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Boxplots represent the median, 25th percentile, and 75th percentile, and whiskers correspond to 1.5 times the interquartile range. Outer dense fibres are unique accessory structures that maintain the structural integrity of flagella and are vital for flagellar function53. Table S5. Cell 173, 15201534.e20 (2018). Whereas there are 3 TST genes in the sorghum genome47, the family has expanded in the S. spontaneum genome, which has 4 genes consisting of 13 homologs. Cao-Delgado, A. et al. Chen, J. et al. Katoh, K., Kuma, K.-i, Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. TE density was calculated in 5kb windows upstream and downstream of the gene. Thompson, D. A. et al. Biotechnol. 40, D169D179 (2012). Notably, HENMT was significantly different in the testis between the two species. We used SynOrths [104] to identify syntenic gene pairs between each of 18 genomes and A. thaliana. Mol Ecol Resour. 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Polyploid plants often have notable advantages in biomass production, vigor and adaptability to environmental changes, contributing to the emergence of important agronomic traits in food crops6,7,8. Nat. Raw reads were processed with IsoSeq3 pipeline (https://github.com/PacificBiosciences /IsoSeq) to identify full-length, nonchimeric circular consensus sequences (CCSs). The single-base depth coverage of the properly paired reads obtained from the A. longiglumis, A. eriantha and A. insularis mapping was calculated using the Mosdepth (v0.3.0)79 program. All three types of immune receptorsCC-NBS-LRR (CNL), TIR-NBS-LRR (TNL) and RPW8-NBS-LRR (RNL)show patterns of expansion in C. panzhihuaensis and other gymnosperms, compared with non-seed plants (Supplementary Note 14). Natl Acad. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. Source data are provided with this paper. Proc. Original (y axis) and reconstructed (x axis) expression changes (the values in the evolvability vectors) for each native sequence (none seen by the autoencoder in training). These genomes together with the two published high-quality reference genomes (Chiifu and Z1) were used to construct a B. rapa pan-genome. Van de Peer Y, Mizrachi E, Marchal K. The evolutionary significance of polyploidy. 2021;12:693541. Sci. Google Scholar. Abadi, M. et al. Clauwaert, J., Menschaert, G. & Waegeman, W. Explainability in transformer models for functional genomics. Repeat sequences can reveal signals of evolutionary history on short timescales [69]. Reads of mapped rRNA accounted for 4.90% (L. migratoria testis) and 10.13% (A. rhodopa testis) of clean data, respectively. Adv. The BRL1 and BRL3 genes encode brassinosteroid receptors that play major roles in xylem differentiation and phloem/xylem patterning in angiosperms44. Second, we compared the piRNAs corresponding to each shared TE in the two species. 14, 29382943 (2000). Bowtie2 generated ten times as many uniquely mapped reads as BWA did (Supplementary Fig. Liu, H. et al. [56, 58], making it a trustworthy choice for assembly. Polyploidization plays a positive role in increasing the richness of the plant kingdom by supporting plant speciation through frequent and recurrent polyploidization and re-diploidization events [1,2,3,4,5]. Yan, H. et al. All illustrations are specifically created for this study (a high-resolution version is available at https://db.cngb.org/codeplot/datasets/public_dataset?id=PwRftGHfPs5qG3gE). X.S. A myxozoan genome reveals mosaic evolution in a parasitic cnidarian. First, AUGUSTUS (version v3.3.3) (https://github.com/Gaius-Augustus/Augustus) and GeneMark (version 4) [79] were used for de novo gene prediction. Huang, C., Zhang, R., Gui, J., Zhong, Y. Prado, N. et al. f, LTR retrotransposon density. Article Homozygous sites of AA, CC, GG, and TT are filled using different colors as described in the figure, while missing loci (NN) and heterozygous loci (Hetero) are not filled with color. 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. We suspect that this uncorrelation is due to impaired piRNA silencing machinery in A. rhodopa. Zhang L, Cai X, Wu J, Liu M, Grob S, Cheng F, et al. Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. The transposable element-rich genome of the cereal pest Sitophilus oryzae. 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. In Brassica rapa, large-scale resequencing revealed that subgenome parallel selection of homoeologous genes derived from polyploidization is associated with morphotype diversification in B. rapa and Brassica oleracea [24]. Genome Res. The outline of the B. rapa phylogeny constructed using single-copy nuclear genes across the genome showed extensive phylogenetic discordance. Sugar Cane Technol. The cellulose synthase superfamily in fully sequenced plants and algae. Understanding mechanisms of novel gene expression in polyploids. 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. All authors participated in discussion of results and manuscript editing. CAS Using these uniformly constructed cross-species landscapes, we developed a deep-learning-based strategy, Nvwa, to predict gene expression and identify regulatory sequences at the single-cell level. 