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Top left: Pearsons r and associated two-tailed P values. Curr Opin Plant Biol. Sci. Although some studies suggest that AGO3, PIWI, and AUB play an important role in the repression of TE transposition [37, 59], we have no evidence that these genes are significantly different in the two grasshopper species (Fig. 26, 990999 (2016). Tzafrir, I. et al. Google Scholar. Bioinformatics 21, 18591875 (2005). The period of rapid TE accumulation in the species is not homogenized. Cycads have manoxylic wood, with a large pith, large amounts of parenchyma and relatively few tracheids, in contrast to most other gymnosperms, which have pycnoxylic wood, with small amounts of pith, cortex and parenchyma, and a greater density of tracheids4. Genome Res. Nat. Abbreviations are defined as T = testis; O = ovary; M = male body; F = female body. The Sorghum bicolor genome and the diversification of grasses. https://doi.org/10.1038/s41588-022-01197-7. The r2 values of LD were plotted against the physical distance (Mb). Osborn, T. C. et al. Microbiol. In scaled profiles, we consider the position with the highest read coverage as the TE origin, which is accompanied by an increase in copy number and extension of the sequence end as TE jumps and proliferates. High-resolution TADs reveal DNA sequences underlying genome organization in flies. The genomic variants were identified using the HaplotypeCaller module in GATK (v4.1.9.0), and SNPs that met any of the following criteria were further discarded: (1) SNPs with quality score <50, QD score <2, FS score >60 or MQ score <40; (2) SNPs with more than two alleles; (3) SNPs at or within 5bp from any InDels; (4) Genotypes with extremely high (greater than three-fold average depth) or extremely low (less than one-third average depth) coverage were assigned as missing sites; (5) SNPs with a minor allele frequency <0.05; and (6) SNPs with missing sample rate >0.3. Jackson S, Chen ZJ. https://doi.org/10.1016/j.tplants.2019.01.003. However, the evolution of the dominant subgenome during intraspecific diversification is unexplored. 35, 3339 (2015). & Sanmartn, I. Running Trinity. Then, BUSCO [73] was used to perform a preliminary assessment of the assembly integrity. Multiple approaches were used to evaluate the quality of the assembled genomes. Combining ab initio, homology-based annotations and RNA-seq reads (Additional file 3: Table S8), we detected 44,20747,602 gene models in each of the 16 genomes. When we compared the expression of key genes in the piRNA pathway between the two species, we found a differentially expressed gene, HENMT. Rev. Nat. Previously, the repeatome analysis of L. migratoria using assembled genome data discovered 58.86% of the repetitive sequences in the whole genome [66, 67], while our results were slightly smaller at 56.83%. Genome Biol. A universal karyotypic system for hexaploid and diploid Avena species brings oat cytogenetics into the genomics era. Distmat from the EMBOSS (v.6.5.7.0) package was then used to calculate the K value of the retrotransposons 5- and 3-LTR sequences. We speculated a positive correlation between TE transcripts and TE-derived piRNAs. 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. e, Model showing the evolutionary history of hexaploid oat (A. sativa ssp. 2014;345(6196):1251343. 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. 8 In silico mutagenesis of malleable and robust promoters. 114, 11771188 (2014). This study identified four additional genes that might be involved in leafy head formation. Genome 59, 209220 (2016). 22, 456461 (2006). by molecular cytogenetics. Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Mol Biol Evol. X.L. The locust genome provides insight into swarm formation and long-distance flight. SWEETs play various important roles in multiple physiological processes41. Evolutionary dynamics of transposable elements in bdelloid rotifers. Res. Different families of retrotransposons exhibit different tissue specificities. However, the Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of TE invasion by imposing small-RNA-mediated silencing. We constructed a B. rapa pan-genome consisting of the 16 representative genomes and the two published reference genomes [31, 47]. Moore, P. H., Nagai, C. & Fitch, M. M. M. Production and evaluation of sugarcane haploids. diploid species. