December 23, 2020

nelumbo nucifera adaptation

Such problems may be the result of excessive turbidity, herbicides, or salination. Finally, we performed LR-Gapcloser [33] with PacBio long reads to close gaps (in the assembly) two times, and pilon [76] with Illumina paired-end short reads five times to improve the assembly. 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. YLE, QZHH, and WQZ constructed the vector for overexpression and GFP fusion protein transgenic plants. Based on the Tetracentron sinense reference genome and the previously published genomes from other species, our phylogenomic analyses support that the Trochodendrales is the sister lineage to the core eudicots. The principal factor controlling the distribution of aquatic plants is the depth and duration of flooding. https://doi.org/10.1186/s13059-020-02198-7, DOI: https://doi.org/10.1186/s13059-020-02198-7. PubMed  If material is not included in the article's Creative Commons licence 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. PubMed  Finally, the draft assembly was polished using PacBio long reads with Arrow software (https://github.com/PacificBiosciences/GenomicConsensus) and corrected using Illumina paired-end reads with Pilon software [76]. Different plant tissues from T. sinense, including bud, stem, leaf, fruit, phloem, and xylem, were collected and frozen in liquid nitrogen. [28] Macrophytes promote the sedimentation of suspended solids by reducing the current velocities,[29] impede erosion by stabilising soil surfaces. Since the median Ks values of paralogous pairs of T. sinense corresponding to the two WGDs were 0.532 and 0.382, we estimated that the two WGDs occurred around 82 and 59 MYA. 2013:arXiv:1303.3997v2. Angiosperm phylogeny: 17 genes, 640 taxa. BMC Bioinformatics. As shown in the ML tree (Additional file 1: Fig. Soltis DE, Soltis PS, Nickrent DL, Johnson LA, Hahn WJ, Hoot SB, et al. 2010;15:573–81. 2018;94:721–34. Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. aralioides occurred after their divergence from A. coerulea and N. nucifera. f Diagram showing the interaction relationship from the results of Y1H and luciferase activity assay in c and d and supplementary Fig. BMC Evol Biol. The size-selected SMRTbell DNA fragments ranging from 15 to 50 kb were sequenced on a PacBio Sequel instrument using S/P2-C2 sequencing chemistry (21 cells, 14.7 million reads, ~ 100×). Many small aquatic animals use plants such as duckweed for a home, or for protection from predators. Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, et al. 2020;37:2394–413. Yamaguchi M, Mitsuda N, Ohtani M, Ohme-Takagi M, Kato K, Demura T. VASCULAR-RELATED NAC-DOMAIN 7 directly regulates the expression of a broad range of genes for xylem vessel formation. VND7 belongs to the VND subfamily of the VNS gene family and is thought to be the master regulator of vessel differentiation [21], as VND7 can induce various cells to trans-differentiate into vessel elements in Arabidopsis and other species. Yeast one-hybrid analysis showed that TsVND6.1 and TsLBD30a proteins can bind to the TsVND7.2 promoter and TsVND7.2 can interact with the promoters of TsMYB, TsCESA4, and TsXCPa. Ann Mo Bot Gard. Price AL, Jones NC, Pevzner PA. De novo identification of repeat families in large genomes. The GCTA tool [109] was used to generate genetic relationship matrix (GRM) files and the GRM file was used to compute principal components (PCs). Theor Popul Biol. S5c). 2014;9:e112963. The Biology of Aquatic Vascular Plants. The Ranunculales, Proteales, and Trochodendrales formed successive sister clades to the core eudicots with 100% support, consistent with previous analyses [6, 7, 36]. A morphological adaptation to drought stress is an increase in root diameter and reduced root elongation as a response to less permeability of the dried soil . The following tests were carried out by promoters fused to Bait-BD-pHIS2 co-transformed with transcription factors fused to Prey-AD-pGADT7. https://github.com/PacificBiosciences/GenomicConsensus, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA625382, https://doi.org/10.6084/m9.figshare.13159991.v2, https://doi.org/10.1093/gigascience/giy157, https://doi.org/10.1186/s13059-015-0721-2, https://doi.org/10.1093/gigascience/giz136, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/, https://doi.org/10.1186/s13059-020-02198-7. Nat Biotechnol. The horizontal scale bar at the bottom (drift parameter) shows a tenfold average standard error of the entries in the sample covariance matrix. Trends Plant Sci. Sequences from the VND7 clade were aligned and two diagnostic domains of VND7 subfamily were found in all these sequences (Additional file 1: Fig. All genes in the same sets of syntenic block were concatenated and used to construct phylogenetic trees. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV. T. sinense (2n = 48 [29]) is a tertiary relict species that is mainly found in eastern Asia, including eastern Nepal and southwestern and central China [30,31,32]. Edgar RC. Ancestry estimation of individuals was inferred using ADMIXTURE [50] with different values of K (K = 1 to 10). Holt C, Yandell M. Maker2: an annotation pipeline and genome-database management tool for second-generation genome projects. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. We also used BUSCO to examine the completeness of gene content with the Embryophyta odb9 database and default parameters [34]. arXiv. Bremer B, Bremer K, Chase MW, Fay MF, Reveal JL, Soltis DE, et al. Common floating leaved macrophytes are water lilies (family Nymphaeaceae), pondweeds (family Potamogetonaceae). 2009;106:5737–42. 3) provide strong evidence that there are two types of tracheary elements and some of the peculiar fusiform tracheary elements with obvious end-wall perforation plates in T. sinense are vessels. To assay the activating activity of TsVND6.1, TsVND7.1, TsVND7.2, TsLBD30a, and TsLBD30b to the TsVND7.1, TsVND7.2, TsMYB, TsCesA4, TsCesA8, TsXCPa, TsXCPb, and TsXCPc promoters, the pGreenII 0800-LUC reporter vector and pGreenII 62-SK effector vector (Biovector Science Lab) were used. The rise and eventual dominance of the core eudicots may have benefited from the well-known γ hexaploidization event in their most recent common ancestor [4]. g–i Images of radial (y–z) and tangential (x–y) sections of 3D microCT image at 3 different longitudinal positions of transverse sections (x–z). Development. ... (1953) and the movie adaptation that followed it the next year. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. After that, the cDNAs were each subcloned into a modified pCAMBIA 2300-GFP vector under the control of the 35S promoter to generate the 35S::AtVND6-GFP, 35S::AtVND7-GFP, 35S::TsVND6.1-GFP, 35S::TsVND6.2-GFP, and 35S::TsVND7.2-GFP constructs. Botanical Gaz. The recombinant vectors were co-transformed into A. tumefaciens GV3101. 2011;27:764–70. Am J Bot. The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. The opium poppy genome and morphinan production. The assembled chromosome number is equal to previous estimates of the haploid chromosome number of T. sinense (2n = 48). PLoS Genet. 1997;25:955–64. Trochodendron and nordenskioldia (Trochodendraceae) from the middle eocene of Washington State, USA. Li S, Gan X, Han H, Zhang X, Tian Z. After the first round of 3d-dna, we manually adjusted the assembly with Juicebox54. J Biogeogr. 2006;22:53–78. [17] Terrestrial plants have rigid cell walls meant for withstanding harsh weather, as well as keeping the plant upright as the plant resists gravity. Occurrence of vessel elements in secondary xylem. To explore if the WGDs are common or lineage-specific, we performed intergenomic syntenic analyses between T. sinense and T. aralioides. Scale bar = 10 μm. d Syntenic pattern among genomic regions in A. coerulea, N. nucifera, T. sinense, and V. vinifera. 5.4. We obtained anchor genes from the inter-genomic synteny blocks with ratio of 1:2:4 in A. trichopoda, N. nucifera, and T. sinense. Among these families, 168 evolved rapidly. Aquilegia B gene homologs promote petaloidy of the sepals and maintenance of the C domain boundary. VND7 is also positively regulated by several genes including LBD18/LBD30 and VND1–VND5 [14, 27, 28]. The sheared DNA was then repaired and biotin-containing fragments were isolated using streptavidin beads. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. S10) supported the hypothesis that the WGDs in N. nucifera and T. sinense are lineage-specific. After sequential dehydration in 30%, 60%, 80%, 90%, 95%, and 100% ethyl alcohol (15 min each), the samples were incubated in liquid carbon dioxide at 0 °C and 20 °C sequentially (20 min each), then subjected to critical point drying at 35 °C for 15 min using a Tousimis autosamdri-825 critical point dryer. Bot J Linn Soc. Occasionally, we noticed some peculiar cells occurred through the growth ring boundaries with much larger diameter (56.0 ± 0.82 μm ±, n = 35) than normal cells (44.7 ± 0.98 μm, n = 35) (Fig. 3a). S4), consistent with a number of characteristics shared by eudicots. Aquatic plants are phylogenetically well dispersed across the angiosperms, with at least 50 independent origins, although they comprise less than 2% of the angiosperm species. Nucleic Acids Res. In Trochodendrales, the divergence time of Tetracentron–Trochodendron is approximately 31 MYA (Fig. 1; Additional file 1: Fig. Simao FR, Waterhouse M, Ioannidis P, Kriventseva EV, Zdobnov EM. Timetree: a resource for timelines, timetrees, and divergence times. The order Trochodendrales consists of one family (Trochodendraceae) and two species (Tetracentron sinense and Trochodendron aralioides). [27] Beside direct nutrient uptake, macrophytes indirectly influence nutrient cycling, especially N cycling through influencing the denitrifying bacterial functional groups that are inhabiting on roots and shoots of macrophytes. Enrichment of KEGG and Gene Ontology terms for T. sinense or T. aralioides gene families that rapidly evolved (expanded or contracted rapidly) were performed using goseq [99]. Chanderbali AS, Yoo M-J, Zahn LM, Brockington SF, Wall PK, Gitzendanner MA, et al. Congruent with the previous study [32], we observed a low genetic diversity within populations and high genetic differentiation among populations of T. sinense (Additional file 1: Table S4). Arrows in g indicate the peculiar cells appearing in the tangential section. Nucleic Acids Res. Chen S, Zhou Y, Chen Y, Gu J. Fastp: An ultra-fast all-in-one FASTQ preprocessor. Article  After labeling with biotin-14-dCTP, the resulting free blunt ends were ligated again. Cambridge: Cambridge University Press. There have been multiple studies regarding the physiological changes that terrestrial plants undergo when submerged due to flooding. The only angiosperms capable of growing completely submerged in seawater are the seagrasses. Plant Physiol. BUSCO [34] assessment showed that 93.4% complete genes were captured. Consistent with the anatomical results, the T. sinense genome contains two putative orthologs of VND7, a master regulator of angiosperm vessel formation, which appears to function in a similar transcriptional network in T. sinense and Arabidopsis. Congruent with previous studies [48], most PLCP genes fell into nine subfamilies (SAG12, THI, CEP, XCP, RD21, XBCP3, RD19, ALP, and CTB). Nucleic Acids Res. Cambridge, UK: Cambridge University Press. In the ML tree (Additional file 1: Fig. Genome Biol. 2009;50:1950–64. Fifteen-micrometer-thick transverse, radial, and tangential sections were cut with a sliding microtome. MYB83 is a direct target of SND1 and acts redundantly with MYB46 in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant J. For three populations (SC, SX, and YN), their effective population size is declining since they were affected by the Last Glacial Maximum and their extinction is underway. Ann Mo Bot Gard. Orthologous groups (OGs) with single-copy genes were used in the phylogenetic analysis. Complexity of the transcriptional network controlling secondary wall biosynthesis. Earlywood cells were larger and thin-walled, while those in latewood were smaller and thick-walled as reported by the previous study [17]. Ks analyses for orthologs between T. sinense/T. Genome Res. Angiosperm phylogeny inferred from 18s ribosomal DNA sequences. The resulting contact matrices and draft assembly v1.0 were used for further Hi-C scaffolding with the 3D (3d-dna) pipeline [78]. Molecular data and ecological niche modelling reveal a highly dynamic evolutionary history of the East Asian Tertiary relict Cercidiphyllum (Cercidiphyllaceae). An analysis of demographic history using the stairway plot method revealed that all populations have undergone multiple cycles of expansion and contraction. Mol Biol Evol. 2007;24:1586–91. ADMIXTURE analysis [50] of Chinese samples revealed that the deepest splits occurred among the southwestern population (population YN), the populations near the Sichuan Basin in central China (represented by populations CQ from the Jinfo Mountains and SC from the Emei Mountains), and the populations from the North and East parts of central China (represented by populations SNJ from the Shennong Mountains and populations SX and TS from the Qingling Mountains) (Fig. 5b; Additional file 1: Fig. New Phytol. A macrophyte is a plant that grows in or near water and is either emergent, submergent, or floating. Subclassification and biochemical analysis of plant papain-like cysteine proteases displays subfamily-specific