[DOI] 10.5524/102216
[Title] Supporting data for "Genomes and demographic histories of the endangered Bretschneidera sinensis (Bretschneideraceae)"
[Release Date] 2022-04-20
[Citation] Zhang, H; Du, X; Dong, C; Zheng, Z; Mu, W; Zhu, M; Yang, Y; Li, X; Hu, H; Shrestha, N; Li, M; Yang, Y (2022): Supporting data for "Genomes and demographic histories of the endangered Bretschneidera sinensis (Bretschneideraceae)" GigaScience Database. http://dx.doi.org/10.5524/102216
[Data Type] Genomic,Transcriptomic
[Dataset Summary] Bretschneidera sinensis is an endangered relic tree species in Bretschneideraceae and is sporadically distributed in eastern Asia. In contrast to its narrow and rare distributions currently, the fossil pollens of Bretschneideraceae were found to be frequent and widespread in the Northern Hemisphere during the Late Miocene. B. sinensis is also a typical mycorrhizal plant and its annual seedlings exhibit high mortality rates in absence of mycorrhizal development. Hence, the chromosome-level high-quality genome of B. sinensis will deeply help us understand the survival and demographic histories of this special relic species.
A total of 25.39 Gb HiFi reads and 109.17 Gb Hi-C reads were used to construct the chromosome-level genome of B. sinensis, which is 1.21 Gb in length with the contig N50 of 64.13 Mb and chromosome N50 of 146.54 Mb. The transposable elements (TEs) identified account for 55.21% of the genome, and 46,686 protein-coding genes were predicted. A lineage-specific whole-genome duplication was detected, and 7,269 lineage-specific expanded gene families with functions related to the specialized endotrophic mycorrhizal adaptation were identified in this species. The effective population size (Ne) of B. sinensis was also inferred and it was oscillated greatly in response to Quaternary climatic changes and decreased rapidly in recent making the Ne size of B. sinensis extremely lower. Our further evolutionary genomic analyses suggested that the developed mycorrhizal adaption might have been repeatedly disrupted by environmental changes caused by Quaternary climatic oscillations. The environmental changes and an already decreased population size during the Holocene may have led to the current rarity of B. sinensis.
This is the first report of the genome sequences for the monotypic family Bretschneideraceae distributed in evergreen forests in eastern Asia. Such a high-quality genomic resource will provide critical clues for comparative genomics studies of this family in the future.
[File Location] https://ftp.cngb.org/pub/gigadb/pub/10.5524/102001_103000/102216/
[File name] - [File Description]
readme_102216.txt - None
Bretschneidera_sinensis_pep.fasta - Bretschneidera sinensis Coding gene translated sequences
Bretschneidera_sinensis_BUSCO_full_table.tsv - Bretschneidera sinensis Full BUSCO results output files
Bretschneidera_sinensis_assembly.fasta - Bretschneidera sinensis Genome assembly
Bretschneidera_sinensis_phylogenetic_tree.nwk - Bretschneidera sinensis Phylogenetic tree files (newick)
Bretschneidera_sinensis_TE.gff - Bretschneidera sinensis Annotation of Transposable elements
Annotation-missing_busco_list.tsv - Bretschneidera sinensis Missing BUSCO results - Annotation
Annotation-short_summary.txt - Bretschneidera sinensis Short summary BUSCO results output files - Annotation
Assembly-missing_busco_list.tsv - Bretschneidera sinensis Missing BUSCO results - Assembly
Assembly-short_summary.txt - Bretschneidera sinensis Short summary BUSCO results output files - Assembly
COG.csv - Functional annotation results from COG
GO.csv - Functional annotation results from GO
KEGG.csv - Functional annotation results from KEGG
KOG.csv - Functional annotation results from KOG
NCBI-NR.csv - Functional annotation results from NCBI-NR
Swiss-prot.csv - Functional annotation results from Swiss-prot
TrEMBL.csv - Functional annotation results from TrEMBL
Figure_1.tif - Image (TIFF format) of Figure 1 in accompanying manuscript showing chromosome features of the Bretschneidera sinensis.
Figure_2.tif - Image (TIFF format) of Figure 2 in accompanying manuscript showing evolution analyses in gene families and repeat elements (TEs).
Figure_3.tif - Image (TIFF format) of Figure 3 in accompanying manuscript showing whole-genome duplication (WGD) analyses in the Bretschneidera sinensis.
Figure_4.tif - Image (TIFF format) of Figure 4 in accompanying manuscript showing demographic history of Bretschneidera sinensis estimated using PSMC.
Figure_S1.tif - Image (TIFF format) of Figure S1 in accompanying manuscript showing genome size estimation for Bretschneidera sinensis by GenomeScope.
Figure_S2.tif - Image (TIFF format) of Figure S2 in accompanying manuscript showing heatmaps for Hi-C assembly in B. sinensis.
Figure_S3.tif - Image (TIFF format) of Figure S3 in accompanying manuscript showing GC ratio of the three species. B. sinensis, C. papaya and M. oleifera that belong to Brassicales.
Figure_S4.tif - Image (TIFF format) of Figure S4 in accompanying manuscript showing the function enrichment analyses of the genes with TE insertions in B. sinensis.
Figure_S5.tif - Image (TIFF format) of Figure S5 in accompanying manuscript showing concatenated and coalescence-based phylogenetic trees.
Figure_S6-01.tif - Image (TIFF format) of Figure S6 in accompanying manuscript showing divergence times among 12 species selected in angiosperm.
Figure_S7.tif - Image (TIFF format) of Figure S7 in accompanying manuscript showing function enrichment analyses of the rapid expansion genes in B. sinensis.
Figure_S8.tif - Image (TIFF format) of Figure S8 in accompanying manuscript showing analysis of whole-genome duplicate event.
Figure_S9.tif - Image (TIFF format) of Figure S9 in accompanying manuscript showing function enrichment analyses of the WGD genes in B. sinensis.
Figure_S10.tif - Image (TIFF format) of Figure S10 in accompanying manuscript showing phylogenetic trees of the RBOH gene families.
Figure_S11.tif - Image (TIFF format) of Figure S11 in accompanying manuscript showing phylogenetic tree of the SAURs gene family.
Bretschneidera_sinensis_genomic.gff - Bretschneidera sinensis Coding gene annotations
Bretschneidera_sinensis_cds.fasta - Bretschneidera sinensis Coding gene nucleotide sequences
[License]
All files and data are distributed under the Creative Commons Attribution-CC0 License unless specifically stated otherwise, see http://gigadb.org/site/term for more details.
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