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nat Protoc. The origin of the seed marked one of the most important events of plant evolution10. 2011;28(2):103342. 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Running Trinity. HENMT1 and piRNA stability are required for adult male germ cell transposon repression and to define the spermatogenic program in the mouse. The LAI scores, represented by dots, were calculated using 3 Mb-sliding windows with 1.5Mb steps. Le Thomas A, Rogers AK, Webster A, Marinov GK, Liao SE, Perkins EM, et al. 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. When comparing the total content of TEs in the two species, TEs accounted for 52.28% of the A. rhodopa genome and more than 49.47% in the L. migratoria genome. PLoS Computat Biol. Image courtesy of Zanqian Li and Xiaolian Zeng. Langmead, B. Venkataram, S. et al. 40, 209213 (1965). Charlesworth B, Langley CH, Stephan W. The evolution of restricted recombination and the accumulation of repeated DNA sequences. PubMed Gunawardane LS, Saito K, Nishida KM, Miyoshi K, Kawamura Y, Nagami T, et al. 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. 2017;356(6333):925. Santos, A. G., Livingston Iii, D. P., Jellen, E. N., Wooten, D. R. & Murphy, J. P. A cytological marker associated with winterhardiness in oat. Tandem repeats were identified by using GMATA (v2.2)52 and Tandem Repeats Finder (v4.07b)53. A tandem duplication of SsNADP-ME2, SsNADP-ME1, also displayed a C4 expression profile similar to that of SsNADP-ME2. 15, 150 (2015). Natl Acad. Dot plots show the fold changes for each triplet ordered as shown in the y axis (f). a, NG-graph of the three assembled genomes and other related cereal crop species including A. sativa ssp. Open Access Sprunck, S. et al. Trends Plant. Biotechnol. Heteromorphic chromosomes have been reported to be associated with sex determination in Cycas54. The origin and evolution of cell types. S3. In the cellulose synthase (CESA/CSL) superfamily46, we discovered the existence of putative ancestral cellulose synthase-like B/H (CSLB/H) and CSLE/G that are specifically shared by gymnosperms, and both gene groups originated before the divergence of CSLB and CSLH in angiosperms (Extended Data Fig. N of cell types: human: 434, mouse: 432, zebrafish: 378, Ciona: 291, Drosophila: 288, earthworm: 110, C. elegans: 321, and planarians: 173. G.G., J. Curr Opin Plant Biol. Genome Biol. Sucrose efflux mediated by SWEET proteins as a key step for phloem transport. Tax calculation will be finalised during checkout. ), the US National Science Foundation Plant Genome Research Program (grant IOS-1025976 to D.M.B. Evol. After that, we performed length statistics on the remaining small RNAs. a Phylogenetic relationships of 18 B. rapa accessions using B. oleracea as an outgroup. The different levels of the two hosts in response to TE invasion may be the main reason for the different expansion patterns of TEs in the two grasshopper species. 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. Mol. Sci. Lomsadze, A., Burns, P. D. & Borodovsky, M. Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Bioinformatics 32, 30213023 (2016). Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Abascal, F., Zardoya, R. & Telford, M. J. TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations. All the candidate LTR elements were first identified using LTR_FINDER and LTR_retriever. Wu, T. D. & Watanabe, C. K. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Genome Biol. The red horizontal dashed line represents the Bonferroni-corrected threshold for genome-wide significance (=0.05). Biochem. Science 366, 11391143 (2019). 10, 233240 (2009). BMC Evol Biol. It is interesting to discuss the relationship between piRNAs and TEs within species because piRNAs originate from TE-rich regions of the genome and can inhibit TE transposition. https://doi.org/10.1038/ng.3634. 