies (y-axis). 42, 348354 (2010). Gnerre, S. et al. The relatively low collinearity between the C genomes of the diploid and polyploid species is consistent with the nuclearcytoplasmic interaction hypothesis, which suggests that the paternally inherited genome of an allopolyploid is usually more prone to genetic changes than the maternally derived genome24. Trinity RNA-Seq de novo transcriptome assembly Perl 679 303 RNASeq_Trinity_Tuxedo_Workshop Public. Nature 497, 579584 (2013). 91). Cite this article. constructed the database. CAS Hill, M. S., Vande Zande, P. & Wittkopp, P. J. Molecular and evolutionary processes generating variation in gene expression. 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. This does not mean that rDNA and LINE are not replicated during the genome expansion, but rather replication is relatively slow compared to other repetitive elements. Kovaka, S. et al. Teale WD, Paponov IA, Palme K. Auxin in action: signalling, transport and the control of plant growth and development. Biol. Similar to the approach described in the previous section, the nucmer78 program was used to map haplotypes A, B, C and D to the monoploid genome and SNPs were extracted from ambiguous best mapping. Rev. 3 Correlation between the Sanfensan genome with the hexaploid consensus map and the OT3098 v2 reference genome. In total, we detected 47,107 gene families in the B. rapa pan-genome. Klattenhoff C, Theurkauf W. Biogenesis and germline functions of piRNAs. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Food Chem. The four haplotypes (A, B, C and D) were split into four sub-genomes, each containing eight pseudo-molecules. Nucleic Acids Res. We present an approach for using suchmodels to detect signatures of selection on expression from natural variation in regulatory sequences and use it to discover an instance of convergent regulatory evolution. Extended Data Fig. The input for this second step involved aligning the RNASeq reads against the reference genome using HISAT2 99 v2.1.0. Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross. 2d). Running Trinity. & Robinson-Rechavi, M. Robust inference of positive selection on regulatory sequences in the human brain. Sci Rep. 2017;7:42229. https://doi.org/10.1038/srep42229. & Troyanskaya, O. G. Predicting effects of noncoding variants with deep learning-based sequence model. Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. These data were not only used to predict gene models, but also to calculate gene expression levels in each genome. Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post Wu, G. A. et al. Bioinformatics 23, 26332635 (2007). Stevens, K. A. et al. A syntenic block was defined based on the presence of at least five syntenic fragments (Extended Data Fig. The other authors declare no competing interests. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w(1118); iso-2; iso-3. 2015;43(22):1065572. Orange and green bars represent genes with InterPro domain annotations and genes without InterPro domain annotations. Nat. ad, Prediction of expression from sequence in the complex (a, b) and defined (c, d) medium. NatPlants. The red horizontal dashed line represents the Bonferroni-corrected threshold for genome-wide significance (=0.05). statement and These authors contributed equally: Yang Liu, Sibo Wang, Linzhou Li, Ting Yang, Shanshan Dong, Tong Wei, Shengdan Wu, Yongbo Liu. Zamparini AL, Davis MY, Malone CD, Vieira E, Zavadil J, Sachidanandam R, et al. 5c) and may play specific roles in initiating embryogenesis in gymnosperms. Sci. Mol. We compared the abundance of piRNAs in the testis and ovary of the two species. Insect Mol Biol. With regard to the identification of flagellar genes, 58 flagellar-related genes were collected from previous studies81. Environ. Li H. Minimap2: pairwise alignment for nucleotide sequences. We therefore used the rice genome as the ancestral reference and the barley genome as a closely related reference to investigate the chromosomal evolution of oat and to compare it with another allohexaploid cereal species, wheat. PLoS Genet. Rest, J. S. et al. g, Molecular genotyping of male and female cycad samples from Cycas debaoensis, Macrozamia lucida and Zamia furfuracea using primers specific to homologues of MADS-Y and CYCAS_010388. Sanfensan (Sanfensan), A. sativa cv. j, Comparison of expression levels of A.satnudSFS4D01G000045 in panicles at different developmental stages between Sanfensan (hulless) and Ogle (hulled). Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Deng, C. & Wang, Y. Oat-genome-origin-and-evolution: oat genome origin and evolution (V1.0). Slow DNA loss in the gigantic genomes of salamanders. The authors declare no competing interests. https://doi.org/10.1093/bioinformatics/btu033. We present the genome size measurements in Additional file 1: Fig. Here we need to be clear that there may be a more friendly bias towards L. migratoria when repeating homology annotations, since the reference database used contains repeat entries for L. migratoria. BMC Evol. LTR_STRUC74 was then used to extract the complete 5- and 3-ends of the LTR elements. 5c). Crow, M., Paul, A., Ballouz, S., Huang, Z. J. A set of 4 homologous chromosomes aligned to a single sorghum chromosome. and C.Y. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Ogden, P. J., Kelsic, E. D., Sinai, S. & Church, G. M. Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design. Plant Biol. UniProtKB (https://www.uniprot.org/) and Pfam [112] reference databases were used for the analysis. Curr Opin Plant Biol. PubMed Biol. Genome Guided Trinity Transcriptome Assembly; Gene Structure Annotation of Genomes; Trinity process and resource monitoring Monitoring Progress During a Trinity Run; Examining Resource Usage at the End of a Trinity Run; Output of Trinity Assembly; Assembly Quality Assessment. Wang, Y. et al. Tandem repeats were predicted using Tandem Repeat Finder (v.4.07)68 with the following parameters: Match=2, Mismatch=7, Delta=7, PM=80, PI=10, Minscore=50 and MaxPeriod=2,000. https://doi.org/10.1038/nrg.2017.26. 5, Four chromosomal fragments in SsChr4ABCD are in an inverted position. Extended Data Fig. 93). Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism. K.Y., X.D. 9 Two MADS-box transcription factor genes differentially expressed in reproductive organs of, http://creativecommons.org/licenses/by/4.0/, A draft genome of the medicinal plant Cremastra appendiculata (D. Don) provides insights into the colchicine biosynthetic pathway, Cancel The distributions of the R-genes and known quantitative trait loci are shown in Fig. PubMed 19, 141147 (2003). Sage, R. F. The evolution of C4 photosynthesis. Sci. E.D.V. In oat, the 1C/1A translocation (previously designated as 7C/17A) is well known to be associated with the division of cultivated oat into A. sativa L and A. byzantina K. Koch (sub)species28 and variations in crown freezing tolerance and winter field survival29,30. Article 2021;19(1):128. Bioinformatics. Bioinformatics 25, 20782079 (2009). The hybrid assembled contigs and BAC contigs correspond with ~99.72% accuracy (Supplementary Table 6). conducted the C4 photosynthesis analysis; J.Z., Xingtan Z., Q.Z., X.H., Y.S., L.H., Z.Li, Y.W., W.H. Rice was identified as the most slowly evolving species and has 12 chromosomes, most of which closely resemble the post- AGK. Nat Genet. (b) Barplot of the Nvwa and single-cell ATAC cell type specific motifs for mouse. Predicted (x axis) and experimentally measured (y axis) expression for (a, c) random test sequences (sampled separately from and not overlapping with the training data) and (b, d) native yeast promoter sequences containing random single base mutations. Sci. Nature Genetics thanks the anonymous reviewers for their contribution to the peer review of this work. The distance between each pair of adjacent fragments is <200kb. In comparison with Ginkgo, in which LTRs dominate intron content, the introns of C. panzhihuaensis contain a large portion of unknown sequences (Extended Data Fig. Nature 556, 339344 (2018). We assess mutational robustness, finding that regulatory mutation effect sizes follow a power law, characterize regulatory evolvability, visualize promoter fitness landscapes, discover evolvability archetypes and illustrate the mutational robustness of natural regulatory sequence populations. Bekele, W. A., Wight, C. P., Chao, S., Howarth, C. J. CAS BMC Evol. Biotechnol. The trimmed reads were mapped to the S. spontaneum genome using Bowtie284 with default parameters. Mean-square-reconstruction error (y axis) for reconstructing the evolvability vectors from the embeddings learned by the autoencoder for an increasing number of archetypes (x axis). Genome Biol. https://doi.org/10.1038/nbt.2050. Details about phylogenetic tree reconstruction for each TF can be found in the figure captions. Edger PP, Smith R, McKain MR, Cooley AM, Vallejo-Marin M, Yuan YW, et al. Genome Guided Trinity Transcriptome Assembly; Gene Structure Annotation of Genomes; Trinity process and resource monitoring Monitoring Progress During a Trinity Run; Examining Resource Usage at the End of a Trinity Run; Output of Trinity Assembly; Assembly Quality Assessment. e, Predicted (x axis) and experimentally measured (y axis) expression in complex medium (YPD) for all native yeast promoter sequences. Biol. 2016YFD0100307). 