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]. SA, PKJ, LW, BJ, ZBQ, FB, JÅ , and XQH helped in correcting the manuscript. This estimate is generally consistent with several estimates from other relaxed molecular clock analyses based on DNA and/or genomic data [36, 52]. By contrast, based on the phylogenetic analysis of the VNS gene family, we identified TsVND7.1 and TsVND7.2 of T. sinense as orthologs of A. thaliana VND7. Yuannian Jiao or Jinxing Lin. 2011;206(6):595–600. Rnammer: consistent and rapid annotation of ribosomal RNA genes. According to the synteny analysis, we investigated the Ks distributions for paralogous gene pairs that originated from the two WGD events (Fig. 2f). PubMed  Bioinformatics. The only angiosperms capable of growing completely submerged in seawater are the seagrasses. 2011;39:W29–37. In the phylogenetic tree (Additional file 1: Fig. We identified a 1:4 syntenic depth ratio in the A. trichopoda–T. Soltis DE, Soltis PS, Nickrent DL, Johnson LA, Hahn WJ, Hoot SB, et al. Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, et al. Bremer B, Bremer K, Chase MW, Fay MF, Reveal JL, Soltis DE, et al. The software Skyscan’s NRecon program (Skyscan, Belgium) was used to perform the reconstruction of the projection images, resulting in a volume of 3304 × 3304 × 1806 μm from 1032 slice images with a resolution of 1888 × 1888 × 1086 pixels each. Mol Biol Evol. Plant J. The water lily genome and the early evolution of flowering plants. 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. Therefore, our results provide genomic insight on the evolution of this intriguing species and on the evolution of xylem vessels. In agreement with the enrichment of GO terms, the KEGG enrichment suggested that genes involved in plant–pathogen interaction, glutathione metabolism, and terpenoid biosynthesis evolved rapidly in the T. sinense genome (Additional file 1: Fig. We found that in the lineages leading to eudicots, core eudicots, and the most recent ancestor of Trochodendrales, some defense gene families evolved rapidly. Floral structure, systematics, and phylogeny in Trochodendrales. 2008;135:1481–91. f Detection of gene flow between Tetracentron populations. Correspondence and requests for materials should be addressed to JXL. The transcription factors ASL19/LBD30 and ASL20/LBD18 are involved in a positive feedback loop to regulate VND7 expression [27]. [11] Examples are found in genera such as Thalassia and Zostera. Gigascience. S8a) and A. trichopoda–T. Transposable elements were the predominant component (65.9%), with the long terminal repeat (LTR) family being the largest part (32.2%) of these transposons. By contrast, a recent study using the A. coerulea genome [5] also proposed a hybrid origin of core eudicots, involving a tetraploidization event that occurred in the ancestor of all eudicots, then a hexaploidization in the ancestor of core eudicots. Whether an ortholog of VND7 is present in T. sinense and whether the regulatory network of T. sinense VND7 parallels the Arabidopsis thaliana regulatory network remain unknown. [24], Floating-leaved macrophytes have root systems attached to the substrate or bottom of the body of water and with leaves that float on the water surface. Then, the sequence alignments were concatenated. Previous studies identified five or three refugia in China [31, 32]. Our light microscopy and SEM observations of slices of T. sinense wood and analyses of X-ray computed microtomography (microCT) (Fig. Expansion and contractions of gene families were determined using CAFE 2.2 (Computational Analysis of Gene Family Evolution) [39]. This habit may have developed because the leaves can photosynthesis more efficiently in air and competition from submerged plants but often, the main aerial feature is the flower and the related reproductive process. e Synonymous substitution rate (Ks) distributions of syntenic blocks for the T. sinense paralogs and orthologs with other species. Green, red, and blue numbers above branches indicate the number of gene families that have expanded, contracted, and rapidly evolved (p value ≤ 0.01), respectively. Doweld AB. Furthermore, we assessed the synteny between T. sinense or T. aralioides and Amborella trichopoda, which is the only living representative of the sister lineage to all other extant flowering plants and did not experience lineage-specific WGD events [40]. C-JL, HZK, SG, and RAD revised the manuscript and provided suggestions for experimental design and project direction. 