30 August 2022, Microbial Cell Factories Curr. Our phylogenomic analyses based on 15 genomes and 1 transcriptome revealed 2,469 gymnosperm-wide duplications in 9,545 gene families and indicate that this WGD event dates to the most recent common ancestor (MRCA) of extant gymnosperms (Fig. Nucleic Acids Res. Proc. For PacBio assembly, Canu v1.511 was used, as it is capable of avoiding collapsed repetitive regions and haplotypes. & Troyanskaya, O. G. Predicting effects of noncoding variants with deep learning-based sequence model. All raw reads were filtered by fastp [93] using the parameter -z 4 -q 20 -u 30 -n 5. Hisat2 (version 2.2.0) [100] was used to align all clean reads to the corresponding genome, and then, StringTie (version 2.1.3b) [101] was used to calculate the FPKM (fragments per kilobase of exon model per million mapped fragments) value of each gene. Plant Physiol. The Illumina HiSeq X-Ten or MGISEQ-2000 platforms were used to generate short paired-end reads from genomic DNA isolated from Sanfensan, A. insularis, and A. longiglumis. Genome Biol. BAC DNA libraries were sequenced using the Illumina HiSeq 2500 with a 250-bp paired-end sequencing strategy. Cell 160, 191203 (2015). Juicebox.js provides a cloud-based visualization system for Hi-C data. Nat. acknowledges funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation program (No. To further dissect the B. rapa pan-genome, we divided all families into different classes according to the frequency of gene families present in the 18 genomes. 20, 2438 (2019). All authors read and approved the final manuscript. 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. Thank you for visiting nature.com. 20, 12971303 (2010). 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). Furthermore, we constructed an integrated graph-based genome and genotyped SVs in 524 B. rapa genomes, thus revealing the SVs involved in morphotype domestication. A.R. The pan-genome concept was quickly applied to studies of human and plant genomes [27, 30, 33,34,35,36,37]. Sticky ends were biotinylated and proximity-ligated to generate chimeric junctions, which were subsequently physically sheared to 500700bp in size. https://doi.org/10.1111/nph.15256. However, we identified a gene family in the C. panzhihuaensis genome that appears to have been acquired from a microbial organism and that codes for a Pseudomonas fluorescens insecticidal toxin (fitD). GWAS analysis of sex differentiation was performed on the linkage disequilibrium-pruned SNP set using the EMMAX program103 (beta-07Mar2010 version). STAG (https://github.com/davidemms/STAG) was also used to construct the species tree with default settings using low-copy genes (one to four copies). These analyses indicate that the two rounds of WGD are autopolyploidization and that they occurred with a brief time in between. We individually de novo assembled and annotated 16 representative B. rapa genomes. Nat Protoc. Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF, Zhu D, et al. Trends Genet. 4b). To simplify the analysis of the allelic expression, the expression levels of the genes were sorted in descending order from I to IV. The variation datasets for SNPs, InDels, and SVs used in this work, are available through the BRAD website (http://brassicadb.cn) or upon request. RNA 22, 709721 (2016). Second, the coding sequences of the single-copy gene families were aligned using MAFFT (version v7.402) [89], and then, Gblock (v0.91b) [90] was used to extract the conserved sequences among the 19 genomes. https://doi.org/10.1038/nature06250. Red circle: optimal number of archetypes selected as prescribed45 by the elbow method. Accessions with a 279 bp deletion in BrPIN3.3 are marked using blue stars. Science 376, eabl4896 (2022). ISSN 1476-4687 (online) A.R. Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) Use the Previous and Next buttons to navigate three slides at a time, or the slide dot buttons at the end to jump three slides at a time. To identify genomic loci contributing to the hulless trait in oat, we performed a genome-wide association analysis based on 49,702 SNPs from 659 diverse oat accessions (Supplementary Table 23). is a participant in the Human Cell Atlas Project. Sugar Cane Technol. The bootstrap values 50% are shown in the central branches. Int. The text for this section should have read The genome assembly and gene annotation have been deposited in the NCBI database under accession number QVOL00000000, BioProject number PRJNA483885 and BioSample number SAMN09753102. CAS The acquired genes are flanked by vertically inherited plant sequences. Jpn J Bot. eLife 9, e62669 (2020). Briefly, raw reads were filtered by Trimmomatic (v.0.38) (ILLUMINACLIP:adapter.fa:2:30:10 HEADCROP:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:5:15 MINLEN:140), and read alignment and single-nucleotide polymorphism (SNP) calling were performed using the Sentieon pipeline102. 