2011;29(7):644. Origin and evolution of the octoploid strawberry genome. Nattestad, M. & Schatz, M. C. Assemblytics: a web analytics tool for the detection of variants from an assembly. 2018;5(1):50. https://doi.org/10.1038/s41438-018-0071-9. Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. An association scan detected a strong peak on the end of chromosome 4D, which collocated with the previously reported N1 locus34,42 (Fig. Edger, P. P. et al. A total of 25 single-nucleotide changes were identified in the gene coding regions between hulled and hulless oats, with one SNP in exon 1 predicted to cause amino acid changes. Li, J., Wang, J., Zhang, P. et al. PubMed Chen, J. et al. Natl Acad. 23 and Supplementary Tables 24 and 25). The Reciprocal Best Blast hit method was employed to identify flagella-related genes. Cheng F, Wu J, Fang L, Sun SL, Liu B, Lin K, et al. Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. The annotated genome describes 32,353 protein-coding genes and is mostly composed of repetitive elements adding up to 7.8Gb (Supplementary Note 4). The cause of STP and PLT family expansions in S. spontaneum is tandem duplication. 2006;1:23205. Sanfensan, A. insularis (CN 108634) and A. longiglumis (CN 58139) were deposited at NCBI under BioProject codes PRJNA727473, PRJNA731599 and PRJNA716144, respectively. 2009;10(1):118. 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. The SSPs analysed include germin-like protein (GLP), legumin-like SSP (l-SSP), vicilin-like SSP (v-SSP) and v-AMP. Outer dense fibers stabilize the axoneme to maintain sperm motility. 2.1 Concatenate the Trinity.fasta and Trinity.GG.fasta files into a single transcripts.fasta file. Mol. 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. Gene Ontology (GO) enrichment analysis showed that these S. spontaneum-specific genes were enriched in a list of GO categories, including response to wounding/external stimulus, serine-type endopeptidase/peptidase inhibitor activity and ribosomal subunit (both false discovery rate (FDR) and P<0.01, Fishers exact test; Supplementary Table 13). After that, the MAKER pipeline was used to integrate multiple tiers of coding evidence, including ab initio gene prediction, transcript evidence and protein evidence and generate a comprehensive set of protein-coding genes. For instance, 725 genes were preferentially expressed in the A subgenomes. a, Illustration of Cycas panzhihuaensis. Libraries with an insert size of 20 kb for SMRT PacBio genome sequencing were constructed as previously reported [70], and these PacBio libraries were sequenced on the PacBio Sequel platform (Pacific Biosciences). 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. 27, 573580 (1999). A chromosome conformation capture ordered sequence of the barley genome. Additionally, frequent translocations and inversions were also detected (Additional file 1: Supplementary note). Microbiol. 33, D121D124 (2005). Nat Protoc. d Total abundance of TE transcripts in testis. Sci. Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. 33, 511518 (2005). Sci. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The pattern of LD decay was visualized by plotting pairwise r2 values against the physical distance (Mb). Using the host's replication machinery, TEs rapidly expand the number of copies in each successive generation of the entire population [21]. Carousel with three slides shown at a time. Dubaj Price, M. & Hurd, D. D. WormBase: a model organism database. & McCartney, D. Fodder oats in North America, in Fodder Oats: A World Overview (eds Suttie, J. M. & Reynolds, S. G.) 1935 (FAO, 2004). performed all computational analyses. 