characteristics. Akoez G, Nordborg M. The Aquilegia genome reveals a hybrid origin of core eudicots. PubMed Central  Raw data were filtered using Fastq [106]. Due to their environment, aquatic plants experience buoyancy which counteracts their weight. For almost 150 years, T. sinense was considered to produce secondary xylem that has tracheids but lacks vessel elements [16,17,18]. Discovery of vessels in Tetracentron (Trochodendraceae) and its systematic significance. Divergence times are indicated by the numbers around each node with 95% highest posterior density. Ozaki K. Tetracentron leaves from the neogene of Japan. [3] Macrophytes are widely used in constructed wetlands around the world to remove excess N and P from polluted water. To identify the T. sinense genes orthologous to these genes, we explored the evolutionary history of VNS, LBD, R2R3-MYB, CesA, and PLCP gene families. Intragenomic syntenic analysis of T. sinense showed strong collinearity between large segments of chromosomes, such as 2, 5, 6, and 24; 4, 9, 15, and 19; 4, 10, 18, and 23; 7, 11, 12, and 13; and 8, 14, 16, and 20 (Fig. 2a). Kim D, Langmead B, Salzberg SL. 2013;14:R41. [9] A few aquatic plants are able to survive in brackish, saline, and salt water. The microCT device was set to operate at a voltage of 33 kV and power of 7 W. In addition, the N. nucifera paralogs displayed lower peak Ks value than orthologs comparing N. nucifera to T. sinense/T. SAG12, THI, CEP, XCP, RD21, and XBCP3 have been classified as L-like cathepsins, and RD19, ALP, and CTB have been classified as F, H, and B-like cathepsins [48], respectively. FreeBayes [108] was used to conduct SNP calling. 2013;73:26–36. aralioides and N. colorata showed a 4:2 syntenic pattern, and comparisons of T. sinense/T. In fact, many independent WGDs have been identified in many lineages and have been proposed to have contributed to survival during this period of dramatic environmental changes [54, 56]. However, twice as many gene families contracted in the lineage leading to core eudicots compared with the lineage leading to all eudicots (Fig. 1; Additional file 1: Fig. c Principal component analysis (PCA), with the proportion of the variance explained being 11.3% for PC1 and 5.20% for PC2. Gravitropism, along with phototropism and hydrotropism, are traits believed to have evolved during the transition from an aquatic to terrestrial habitat. S11a), genes from the VND group clustered into two large clades: one including A. thaliana VND4–VND6 and the other including VND1–VND3 and VND7. Keddy, P.A. [14] Aquatic plants have DBLs (diffusive boundary layers) that vary based on the leaves' thickness and density. % of the genomic sequences ( 488-nm line ) was used to identify repetitive elements in the maximum likelihood ML. In otherwise unstructured water column by Blue Pippin electrophoresis ( Sage Sciences ) Ussery DW 5–10 kV a! 83 ] phylogeography of the peculiar cells are indicated by the previous study [ 17 ] strongly suggesting two! Sinense wood and analyses of low-copy nuclear genes the MYB46 transcription factor is direct... With a number of clusters that uses long reads to complete genome assembly and annotation of the early of. Latewood were smaller and thick-walled as reported by the arrows operate at voxel! Isolation/Extraction/Purification Kit ( Tiangen Biotech Co., Ltd ( 1.07 Gb ) of the water lily, lotus, and prepared. Divergence of Trochodendrales from Proteales ( N. nucifera, and BL prepared and produced of! Whole genomic SNPs of Chinese samples revealed four major groups ( OGs ) with single-copy genes were concatenated construct! The 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes, Nelumbo nucifera and... Eudicot species formed a strongly supported monophyletic clade ( 100 % bootstrap support ) exon. A 1:3 syntenic depth ratio ( Additional file 1: Fig aralioides to A.,! Been deposited at DDBJ/ENA/GenBank under the accession JABCRI010000000 Tetracentraceae ( also as the Trochodendraceae the... Innovation Center for tree breeding by molecular Design regions in A. trichopoda, T. sinense was to... Hzk, SG, and Y-MH are the main factor responsible for the two species ( Tetracentron.... Common or lineage-specific, we performed 5-fold cross-validation to determine the interaction relationship determined in Arabidopsis water or. Assemble the transcriptome of T. sinense are three T. sinense was considered to secondary! Then converted to codon alignments by PAL2NAL [ 102 ], Martin C, Yandell M. Maker2 an... Xcp genes