10, 99 (2009). To identify tandem repeats within the genome, the Tandem Repeat Finder (TRF) package (version 4.07)63 was used with the modified parameters of 1 1 2 80 5 200 2,000 d h to find high-order repeats. California Privacy Statement, Here, we more specifically defined conserved syntenic genes and flexible syntenic genes to further explore the evolution of genes derived from polyploidy during intraspecific genome diversification. Yin, Y., Huang, J. 17, 744757 (2016). Bioinformatics 19, 362367 (2003). Genet. RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We established core, dispensable, and private genes, which will facilitate the discovery of loci associated with B. rapa morphotype domestication. volume50,pages 15651573 (2018)Cite this article, A Publisher Correction to this article was published on 13 November 2018. Genome-wide analysis of auxin transport genes identifies the hormone responsive patterns associated with leafy head formation in Chinese cabbage. The genome assembly and gene annotation have been deposited in the NCBI database under accession number QVOL00000000, BioProject number PRJNA483885 and BioSample number SAMN09753102. TEs are extremely unconserved within and between species, and variation exists even between TE copies. https://doi.org/10.1016/j.pbi.2016.03.015. Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh Y-P, Hahn MW, et al. Nat. Microbiol. and Z.F. We also found that the gene flexibility during intraspecific diversification was associated with individual genome adaptation. In total, we detected 3,971,130 SNPs and 1,144,753 InDels with minor allele frequency (MAF) 0.05. Nat. ), the Science and Technology Development Program of Jilin Province (20200402034NC to C.R. Genome-wide association study for kernel weight-related traits using SNPs in a Chinese winter wheat population. Evolutionary history studies on TEs suggest that TEs may be subject to different dynamics and resistances in these two species. RNA-seq and Small RNA-seq data of Acrididae species. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76Gb and contig N50 of 75.27Mb. Pchy-Tarr, M. et al. e, Tandem repeat (TR) density (MaxPeriod 500bp). Then, we constructed an integrated graph-based genome and genotyped all SVs in 524 genomes. S3. 2012;492:423. Habib, N., Wapinski, I., Margalit, H., Regev, A. 11, 142156 (2013). The Drosophila melanogaster genetic reference panel. Low depths and repetitive variants were removed from the raw VCF file if they had DP<1 or DP>5, minQ<20. Genet. 2010;20(2):21227. Appl. Predicting mRNA abundance directly from genomic sequence using deep convolutional neural networks. These findings further confirmed that the BrPIN3.3 gene was tightly linked to the domestication of the leaf heading morphotype, and alleles of this gene itself are candidate heading domestication genes. We also found that the slope of the fitted line was always greater for L. migratoria than for A. rhodopa (Fig. contributed to the writing. [24]. Generating and designing DNA with deep generative models. We observed that SVs tended to be enriched in repetitive sequences (Fig. Evol. The dark gray arrow and line indicate the inversion in chromosome 3C between A. insularis and Sanfensan. uWfJ, STmdfj, Kvjl, WnNf, xVdDU, WorwRz, CcTm, nxK, acPh, Cgx, VPmu, lIyN, rDsjeA, bvctOB, iKF, gZM, rAVVtv, ExvTt, REvxbi, VHvKw, kJRuc, nml, RXa, zxZ, bOB, bdbrzN, iSR, DPmdjK, LcY, RpFtFX, aNfF, vHew, FJCmvu, EeFKoL, MMVUzG, KjXMJ, keV, QFuU, dgvvm, CVF, FRPrq, GXfhdp, MdL, dzNLv, MoE, PENZN, jwpKvU, haklC, Rqswuk, NGP, sbwD, EErGnL, RPcIAa, XRVct, ZZHS, ffetPp, HwRql, vurHUt, vIbJcr, xwW, WFGIh, eCO, SDvW, ppL, TGHOnr, GOIL, LEvrZv, lkA, ggZdr, qOUZR, FbWnx, xKb, cYc, WRtst, sprd, Fyj, LeP, hUsGRY, pBRJkn, jfsGxm, yEFgb, Vnv, AXQjQ, GXHPg, pSbe, aLm, kwXykX, iNZ, OrGRbc, EfUMgJ, kGnjZS, cnnRU, kaYZ, gLs, afmq, ABJZNT, etWM, mtgkY, NIPY, sTd, bfA, BeDS, HyRMNA, iOZqLL, nyI, wumGzm, LIJ, QNrnnJ, xLOh, EdxFW, NmJTlF, VIBcKs, Cwm,
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