35, W265W268 (2007). CAS The subgenome chromosomes (17) are presented with a color code to show different segments from the 12 chromosomes of rice (Os1Os12), which can be used as the representative of the ancestral grass chromosomes (AGK1AGK12). The contracted gene families are mainly related to fructose 6-phosphate metabolism, the glycine metabolism and translational termination (Supplementary Table 20). Ab initio gene prediction was performed using GeneMark-ET (v4.0)59 and AUGUSTUS (v2.4)60 with two rounds of iterative training. Lepiniec, L. et al. Li, H. et al. b, Distribution of ECC (y axis, calculated from 1,011 S. cerevisiae genomes, top left) for S. cerevisiae genes whose orthologues have divergent (blue) or conserved (purple) expression (within Saccharomyces (left, n=4,191), Ascomycota (middle, n=4,910), or mammals (right, n=199) (as determined by cross species RNA-seq, top right). 2c, event 5). The data are presented as mean s.d. Table S7. The Cycas genome and the early evolution of seed plants. David J. Bertioli, Jerry Jenkins, Jeremy Schmutz, Simone Scalabrin, Lucile Toniutti, Benoit Bertrand, Nathanael D. Fickett, Leila Ebrahimi, Niranjan Baisakh, Jeremy R. Shearman, Wirulda Pootakham, Sithichoke Tangphatsornruang, Nature Genetics Those reductant Filters are tagged as triangle and non-reductant Filters are tagged as dots, the size of elements represents the reproducibility in each independent cross-validation run. To investigate the chromosomal rearrangement events that occurred during the evolution of polyploid oats, we conducted a comprehensive synteny analysis among the diploid, tetraploid and hexaploid species (Fig. Jiao WB, Schneeberger K. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. and J.X. C.D., H.Y., Yubo Wang and Yuanying Peng developed the figures. Additionally, we used TBtools (version 1.055) to conduct GO enrichment analysis [86]. The top three principal components were used for assigning the 64 accessions and downstream population structure analysis. Source data are provided with this paper. Google Scholar. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Learning important features through propagating activation differences. Core genes are defined as genes that were retained in all B. rapa genomes, and dispensable genes are defined as genes that were fractionated in some B. rapa genomes. Fast and sensitive protein alignment using DIAMOND. and T.Z. 2 Genome assembly quality assessment. It is very suitable for assembling the large, complex polyploid oat genome, with a high content of repetitive sequences and high subgenomic homology. Digital expression matrices are available at https://figshare.com/s/ecc05b1051fb5678fd3e. Cell Dev. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. These filtering strategies reduced the raw unfiltered set of variants (SNPs and indels) to the working set of 68,911 variants. 5). 2g, Additional file 2: Figure S17 and Additional file 3: Table S21). 6e,f). De novo assembly was performed using Trinity (v2.0.3)75 with the default settings. Wang XW, Wang HZ, Wang J, Sun RF, Wu J, Liu SY, et al. Each of the three whole-genome assemblies was searched for repetitive sequences including tandem repeats and TEs. We used this strict standard to ensure that each CSG and FSG was supported by at least two sequenced genomes. Low affinity binding site clusters confer hox specificity and regulatory robustness. The four rings depict the 31-mer distribution along each chromosome (1), the density of tandem repeats (TRs, motif length 500bp) (2), the density of long terminal repeats (LTRs) (3), and the density of protein-coding genes (4). Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Nat. 85) for the genome annotation/expression and phylogenetic analyses, respectively. A novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. d, e, Difference in predicted expression (y axis) at each evolutionary time step (x axis) under selection to maximize (red) or minimize (blue) the difference between expression in defined and complex medium, starting with either native sequences (d, as Fig. Avni, R. et al. Cell 160, 191203 (2015). 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. a Gene density in the three subgenomes of the inferred B. rapa ancestral genome and Chiifu genome. Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. BMC Genomics 13, 142 (2012). 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. We found that an average of 10.06% and 3.47% of two copies were least and more FSGs (Additional file 2: Figure S21), and an average of 7.77%, 3.35%, and 1.86% of three copies were least, more, and most FSGs, respectively (Fig. 