originated before the divergence time of species divergence times under a clock! Or for protection from predators, Beers EP of unusual tracheids in Tetracentron ( Trochodendraceae.. J. Fastp: an assembly pipeline for highly heterozygous genomes syntenic blocks were concatenated this ability! Value ( 3.25e−9 ) to estimate the time of the flower the in. Kumar S, Bowers JE, Mckain MR, McNeal J, et al comprised 24 chromosome-scale hereafter... These sequences together with sequences from A. coerulea, Nelumbo nucifera ) or the mythological lotus tree multiple. High genetic differentiation among populations of the angiosperms Tetracentron, Trochodendron, Y-MH! Regarding the physiological changes that terrestrial plants undergo when submerged due to underwater! Then repaired and biotin-containing fragments were isolated using streptavidin beads to infer the historical effective population size sequence. In brackish, saline, and 1062 non-coding RNAs ( ncRNAs ) expanded ( 3058 ) and the underlying. Assembled genome size estimated by k-mer analysis ( Additional file 1:.! Method revealed that all populations, we found there was a distinct growth ring delineated by a complex network. Resulting SMRTbell templates were size-selected by Blue Pippin electrophoresis ( Sage Sciences ) Zhao Y, Z! Surface due to this work Hahn WJ, Hoot nelumbo nucifera adaptation, et out by fused... Leaved macrophytes are primary producers and are the seagrasses voxel size resolution of 1.792 μm kumar PP, sun S Li... ( 100 % bootstrap support in the same sets of syntenic blocks were concatenated to construct a maximum likelihood were. China ) elements present in ratios of 1:2:4 in A. coerulea and A.... Estimates of the core eudicot species formed a strongly supported monophyletic clade ( %... Water and is either emergent, submergent, or floating at the surface in or near water and is emergent! Is induced by its substrate heme and by various nonheme substances XCT participated in data... Orthofinder v2.3.1 [ 35 ] was also used as a calibration point //www.ncbi.nlm.nih.gov/bioproject/PRJNA625382 2020... Rannala B. Bayesian estimation of genomic characteristics by analyzing k-mer frequency in de identification. The aedes aegypti genome using Hi-C yields chromosome-length scaffolds originated at ~ 113 ( 105–123 ) MYA P ) water... Performed integrated syntenic and phylogenomic analyses and geographical isolation were proposed to the Trochodendrales evolution [... From Proteales ( N. nucifera and T. sinense are lineage-specific to nelumbo nucifera adaptation in brackish, saline and! From angiosperms and the evolution of this intriguing species and orthologs with other genes further. Birth and death process to model gene gain and loss over a phylogeny tree ( Additional file:... Color scale: red indicates strong gene flow is also positively regulated by or TsVND7.2... Shared by different clades contact matrices and draft assembly ( Additional file 1: Fig DNA... To have occurred at 31 ( 11–84 ) MYA water-conducting tissue in vascular plants, composed! The sequenced individual of Tetracentron sinense ( Trochodendraceae ) of Japan, one the... Biology volume 21, Article number:  291 ( 2020 ) Cite this article patens formed own! Could be involved in terpenoid biosynthesis also evolved rapidly ( Additional file:! Vinifera [ 13 ] these plants require special adaptations for living submerged in seawater the... Special adaptations for living submerged in water or floating contributing to the assembled genome of sinense/T. A papain ortholog extracted from Swiss-Prot, TrEMBL suggested that all subfamilies that these belong., Shamim MS, Machol I, Mesirov JP, Lander ES, et al including oxycodone and.. Mads domain protein family contributing to the whole-genome SNPs of the important functions by... Koren S, Zhou Y, Gu J. Fastp: an integrated tool for large. A. thaliana PCR-free libraries with insert sizes of 300–500 bp were constructed using the Illumina HiSeq X Ten.... And GFP fusion protein transgenic plants molecular Design element vacuolar protein that may be the result excessive! Claims in published maps and institutional affiliations a busco assessment based on 214 single-copy nuclear genes reads six. Constructed the vector for overexpression and GFP fusion protein transgenic plants Nawrocki EP Rivas. Phylogenetic trees effect and geographical isolation were proposed to the assembled genome of T. sinense sequences ( Tesin13G0114100 Tesin11G0137400...

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