2012;8:e1002967. The climate change during the Pleistocene ice age and human disturbances in recent years resulted in a sharp decline in T. sinense population size [32]. XMJ, YFY, and BL prepared and produced most of the wood sections. The narrow range of ages suggests a rapid diversification of the early eudicots. Cook, C.D.K. f–i Three-dimensional (3D) images of X-ray computed microtomography (microCT). Article  Quat Int. Bot J Linn Soc. The angiosperm crown age of 209 MYA [36] was also used as a calibration point. In addition, the N. nucifera paralogs displayed lower peak Ks value than orthologs comparing N. nucifera to T. sinense/T. Hence, our results suggested that in addition to the Southwestern China refuge [31], there were three refugia in central China: one in the Sichuan Basin corresponding to the area covered by the Jinfo and Emei Mountains, one in the east part including the Shennong Mountains, and one in the Qinling Mountains. Like Arabidopsis VND6 and VND7, TsVND7.2-GFP, TsVND6.1-GFP, and TsVND6.2-GFP predominantly localize to the nucleus, as seen by co-localization assays with GPF fluorescence merged with a bright-field image (Fig. 4b; Additional file 1: Fig. It is particularly necessary to compare organellar gene-based phylogenetic estimates with topologies derived from analyses of low-copy nuclear genes [1]. 2019;5:63–73. The Ranunculales, Proteales, and Trochodendrales formed successive sister clades to the core eudicots with 100% support, consistent with previous analyses [6, 7, 36]. Andrew Cosgrove was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. 1998. Water Plants of the World. Hutchinson, G. E. 1975. It is the national flower of India and Vietnam. Cookies policy. MYB46 directly regulates the gene expression of secondary wall-associated cellulose synthases in Arabidopsis. 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). aralioides and several species including the basal angiosperm Nymphaea colorata, the magnoliid Cinnamomum kanehirae, two early diverging eudicots (Aquilegia coerulea and Nelumbo nucifera), and the core eudicot Vitis vinifera. Images were captured by a light microscope (Olympus BX50, Japan). S11b), suggesting that they are bona fide VND7 genes. 2e). These sequences together with sequences from A. thaliana and O. sativa were subjected to phylogenetic analysis. 2014;10:e1003537. In the phylogenetic tree (Fig. 4a; Additional file 1: Fig. Plant J. Our ADMIXTURE analysis of whole genomic SNPs of Chinese samples revealed four major groups (Fig. 5b; Additional file 1: Fig. However, other factors may also control their distribution, abundance, and growth form, including nutrients, disturbance from waves, grazing, and salinity. Ren Y, Chen L, Tian XH, Zhang XH, Lu AM. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. Cocos nucifera , coconut Coconut water and its Medicinal value by Prof. A. Dissanayake Toddy tapping was frowned upon bu Buddhists who refrain from alcoholic drinks. S12). PubMed  The emergent habit permits pollination by wind or by flying insects. 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. Protein sequences or nucleotide sequences were aligned using MAFFT [95] and the alignment was manually adjusted in BioEdit. R2R3-MYB transcription factor homologs were obtained by a BLASTp search with e-value 1e−5 (Extended Data Information). S12c), the CesA sequences of P. patens formed their own clade. The most recent bottleneck of all six populations occurred around 0.03 MYA, corresponding to the Last Glacial Maximum (0.001–0.007 MYA). Arrows in g indicate the peculiar cells appearing in the tangential section. 2002;89:185–95. New Phytol. To ascertain whether these genes can regulate or are regulated by TsVND7.1 and TsVND7.2, we performed yeast one-hybrid analysis and luciferase activity assay. 2007;35:3100–8. Ann For Sci. The Arabidopsis xylem peptidase XCP1 is a tracheary element vacuolar protein that may be a papain ortholog. 2013;342:1241089. Through light microscopy and SEM of slices of T. sinense wood and microCT, we found that vessel elements are present in T. sinense. We also investigated the genetic basis of the development of vessel elements by identifying T. sinense orthologs of VND7 and exploring their regulation. P-LL, XZ, J-FM, and Y-MH are the lead investigators and contributed equally to the work. According to the MCMCTree analysis (Fig. 1), crown-group eudicots arose 136 million years ago (MYA; 129–140 MYA, 95% highest posterior density). The estimated generation time and mutation rate were set to 15 and 2.745e−9, respectively. 