[DOI] 10.5524/100752

[Title] Genome data for the draft assembly of the Chinese tertiary relict tree, <i>Nyssa yunnanensis</i>.

[Release Date] 2020-07-31

[Citation] Mu, W; Wei, J; Yang, T; Fan, Y; Cheng, L; Yang, J; Mu, R; Liu, J; Zhao, J; Sun, W; Xu, X; Liu, X; Drmanac, R; Liu, H (2020): Genome data for the draft assembly of the Chinese tertiary relict tree, <i>Nyssa yunnanensis</i>. GigaScience Database. http://dx.doi.org/10.5524/100752

[Data Type] Genomic,Transcriptomic

[Dataset Summary]  <i>Nyssa yunnanensis</i> is a deciduous tree species in the family <i>Nayssaceae</i> within the order <i>Cornales</i>. With only eight individuals across two geographic sites recorded in the Yunnan province of China, this species was listed as a national grade-I protected species in China in 1999. It is also one of the 120 species in the <i>Implementation Plan of Rescuing and Conserving China&rsquo;s Plant Species with Extremely Small Populations (PSESP)</i> (2011-2-15). <i>N. yunnanensis</i> has also been evaluated as Critically Endangered in the IUCN red list and Threatened Species List of China's Higher Plants. Hence understanding the genomic characteristics of this highly endangered Tertiary relict tree species is essential, especially for developing conservation strategies.<br />Here we present the draft genome assembly of <i>N. yunnanensis</i>. Using 10X genomics linked-reads sequencing data. We carried out the <i>de novo</i> assembly and annotation analysis. The <i>N. yunnanensis</i> genome assembly is 1475 Mb in length containing 288,519 scaffolds with an scaffold N50 length of 985.59 kb. 799.51 Mb of the assembled genome was identified as repetitive elements, accounting for 54.24% of the sequenced genome and a total of 39,803 protein-coding genes were predicted. <br />The genomic data of <i>N. yunnanensis</i> provided in this study will provide basic information for future genomic and evolutionary studies. With the genomic characteristics of <i>N. yunnanensis</i> available, our study might also facilitate future conservation biology studies to help protect this extremely threatened tree species.

[File Location] ftp://parrot.genomics.cn/gigadb/pub/10.5524/100001_101000/100752/

[File name] - [File Description]
RNA_mapping.bam.stat  -  the stat file of the RNA mapping bam file
Nyssa_yunnanensis.gff  -  Coding gene annotations
Nyssa_yunnanensis.repeat.gff  -  Repeats annotations
BUSCO.tar.gz  -  BUSCO full output file
readme_100752.txt  -  None
Nyssa_yunnanensis.fa  -  the assembly fasta file
Nyssa_yunnanensis.cds.fa  -  the coding sequences fasta file
Nyssa_yunnanensis.pep.fa  -  the protein translation of the coding sequences fasta file
RNA_mapping.bam  -  the RNA mapping bam file (BWA)


[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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