Additional file 1 of The Sapria himalayana genome provides new insights into the lifestyle of endoparasitic plants
Creators: name: Guo, Xuelian
name: Hu, Xiaodi
name: Li, Jianwu
name: Shao, Bingyi
name: Wang, Yajun
name: Wang, Long
name: Li, Kui
name: Lin, Dongliang
name: Wang, Hanchen
name: Gao, Zhiyuan
name: Jiao, Yuannian
name: Wen, Yingying
name: Ji, Hongyu
name: Ma, Chongbo
name: Ge, Song
name: Jiang, Wenkai
name: Jin, Xiaohua
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 1: Fig. S1. Evaluation of Sapria himalayana genome by k-mer analysis. X-axis shows the k-mer depth, and Y-axis depicts the k-mer frequency. The genome size of S. himalayana was estimated as 2,822.01 Mb. Fig. S2. Schematic diagram on stratified sampling from flower bud of Sapria himalayana. Tissues from the second, fourth, sixth, and eighth layers were used for RNA-seq and Iso-seq. The outermost host bark was removed prior to sampling. Fig. S3. Functional enrichment analysis of species-specific genes in Sapria himalayana. MapMan categories of significantly enriched genes are displayed using the logarithmic values of their P-values. Fig. S4. Phylogenetic tree of MADS-box gene family. Species names are abbreviated as follows: Arabidopsis thaliana, Manihot esculenta, Populus trichocarpa, Rafflesia cantleyi, and Sapria himalayana. Genes from S. himalayana and R. cantleyi are highlighted in red and brown colors, respectively. BS &gt; 50% are shown. Fig. S5. Phylogenetic inference and sequence similarity of TOMATO MADS-BOX GENE6and FRUITFUL-like.Neighbor-joining tree of the newly isolated euAP3 and TM6homologs.Neighbor-joining tree of FRUITFUL-likehomologs in represent species. Information on gene sequences is provided in Table S14. Fig. S6. Heatmap showing the log2-tranformed expression profile of genes regulating flowering time. Host-derived mRNAs are highlighted in purple. Fig. S7. Phylogenetic tree of acetyl-CoA carboxylase . Species names are abbreviated as follows: Arabidopsis thaliana , Cucumis sativus , Eucalyptus grandis , Glycine max , Gossypium raimendii , Manihot esculenta , Mimulus guttatus , Oryza sativa , Papaver somniferum , Populus trichocarpa , Quercus robur , Sapria himalayana , and Vitis vinifera . Fig. S8. Horizontal gene transferevents in the nuclear genome of Sapria himalayana. Species names are abbreviated as follows: Arabidopsis thaliana, Cucumis sativus, Cuscuta australis , Eucalyptus grandis, Glycine max, Gossypium raimendii, Manihot esculenta, Mimulus guttatus, Oryza sativa, Papaver somniferum, Populus trichocarpa , Quercus robur, S. himalayanaand Vitis vinifera. HGT events are highlighted in red. Fig. S9. Overview of intron sequences in HGTs.72 HGTs with at least one intron and 26 HGTs without intron.The average value of identity of intron sequence searched on nucleotidedatabase at NCBI website using BLASTN. 79introns from Vitaceae, with average identity was 84.67%, 16introns from other species, with average identity was 84.62%, and origins of other introns was uncertain. Fig. S10. Gene structure of selected introns in four sequences. Yellow and green bars represent coding sequences; the vertical dashed lines represent the intron position, the boxes represent introns; The value of sequence identity between introns enclosed in square bracket displayed on line. The total number of introns per coding sequence showed at the right of the bar box. D, genes in donor, substituted by Vitis vinifera; H, HGT genes in Sapria himalayana; V, vertical genes in S. himalayana; VR, related sequences of the vertical gene in Populus trichocarpa.The intron positions of three selected introns were highly conserved in D, H, VR sequences, but the V sequence was intronless.The intron positions of two selected introns were highly conserved in D, H, V, VR sequences, but the first intron position of H sequence had changed.the V sequence has been lost, and the H sequences was intronless. Fig. S11. Comparisons of characteristics among foreign genesin Sapria himalayana , Vertical genes in S. himalayana , genes in donor species, and genes in relative species.Average number of introns per gene.Average of total intron length per gene.Average CDS length per gene.Average gene length. Fig. S12. Scatterplot of enriched GO terms in the nuclear horizontal gene transferdataset of Sapria himalayana. MF, molecular function; BP, biological process. Bubble color indicates the P-value of the GO term; bubble size indicates the frequency of the GO term in the GOA database. Fig. S13. HGT eventsin the mitochondrial genome of Sapria himalayana. Fig. S14. Comparison of mitochondrial protein-coding gene content between Sapria himalayana and representative angiosperms. Colors indicate native, foreign, and absentgenes. The presence of both native and foreign copies of a gene is depicted by a subdivided rectangle. The nad5 gene of Lophophyphytum mirabile is chimeric []. The tree depicts the best estimate of relationships among the plant species. Only intact genes are shown; pseudogenes were not included. Fig. S15. Evolution of KARRIKIN INSENSITIVE2 genes in Sapria himalayana. The phylogenetic tree indicates the relationship among the KAI2 genes in represent species. Conserved, intermediate, and divergentclades are shown in rose, indigo, and purple, respectively. Species names are abbreviated as follows: Arabidopsis thaliana , Cuscuta australis , Cuscutacampestris , Coffea canephora , Cucumis sativus , Ipomoea nil , Jatropha curcas, Lindenbergia luchunensis , Linum usitatissimum , Mimulus guttatus , Manihotesculenta , Mimulus guttatus , Orobanche cumana , Phelipanche aegyptiaca , Papaver somniferum , Populus trichocarpa , Ricinus communis , Striga asiatica , S. himalayana , Sesamum indicum , Solanum lycopersicum , and Vitis vinifera . Genes in S. himalayana are highlighted in red. Figure S16. Overview of gene expression. The transcriptome data of bract, sepal, petal, and reproductive diskproduced in our study, were used to quantify the expression level of gene in our study and Cai et al. [], respectively.The overview of gene expression in our study. Gene with expression and without expression was highlighted in red and blue, respectively.The overview of gene expression in Cai et al. []. Gene with expression and without expression was highlighted in red and green, respectively. Fig. S17. Intron length disparity. Intron length distribution of genesand HGTsin Sapria himalayana genome. 7256genes had at least one long intron. Fig. S18. Number of nuclear-encoded plastid-targeting genes in different categories from Sapria himalayana genome. Fig. S19. Principal component analysis among samples from unopened flower bud of Sapria himalayana.All samples for transcriptome.Removal of abnormal samples for transcriptome. Fig. S20. Sequencing depths of intact mitochondrial protein-coding genes in Sapria himalayana. Sdh4_N represents the vertical copy of sdh4, and sdh4-F represents the foreign copy.