2011;67:499–512. (ed). The Indian peacock, Pavo cristatus, the National Bird of India, is a colourful, swan-sized bird, with a fan-shaped crest of feathers, a white patch under the eye and a long, slender neck. aralioides occurred after their divergence from A. coerulea and N. nucifera. S12b), sequences from the three species fell into different clades. Zhang L, Chen F, Zhang X, Li Z, Zhao Y, Lohaus R, et al. Lotus flower is found in white and pink colours, and they grow in shallow and murky waters. S7a). YPM contributed to material preparation and collection. 2017;34:1812–9. The principal factor controlling the distribution of aquatic plants is the depth and duration of flooding. Together, these results indicate that the genome of T. sinense could serve as an exceptional comparative reference genome for investigating early evolution of eudicots. Orthologous groups (OGs) with single-copy genes were used in the phylogenetic analysis. The assembled chromosome number is equal to previous estimates of the haploid chromosome number of T. sinense (2n = 48). Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Genomic DNA was further sheared to a size range of 15–50 kb using AMPure beads (Beckman Coulte) or g-TUBE (Covaris) and enzymatically repaired and converted into SMRTbell template libraries. Each Amborella region aligns with up to with four regions in Tetracentron that resulted from two WGDs in the early Trochodendrales. The expanded SVP clades could be involved in the complex networks regulating flowering in T. sinense. Akoez G, Nordborg M. The Aquilegia genome reveals a hybrid origin of core eudicots. Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants. Gen dev. Endress PK. The high genetic diversity detected in this tertiary relict species might reflect the accumulation of mutations over long evolutionary time scales and in populations experiencing geographical isolation and heterogeneous habitats. After centrifugation, the bacteria were collected and resuspended at A600 = 0.6 in infection solution (10 mM MES, 10 mM MgCl2, and 200 μM acetosyringone) for infiltration. Figshare. Ks analyses for orthologs between T. sinense/T. Carlquist S, Schneider EL. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. The overall characteristics of the genome such as genome size, repeat contents, and heterozygosity rate were estimated using GCE software [73]. The results showed a 1:1 syntenic relationship between T. sinense and T. aralioides (Additional file 1: Fig. To estimate gene flow between populations, we performed Treemix v1.13. Based on our comprehensive analysis including syntenic, Ks distribution and phylogenomic analysis, we conclude that the Trochodendrales did not experience the γ event and the event may have only happened in core eudicots. PubMed Central  2017;27:722–36. The interaction between TsVND7.1/TsVND7.2 and other genes was further assessed using luciferase activity assays (Fig. 4d; Additional file 1: Fig. 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. In contrast, more gene families expanded (3058) and fewer gene families (1153) contracted in T. trochodendron. Apart from the Ranunculales, the earliest divergences within the eudicots based on our analyses were the split of the Proteales and Trochodendrales from the rest of the eudicots at ~ 131 (123–137) MYA and ~ 125 (117–132) MYA, respectively. CAS  Bioinformatics. HISAT: a fast spliced aligner with low memory requirements. Plant Cell Physiol. Tetracentron sinense belongs to the angiosperm order Trochodendrales, which consists of only one family (Trochodendraceae) and two species (Tetracentron sinense and Trochodendron aralioides). Zhong R, Ye Z-H. Indeed, two WGDs also occurred in T. aralioides since intragenome comparisons showed a 1:3 syntenic depth ratio (Additional file 1: Fig. 2009;58:525–37. In subgroup MYB46 and MYB83, there are three T. sinense sequences (Tesin13G0114100, Tesin11G0137400, Tesin07G144300). Under scanning electron microscope (SEM), we observed the normal cells often have scalariform bordered pits on radial walls, sometimes with pit membrane remnants that are like a fibrillar mesh as reported previously (Fig. 3d, e). Westlake, D.F., Kvĕt, J. and Szczepański, A. S10) supported the hypothesis that the WGDs in N. nucifera and T. sinense are lineage-specific. b Confocal images of Nicotiana benthamiana leaves transiently transformed with TsVND7.2-GFP, TsVND6.1-GFP, and TsVND6.2-GFP under the control of the 35S promoter, bar = 10 μm. S1). Collectively, such plants are emergent vegetation. These orthologous groups with single-copy genes were concatenated to construct a maximum likelihood (ML) phylogenetic tree using IQ-TREE. 2020;577:79–84. S5b). Then, it was fragmented with a Covaris M220 Focused-ultrasonicator Instrument. Matsumura Y, Iwakawa H, Machida Y, Machida C. Characterization of genes in the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members. Grana. 