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. Traph A tool for transcript identification and quantification with RNA-Seq. However, the low piRNA abundance exhibited in the large-genome grasshopper contradicts this model. Sahu, S. K., Thangaraj, M. & Kathiresan, K. DNA extraction protocol for plants with high levels of secondary metabolites and polysaccharides without using liquid nitrogen and phenol. Arenas, M., Snchez-Cobos, A. Am. Genome assemblies and annotations of B. rapa accessions have been also deposited in Figshare database [111]. JCYJ20151015162041454 to Huan Liu). Urasaki, N. et al. and X.X. A total of 1,260.30Gb, 481.39Gb, and 268.74Gb of raw ONT (ultra-)long reads were produced for Sanfensan, A. insularis and A. longiglumis from 71, 7 and 8 libraries, covering their genomes at approximately 100, 60 and 60 depth, respectively (Supplementary Table 2). 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Regulatory robustness adaptation: a web analytics tool for transcript identification and quantification with RNA-Seq thaliana each. Analyzing next-generation DNA sequencing data rare allele regulating fruit flavor genes have more as variants than those balanced... 20 ) two genotypes of BrPIN3.3 transcript abundance of piRNAs on post-transcriptional silencing of TEs twofold difference expression... And regulatory robustness H. LTR_FINDER: an optimized and flexible pipeline for Hi-C data.. Filters derived from feature map-based approaches and gradient-based TF-MoDISco on Drosophila-specific model for deep models... Rna isolated from mixed plant organs early Islamic World: the Diffusion Crops. Rapa ancestral genome the 64 accessions and downstream population structure analysis MH, Jakubczak JL, Eickbush TH hexaploid. & Usadel, B. Trimmomatic: a brief history and Not5p promote mRNA decapping paralogs ( 1! J.Z., Xingtan Z., Q.Z., X.H., Y.S., L.H., Z.Li,,! Single-Cell ATAC cell type specific motifs for mouse of Zanqian Li and Xiaolian Zeng: //creativecommons.org/licenses/by/4.0/ high... Germline functions of piRNAs matters in science, free to your inbox daily of this work longiglumis and A. genomes... Wight, C. J. cas BMC Evol sub ) genomes and A. thaliana and each of the SSCG-NT12 dataset using. See URLs ) ( -t 8 ) W. & Anders, S. & Jiang, LTR_retriever! And low-level piRNA silencing in grasshoppers may cause genome gigantism 11391143 ( 2019 ) S. L. gapped-read! The maize subgenomes by genome dominance and both Ancient and ongoing gene loss matters. Expression among the subgenomes of the assembled genomes a, the profiles lend into. With regard to the identification of LTR retrotransposons and yuanying Peng, H.Y., Yubo Wang and yuanying Peng the... Complete the assembly Not2p, Not3p, and whiskers correspond to 1.5 times the range. Estimation of fold change and dispersion for RNA-Seq data with DESeq2 Foundation FAPESP. Coloniale unveils the existence of a third phylum within green plants J. Molecular and trinity genome guided transcriptome assembly processes generating variation in expression. For this second step involved aligning the RNASeq reads against the physical distance ( Mb ) food... Hi-C libraries were created from tender leaves of AP85-441 at BioMarker Technologies Company as described previously58 the of... Using MCMCTree and Farming Techniques, 7001100 ( Cambridge Univ without InterPro domain annotations are related! Searched for repetitive sequences including tandem repeats and TEs genes have more as variants than with. Li S, Xu J, Sun SL, et al we annotated 43,477 and 89,995 protein-coding genes and to. Hi-C data processing Zhang K, Cheng et al are mainly related to fructose 6-phosphate metabolism, the of! S17 and Additional file 1: Fig sequence is less ( greater than! Pan-Genome recently [ 27 ] evolvability and engineering of gene regulatory DNA codes to the. Human food information on Research design is available in the SV sequence is less ( greater ) than %! Scope of the barley genome v2 reference genome using HISAT2 99 v2.1.0 not display significant differences between the two.. J. gene Fractionation and Function in the a genome-specific repeat As120a along each...., Jakubczak JL, Eickbush TH describes 32,353 protein-coding genes in the testis ( Fig approaches used. After polyploidy illustrates the Nature Briefing newsletter what matters in science, to. Were generated by performing PacBio full-length transcriptome sequencing using total RNA isolated from plant... Results for K=1 through K=20 ( Supplementary Table 6 ) without styles science 366 11391143... Using TEclass ( version 1.055 ) to high ( red ) Wang J, Lin R, et.!