[DOI] 10.5524/102200

[Title] Supporting data for "A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree"

[Release Date] 2022-03-25

[Citation] He, J; Bao, S; Deng, J; Li, Q; Ma, S; Liu, Y; Cui, Y; Zhu, Y; Wei, X; Ding, X; Ke, K; Chen, C (2022): Supporting data for "A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree" GigaScience Database. http://dx.doi.org/10.5524/102200

[Data Type] Genomic,Transcriptomic

[Dataset Summary]  <i>Artocarpus nanchuanensis</i> (Moraceae), which is naturally distributed in China, is a representative and extremely endangered tree species. In this study, we obtained a high-quality chromosome-scale genome assembly and annotation information for <i>A. nanchuanensis</i> using integrated approaches, including Illumina, Nanopore sequencing platform and Hi-C. A total of 128.71 gigabases (Gb) of raw Nanopore reads were generated from 20 kb libraries, and 123.38 Gb of clean reads were obtained after filtration with 160.34x coverage depth and a 17.48 kb average read length. The final assembled <i>A. nanchuanensis</i> genome was 769.44 Mb with a 2.09 Mb contig N50, and 99.62% (766.50 Mb) of the assembled data was assigned to 28 pseudochromosomes. 39,596 genes (95.10%, 39,596/41636) were successfully annotated, and 129 metabolic pathways were detected. Plants disease resistance/insect resistance genes, plant-pathogen interaction metabolic pathways, and abundant biosynthesis pathways of vitamins, flavonoid and gingerol were detected. Unigene reveals the basis of species-specific functions, and gene family in contraction and expansion generally implies strong functional differences in the evolution. Compared with other related species, a total of 512 unigenes, 309 gene families in contraction and 559 gene families in expansion were detected in <i>A. nanchuanensis</i>. This <i>A. nanchuanensis</i> genome information provides an important resource to expand our understanding of the unique biological processes, nutritional and medicinal benefits, and evolutionary relationship of this species. The study of gene function and metabolic pathway in <i>A. nanchuanensis</i> may reveal the theoretical basis of special trait in <i>A. nanchuanensis</i>, and promote the study and utilization of its rare medicinal value.

[File Location] https://ftp.cngb.org/pub/gigadb/pub/10.5524/102001_103000/102200/

[File name] - [File Description]
Chr_genome_final_gene.gff3  -  Coding gene annotations of of Artocarpus nanchuanensis
readme_102200.txt  -  None
Chr_genome_final_gene.gff3.cds  -  Coding gene nucleotide sequences of Artocarpus nanchuanensis
Chr_genome_final_gene.gff3.pep  -  Coding gene translated sequences of Artocarpus nanchuanensis
Chr_genome_miRNA.gff3  -  miRNA annotations of Artocarpus nanchuanensis
Chr_genome_pseudogene.gff3  -  pseudogene annotations of Artocarpus nanchuanensis
Chr_genome_repeat.gff3  -  repeat annotations of Artocarpus nanchuanensis
Chr_genome_rRNA.gff3  -  rRNA annotations of Artocarpus nanchuanensis
Chr_genome_tRNA.gff3  -  tRNA annotations of Artocarpus nanchuanensis
full_table-2.tsv  -  BUSCO results of Artocarpus nanchuanensis - full table
phyml_tree.newick  -  Phylogenetic analysis of A. nanchuanensis and related species.
missing_busco_list.tsv  -  BUSCO results of Artocarpus nanchuanensis - missing BUSCO list
Chr_genome_snoRNA.gff3  -  snoRNA annotations of Artocarpus nanchuanensis
Chr_genome_snRNA.gff3  -  snRNA annotations of Artocarpus nanchuanensis
Lachesis_assembly_changed.fa  -  Artocarpus nanchuanensis genome assembly, scaffold level
Chr_genome_final.fa  -  Artocarpus nanchuanensis final chromosome level genome assembly
busco_short-summary.txt  -  BUSCO results of Artocarpus nanchuanensis - short summary
bioinformatics-methods.txt  -  Bioinformatics methods and analysis performed
Chrun.fa  -  unassigned scaffold fasta sequences
LG19.fa    -  Sequence assembly - chromosome 19
LG20.fa    -  Sequence assembly - chromosome 20
LG21.fa    -  Sequence assembly - chromosome 21
LG05.fa    -  Sequence assembly - chromosome 5
LG06.fa    -  Sequence assembly - chromosome 6
LG07.fa    -  Sequence assembly - chromosome 7
LG28.fa    -  Sequence assembly - chromosome 28
LG27.fa    -  Sequence assembly - chromosome 27
LG26.fa    -  Sequence assembly - chromosome 26
LG25.fa    -  Sequence assembly - chromosome 25
LG24.fa    -  Sequence assembly - chromosome 24
LG23.fa    -  Sequence assembly - chromosome 23
LG22.fa    -  Sequence assembly - chromosome 22
LG08.fa    -  Sequence assembly - chromosome 8
LG09.fa    -  Sequence assembly - chromosome 9
LG02.fa    -  Sequence assembly - chromosome 2
LG03.fa    -  Sequence assembly - chromosome 3
LG04.fa    -  Sequence assembly - chromosome 4
LG14.fa    -  Sequence assembly - chromosome 14
LG13.fa    -  Sequence assembly - chromosome 13
LG12.fa    -  Sequence assembly - chromosome 12
LG11.fa    -  Sequence assembly - chromosome 11
LG10.fa    -  Sequence assembly - chromosome 10
LG18.fa    -  Sequence assembly - chromosome 18
LG17.fa    -  Sequence assembly - chromosome 17
LG16.fa    -  Sequence assembly - chromosome 16
LG15.fa    -  Sequence assembly - chromosome 15
LG01.fa    -  Sequence assembly - chromosome 1
phyml_tree.fa  -  sequence alignment used to create the phylogenetic tree


[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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