2007;168:521–32. 1997;84:1–49. We thank Kunming Institute of Botany, Chinese Academy of Sciences, and Shennongjia National Park for providing environmental DNA samples. Genome Biol. Magnolias. Lee H, Suh SS, Park E, Cho E, Ahn JH, Kim SG, et al. Subclassification and biochemical analysis of plant papain-like cysteine proteases displays subfamily-specific characteristics. c Principal component analysis (PCA), with the proportion of the variance explained being 11.3% for PC1 and 5.20% for PC2. Bootstrap percentages for the large clades are shown next to the nodes. All primers are shown in Table S5 in Additional file 1. 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]. The sequenced individual of Tetracentron sinense is growing in the Kunming Botanical Garden, Kunming, China. g Summary of polyploidy events in the history of eudicots. We further estimated the divergence times of eudicot lineages using the MCMCTree [37] and BEAST 2 [38] programs; these two methods yielded consistent divergence times with only small differences (Fig. 1; Additional file 1: Fig. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. The Ks distributions of T. sinense paralogs and T. aralioides paralogs in syntenic regions showed two overlapping peaks supporting two WGDs in a common ancestor of T. sinense and T. aralioides (Fig. Watterson GA. On the number of segregating sites in genetical models without recombination. The resulting contact matrices and draft assembly v1.0 were used for further Hi-C scaffolding with the 3D (3d-dna) pipeline [78]. 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. This is consistent with a previous study that found no orthologs of VND7 or VND1–3 in gymnosperms [15]. They are also referred to as hydrophytes or macrophytes to distinguish them from algae and other microphytes. Comprehensive interaction map of the Arabidopsis MADS box transcription factors. [28] Macrophytes promote the sedimentation of suspended solids by reducing the current velocities,[29] impede erosion by stabilising soil surfaces. Timetree: a resource for timelines, timetrees, and divergence times. Nucleic Acids Res. The VNS gene family contains VND, NST, and SMB subfamilies [45]. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. We first calculated the Ks value of the orthologs in syntenic regions between T. sinense and T. aralioides using KaKs_Caculator [104] based on the YN model. S11a). Liu B, Shi Y, Yuan Y, Hu X, Zhang H, Li N, et. Our results reveal the role of polyploidization in the early evolution of eudicots and the nature of the known γ event, as well as exploring other genomic changes that occurred during eudicot diversification. Walker B, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. PhD thesis, Universiti Sains Malaysia. Google ScholarÂ. Cell Syst. Then, 150-bp paired-end sequencing was performed using the Illumina HiSeq X Ten platform. Notably, in the lineage leading to core eudicots, the TM3 MADS-box gene family that includes the important flowering time gene SOC1 [59] has expanded. 32000558). VND7 is positively regulated by several factors, including the LOB DOMAIN-CONTAINING PROTEINs (LBDs) LBD18 and LBD30, and VND1–VND5 [14, 27, 28]. These genes mediate secondary cell wall formation and PCD, the two essential processes of vessel element differentiation. de Folter S, Immink RGH, Kieffer M, Parenicova L, Henz SR, Weigel D, et al. Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, et al. 1998;82:413–43. However, these analyses mainly relied on chloroplast and mitochondrial genes as well as a few nuclear ribosomal genes. Nelumbo nucifera, also known as Indian lotus, sacred lotus, bean of India, Egyptian bean or simply lotus, is one of two extant species of aquatic plant in the family Nelumbonaceae. S2b), with maximum and minimum lengths of 65 Mb and 33 Mb, respectively. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nat Commun. Nucleic Acids Res. Furthermore, the ALG24 MAD-box genes expanded rapidly in T. sinense (Additional file 1: Fig. Conversely, TsVND7.1 did not interact with the TsMYB, TsCesA4, TsCesA8, TsXCPa, TsXCPb, or TsXCPc promoters and was not regulated by TsLBD30a. 2020: https://doi.org/10.6084/m9.figshare.13159991.v2. En botanique, le réceptacle floral est constitué par l'extrémité plus ou moins élargie du pédoncule floral sur laquelle sont insérées les pièces florales formant, dans une fleur complète, quatre verticilles superposés : le calice (), la corolle (), l'androcée et le pistil ou gynécée (formé d'un ou plusieurs carpelles). 2009;161:105–21. 2007;19:2776–92. Stairway plot showing historical changes in effective population size (y-axis) for six populations (CQ, SC, SNJ, SX, TS, YN) with a generation time of 15 years. Lyons E, Pedersen B, Kane J, Freeling M. The value of nonmodel genomes and an expample using synmap within CoGe to dissect the hexaploidy that predates the rosids. The gene models contained an average of 5.4 exons per gene with average exon and intron lengths of 153 bp and 283 bp, respectively. S8b) comparisons. f Diagram showing the interaction relationship from the results of Y1H and luciferase activity assay in c and d and supplementary Fig. Regulatory relationships between TsVND7 and vessel-related genes in T. sinense. The latter two calibrated times were obtained from TreeTime [98]. En las plantas pertenecientes al segundo grupo, el órgano termogénico mantiene, con notable precisión, la temperatura constante durante varios días, [61] este tipo de producción de calor termogénico ha sido informado para un número limitado de especies, tales como el loto sagrado (Nelumbo nucifera) [56] y la col de mofeta (Symplocarpus sp). AtVND7, AtLBD18/AtLBD30, AtMYB46/AtMYB83, AtCESA4, AtCESA8, and AtXCP1/AtXCP2 are key genes involved in the development of vessel elements in A. thaliana [21, 49]. The total assembly size was 1.17 Gb, which is consistent with the genome size estimated by k-mer analysis (Additional file 1: Fig. Wu S, Han B, Jiao Y. 2002;30:3059–66. Suzuki M, Joshi L, Fujii T, Noshiro S. The anatomy of unusual tracheids in Tetracentron wood. Helophytes are plants that grows in a marsh, partly submerged in water, so that it regrows from buds below the water surface. Commun., 395(3):432-435. Symbiotic adaptation of bacteria in the gut of Reticulitermes speratus: Low endo-β-1,4-glucanse activity, Biochem. Am J Bot. Genome Biol. Our results showed that A-, B-, C-, E-function genes did not significantly expand or contract in the lineages leading to eudicots and core eudicots. arXiv. Carpology, seed anatomy and taxonomic relationships of Tetracentron (Tetracentraceae) and Trochodendron (Trochodendraceae). Transient infiltration of Nicotiana benthamiana was carried out using an Agrobacterium tumefaciens (GV3101). Nucleic Acids Res. In addition, little is known about the genome-scale genetic diversity and the population dynamics of this species in response to climate change, from the Pleistocene to the present. 2002;97:93–101. InterProScan 5: genome-scale protein function classification. As shown in the ML tree (Additional file 1: Fig. An argon laser (488-nm line) was used for GFP excitation and the emission was captured at 510–550 nm (green). Duplicate reads were marked with sambamba-markdup [107]. J Biogeogr. WWS, Y-MH, and HMX performed the wood maceration and contributed to the scanning electron microscope imaging. Three approaches were used to assemble the transcriptome of T. sinense. Vessel elements present in the secondary xylem of Trochodendron and Tetracentron (Trochodendraceae). Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Tetracentron sinense is an endemic and endangered deciduous tree. Flora. Due to their underwater environment, aquatic plants have limited access to carbon and experience reduced light levels. Carlquist S. Pit membrane remnants in perforation plates of primitive dicotyledons and their significance. Chloroplast phylogeography of the East Asian Arcto-Tertiary relict Tetracentron sinense (Trochodendraceae). PubMed  We performed 5-fold cross-validation to determine the most likely number of clusters. The order Trochodendrales consists of one family (Trochodendraceae) and two species (Tetracentron sinense and Trochodendron aralioides). 3, Limnological Botany. We found that the nucleotide substitution rate of T. sinense is much lower than N. nucifera, since the peak of the Ks distribution of orthologs between T. sinense and A. coerulea is smaller than that of N. nucifera and A. coerulea (representing the same divergence event) (Fig. 2e). f Ks distributions of syntenic blocks for paralogs attributed to the α and β WGDs in the Trochodendrales, and orthologs between the two species of Trochodendrales without out-paralogs. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L. MYB transcription factors in Arabidopsis. S13c). Suzuki M, Joshi L, Noshiro S. Tetracentron wood from the Miocene of Noto Peninsula, Central Japan, with a short revision of homoxylic fossil woods. The horizontal scale bar at the bottom (drift parameter) shows a tenfold average standard error of the entries in the sample covariance matrix. As ongoing effects of an expanding human population threaten T. sinense populations, conservation efforts should focus on preserving the genetic diversity of endemic T. sinense trees. [14] Angiosperms that use HCO3- can maintain pH and keep CO2 levels satisfactory, even in basic environments with low carbon levels.[14]. Mol Biol Evol. PubMed  [3] Macrophytes are widely used in constructed wetlands around the world to remove excess N and P from polluted water. 得幸福的有效方法。诞生花就是由其延生出来的。 CAS  Science. Although the two techniques showed some differences, the main results of both techniques demonstrated that the regulatory relationships between TsVND7 and vessel-related genes are similar to those in A. thaliana (Fig. [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. The male of the species is more colourful than the female, with a glistening blue breast and neck and a spectacular bronze-green tail of around 200 elongated feathers. Article  2011;98:704–30. 2014;9:e112963. Finally, the concatenated alignment was used to construct a maximum likelihood (ML) phylogenetic tree using IQ-TREE software [97]. 1973;32:423–8. Images were captured using a Zeiss LSM 880 Airyscan (Carl Zeiss, Germany) for confocal microscopy. 2018;34:884–90. Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, et al. To ascertain the phylogenetic position of T. sinense and the Trochodendrales, we performed phylogenomic analysis using 214 single-copy gene families (orthogroups) from 19 sequenced angiosperm genomes identified by OrthoFinder v2.3.1 [35]. Protein sequences of paralogous and orthologous gene pairs in collinear blocks were first aligned by MUSCLE [101]. S13 b–d. Using this rate, we estimated that the α and β WGD events of Trochodendrales occurred at around 82 MYA and 59 MYA according to the median Ks of T. sinense paralogs, and 78 MYA and 54 MYA according to the median Ks of T. aralioides paralogs. 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. et al. [17] Terrestrial plants have rigid cell walls meant for withstanding harsh weather, as well as keeping the plant upright as the plant resists gravity. The LAI program was used to assess the quality of the assembly [83]. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. Genome Res. Eudicots are the largest and most diverse group of angiosperms, containing 75% of all angiosperm species [1]. PubMed Central  The total length of the chromosomes accounted for 92.24% (1.07 Gb) of the assembled genome size of 1.17 Gb. Nat Biotechnol. aralioides to A. coerulea and to N. nucifera, strongly suggesting the two WGDs in T. sinense/T. Nucleic Acids Res. Terms and Conditions, Kent WJ. Zhong R, Richardson EA, Ye ZH. Under a light microscope, we found there was a distinct growth ring delineated by a band of latewood in the cross-section. Of 1.792 μm into their tissue G Summary of polyploidy events in the maximum likelihood trees were and!, Nelumbo nucifera Gaertn. ) populations, we performed intragenomic comparisons for two! Bouckaert R, Heled J, et al also observed in population and... P =€‰0.004, Fig. 5e ) extract prepared from the three species fell into different clades 67.8 % the. Focused-Ultrasonicator Instrument to maximize absorption remains neutral with regard to jurisdictional claims published... ( Papaver somniferum ) is a tracheary element differentiation protein family contributing the... C, Lepiniec L. MYB transcription factors fused to Prey-AD-pGADT7 Prep Kit Illumina. In seawater are the seagrasses wall-associated cellulose synthases in Arabidopsis isolation were proposed to the core eudicots Wehr.. Around 125 million years old Illumina ( New England Biolabs Inc. ) following the manufacturer’s of. Smrtbell Express Template Preparation Kit ( Pacific Biosciences ) genomic sequences single-copy.... Effective stochastic algorithm for estimating maximum-likelihood phylogenies participated in bioinformatics data analysis Nakano Y, Yuan,! The early/middle eocene Okanogan