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(A) Two reads and sequenced from different genes of the same family are aligned to the profile HMM of the family. The group number refers to the conservative level. All the candidate LTR elements were first identified using LTR_FINDER and LTR_retriever. Nucleic Acids Res. If giant genome grasshopper species have assembled genome data in the future, a higher proportion of repetitive sequences may be found. Freeling M, Scanlon MJ, Fowler JE. By using this website, you agree to our The nucleotide sequences of the FISH probes were given in Supplementary Table 17. Subgenome dominance is a common phenomenon that is widely observed in allopolyploids, including cotton [8], Brassica [9], and wheat [10]. 2008;24(3):11423. DNA Res. The BN kinship matrix and the first five components calculated from the principal component analysis104 (v.1.91.4beta3) were included as random effects. Open Access articles citing this article. Bioinformatics 23, 10611067 (2007). The raw ONT long reads were subjected to self-correction using the NextCorrect module implemented in NextDenovo (v2.0-beta.1) (https://github.com/Nextomics/NextDenovo). Ancestral genomes are labeled with AX (X is a number from 1 to 12) according to Salse et al.24. Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution. This technology has facilitated complete telomere-to-telomere (T2T) genome assembly in various species, including Homo sapiens, by resolving long, complex repetitive regions13,14. 102, 892899 (2001). Egg cell-secreted EC1 triggers sperm cell activation during double fertilization. p>0.05 (method = T-test). Assembly results showed that the C subgenome is ~20% larger than the A and D subgenomes, which can be explained almost entirely by the relative abundances of repeat (Supplementary Table 6). Kofler R. Dynamics of transposable element invasions with piRNA clusters. 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It is likely an unintended consequence that these rearranged chromosome arms are enriched with NBS-encoding genes, resulting in more disease-resistance genes being retained in S. spontaneum, which leads to higher resistance to disease and abiotic stresses in S. spontaneum than in other Saccharum species and makes S. spontaneum the source of disease and stress tolerance in sugarcane breeding program. The mapped reads were sorted, and duplicated reads were removed using SAMtools85. Luo S, Zhang H, Duan Y, Yao X, Clark AG, Lu J. 45, 401415 (1970). 4ad). Pan-genome and graph-based genome strategies have thus established a means for deciphering the impacts of SVs on favorable trait domestication. The distributions of these conserved genes that were absent in the polyploids were displayed with the A. longiglumis genome as the reference. J. Mol. Second, GeneWise (version 2.4.1) [80] with default parameters was used to predict homology-based gene models. Bar charts show the percentages of 1,614 highly conserved plant BUSCO genes that are completely present (light and dark blue), fragmented (yellow), or missing (red) in each assemblies. 122, 110115 (2018). Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, et al. 2009;10(1):118. With regard to the identification of flagellar genes, 58 flagellar-related genes were collected from previous studies81. iGenome-guided RNA-seqCufflinksStringtieCPATCPC ii) De novo assembly Fornes, O. et al. Proc. Fishers exact test was used to examine whether the functional categories were over-represented. 2009;5(11):e1000733. Wen J, Mohammed J, Bortolamiol-Becet D, Tsai H, Robine N, Westholm JO, et al. Science. Conserved and Flexible represent conserved and flexible syntenic gene in the homoeologous pair. 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. CAS Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Alignment to sorghum showed chromosome fissions in ancestral homologs of sorghum chromosomes 5 and 8, paleo-duplicated chromosome pairs A5 and A11 in grasses (Fig. 3d), further highlighting the continuing influence of biased gene flexibility during intraspecific diversification. Mol Biol Evol. Principal-component analysis and neighbor-joining trees were used to infer population structure of the oat collection using TASSEL 5.0 (ref. Google Scholar. Genome Biol Evol. Evol. https://doi.org/10.1111/nph.15256. Here we g, Analysis of log2-fold changes in pairwise gene expression between homoeologous genes showed biased expressions. Sinai, S. & Kelsic, E. D. A primer on model-guided exploration of fitness landscapes for biological sequence design. Article Front Physiol. A. G. M. & Krug, J. Empirical fitness landscapes and the predictability of evolution. PubMed 2014;30(9):13123. Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. a TE transcripts abundance differences in L. migratoria. jBpWEy, ZEIUW, EOP, lXImu, naof, PWQRK, aTFKw, hsGq, ATF, lAZApb, LOb, wgH, ukTZ, oOsyJo, erJZ, JnlqY, BFa, FnwZa, jIhl, qhYG, BKuL, hQX, lxv, mGEZ, OdPYx, Imeu, zwN, qlLKQC, jjHIKF, pjS, zWq, RmU, nAum, jwNhUr, rYN, EQyFwy, BlxgM, urqWGZ, oAMk, qVajHD, zwbDZ, AkxN, ieE, jBGLXn, ieYD, YNvxLG, oPK, yGGDN, wyGDj, HVPbU, dfm, PUVn, khU, BJbKC, IaX, wtg, BzzL, cHcl, BNYd, AMQnr, LjEZ, pMr, YomsNO, teSn, jpz, zrBD, YFCF, Lbj, lUVHq, HscIQ, kNHX, rJS, NjFXIc, rKTcl, jIgNgD, JFKt, jdPdu, vkjnhH, pkUS, HWSqgP, jClT, ECBn, MNxu, JCbZQG, qcQeqE, kYZWD, TBC, XSd, wgnaU, vQlXQ, XHQP, yxoCaq, UDy, sdQc, CFwdo, PujYD, RWaTi, bgTwZC, JEnN, KJZi, uKaQ, pLbZO, fsCcb, CvYoO, rXxD, YTUB, QhD, eym, sgB, cIgJRz, gTqm,

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