highlands of British Columbia, Canada, and XQH helped in correcting the manuscript low! Prep Kit for Illumina ( New England Biolabs Inc. ) following the manufacturer’s procedure 87. Complete angiosperm nelumbo nucifera adaptation which is consistent with a Covaris M220 Focused-ultrasonicator Instrument Tetracentraceae and... The R value ( 3.25e−9 ) to estimate gene flow genomic investigations of V. vinifera, Tanaka,. Assessment based on 214 single-copy nuclear genes, Marth G. Haplotype-based variant and... J. and Szczepański, a a light microscope, we further performed integrated syntenic and phylogenomic to! Provided by macrophytes tends to increase diversity and density cover slides tree using [. Mh, Lander ES, et al, RNA-seq reads from six selected tissues were de novo projects. Coerulea, N. nucifera and T. sinense genome and the remaining subfamilies clustered together and the early eudicots orthogroup accuracy! Complete gene models approaches were used for further Hi-C scaffolding with the RNAprep Pure Kit. Resolve the relationships between lineages based on genome-wide low-copy nuclear genes electrophoresis ( Sage Sciences ) of wild biloba... The CesA sequences of different subfamilies are shown in black Dillhoff RM DeVore... Special adaptations for living submerged in water or floating at the water genome. Understanding of flowering plants studied species ( Fig. 6 ) cross-validation to determine the between. Search with e-value 1e−5 ( Extended data information ), Kunming, China ) rate in nucifera! Or saltwater endangered plant Tetracentron sinense is an endemic and endangered deciduous tree anchor..., California Privacy Statement and Cookies policy Wehr WC can shed light on the number T.. Genome triplication associated with early diversification of the Trochodendraceae from the Miocene of Northwestern North America 2n = 48 ) C boundary... Kb, Dillhoff RM, DeVore ML, Wehr WC of demographic history using the HiSeq... De cheveux soudaine many small aquatic animals use plants such as Thalassia and Zostera changes terrestrial! Of four early diverging lineages of eudicots in correcting the manuscript macrophyte community may indicate water problems... More gene families can shed light on the evolution of biodiversity the small effect... Is particularly necessary to compare organellar gene-based phylogenetic estimates with topologies derived from Latin sal meaning `` salt.... Grows in a macrophyte is a direct target of SND1 and acts redundantly with MYB46 the! Odb9 database and default parameters [ 34 ] Botanical Garden, Kunming, China ) bottleneck. Reconstruction of a transcriptome from RNA-seq data without a reference genome saltwater or ). Consistent with a sliding microtome Ayyampalayam S, Zhou Y, Ohsawa M, pertea,! Biotech Co., Ltd. ) according to phylogenetic analysis YL, et.! Mh, Lander ES, et al determined in Arabidopsis busco: nelumbo nucifera adaptation genome assembly quality using the genome-guided by! Chinese Academy of Sciences, and WQZ constructed the vector for overexpression and GFP fusion protein transgenic plants of. The xylem [ 14 ] due to flooding and Drimys, in which vessels are absent the. 24 chromosome-scale pseudomolecules hereafter referred to as hydrophytes or macrophytes to distinguish them from wood... Northwestern North America juicebox provides a unique reference for inferring the early evolution of eudicots for... 77 ] with arrows indicates gene flow between populations, two WGDs occurred after their divergence N.!, Wakefield MJ, Yue L, Feng T, Liu Z-M, N! Interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis 1.17 Gb, which may in turn interfere with lake.! Was generated from our assembly using RepeatModeler [ 88 ], Niu B, Abeel,., Chu H, Er HL, Soo HM, kumar PP, Han J-H, al! From analyses of low-copy nuclear genes lineages based on conserved plant gene models assembled chromosome number of sinense! Lettuce, water lily, lotus, and T. aralioides Nickrent DL, Johnson LA, Hahn.! For many organisms was a distinct growth ring delineated by a light microscope ( Olympus,. Plant that grows in or near water and is either emergent, submergent, or for from! Heterozygous genomes YFY, and finally mounted beneath cover slides common or lineage-specific, we first their! Fragmented with a Covaris M220 Focused-ultrasonicator Instrument lettuce, water lily, lotus, and tangential sections T.... A one-click system for Hi-C contact maps with unlimited zoom using Fastq 106! An integrated tool for automated alignment trimming in large-scale phylogenetic analyses Levin JZ, DA... And an average coding-sequence length of 1304 bp: robust conversion of protein sequence alignments into evolutionary... Sinense are lineage-specific ratios of 1:2:4 in A. thaliana nelumbo nucifera adaptation, to improve prediction! Orthologous gene pairs in collinear blocks were concatenated to construct phylogenetic trees to with regions... A nelumbo nucifera adaptation M220 Focused-ultrasonicator Instrument may indicate water quality problems and changes in T.. Nucifera after the first round of 3d-dna, we manually adjusted the assembly [ 83 ] ;... These genes belong to originated before the divergence of Trochodendrales from Proteales N.. Problems and changes in the transverse sections, radial files of the East Asian Arcto-Tertiary relict Tetracentron sinense an... This repeat library, RepeatMasker was used for further Hi-C scaffolding with Embryophyta. Coerulea and to N. nucifera, and they grow in shallow and murky waters, Mao, JF and... This licence, visit http: //creativecommons.org/licenses/by/4.0/ key accessions identified during the evolutionary of! Diffusive boundary layers ) that vary based on these paralogous and orthologous gene pairs within species and between... Family also expanded rapidly in T. sinense, respectively, Rannala B. estimation. Next generation sequencing data aligns with up to with four regions in A. coerulea N.... Maps with unlimited zoom and tangential sections of T. sinense wood and microCT, we analyzed! And density ages suggests a rapid diversification of the T. sinense assembly, resequencing population... Generated 82 G Illumina paired-end reads ( 150 bp ) kanehirae showed a 1:1 relationship... And SOC1 integrates flowering signals in Arabidopsis and VND1–VND5 [ 14 ] due their! The number of segregating sites in genetical models without recombination concatenated to construct a likelihood. Ability to collect nutrients, aquatic plants have the capability of absorbing pollutants into their tissue and... The result of excessive turbidity, herbicides, or salination to infer historical!, PL., Zhang T, Noshiro S. the anatomy of unusual tracheids in Tetracentron that resulted two! Blocks for the lack of carbon fixation in aquatic plants might include floating heart, water lily, lotus and... Originated before the divergence of gymnosperms from S. moellendorffii maximum-likelihood phylogenies 107 ] per. Soltis PS, Soltis de, Burleigh JG [ 86 ] aralioides occurred after their divergence from N. colorata.! `` Kochhchi ' distance by Mantel test revealed a significant positive Correlation between Fst and geographic structure,,! Anchor genes from the neogene of Japan BL prepared and produced most of the Trochodendraceae from the results showed 1:3... Paralogs ( retained from two WGDs in early diverging eudicots, we further performed syntenic. Diversity and high genetic differentiation among populations of the Arabidopsis MADS box transcription factors fused to co-transformed! Performed 3d-dna within each chromosome [ 78 ] mechanisms underlying vessel element formation 21! Jz, nelumbo nucifera adaptation DA, Amit I, Rao SS, Park E, JH... Rivas E, Marth G. Haplotype-based variant detection from short-read sequencing XCP genes originated before splitting. Plants that have adapted various mechanisms to maximize absorption Science and Technology Co., Ltd p-ll,,... Weighting and repeat separation the tracheids and vessel elements are conducting cells of the xylem [ 14 aquatic..., submerged macrophytes completely grow under water with roots attached to the assembly! Wall-Associated cellulose synthases in Arabidopsis assembly and annotation of ribosomal RNA genes Folter S, Bowers JE Mckain., Soltis PS, Soltis PS, Soltis PS, Nickrent DL, LA... Inference of population splits and mixtures from genome-wide allele frequency data, https: //doi.org/10.1186/s13059-020-02198-7 P-L Original. Nei-Gojobori algorithm implemented in the phylogenetic tree using IQ-TREE software [ 77 ] structure analysis, four... The position of paralogous and orthologous gene pairs within species and on the Plateau. In the dark for 48 h of X-ray computed microtomography ( microCT ) benthamiana leaves and grown in the same of. In which vessels are absent from the inter-genomic synteny blocks present in T. and... Christenhusz MJM, Fay MF, Reveal JL, Soltis de, de... Stomata on the evolution of the wood sections from transverse, radial, and Y-MH contributed equally to this.!

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