Genome data for the draft assembly of the Chinese tertiary relict tree, Nyssa yunnanensis.

Dataset type: Genomic, Transcriptomic
Data released on July 31, 2020

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, Nyssa yunnanensis. GigaScience Database. http://dx.doi.org/10.5524/100752

DOI10.5524/100752

Nyssa yunnanensis is a deciduous tree species in the family Nayssaceae within the order Cornales. 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 Implementation Plan of Rescuing and Conserving China’s Plant Species with Extremely Small Populations (PSESP) (2011-2-15). N. yunnanensis 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.
Here we present the draft genome assembly of N. yunnanensis. Using 10X genomics linked-reads sequencing data. We carried out the de novo assembly and annotation analysis. The N. yunnanensis 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.
The genomic data of N. yunnanensis provided in this study will provide basic information for future genomic and evolutionary studies. With the genomic characteristics of N. yunnanensis available, our study might also facilitate future conservation biology studies to help protect this extremely threatened tree species.

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Related datasets:

doi:10.5524/100752 IsNewVersionOf doi:10.5524/101352

Accessions (data generated as part of this study):

BioSample: SAMN14929538
BioSample: SAMN08770557





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
RL0289161873  Nyssa yunnanensis Description:DNA extracted from leaves of Nyssaceae...
Geographic location (country and/or sea,region):Ru...
Geographic location (latitude and longitude):24.05...
...
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RL0289_RNA161873  Nyssa yunnanensis Description:RNA extracted from leaves of Nyssaceae...
Geographic location (country and/or sea,region):Ru...
Geographic location (latitude and longitude):24.05...
...
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Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
OtherTAR36.7 MB2020-05-17
Coding SequenceFASTA39.99 MB2020-05-17
Genome sequenceFASTA1.41 GB2020-05-17
annotationGFF15.95 MB2020-05-17
protein sequenceFASTA16.29 MB2020-05-17
annotationGFF454.24 MB2020-05-17
readmeTEXT2.87 KB2020-05-17
AlignmentsBAM7.62 GB2020-05-17
AlignmentsUNKNOWN0.44 KB2020-05-17
Displaying 1-9 of 9 File(s).
Funding body Awardee Award ID Comments
Yunnan Innovation Team Program Weibang Sun 2019HC015 for conservation and utilization of PSESP
National Key R&D Program of China H Liu 2019YFC1711000
Shenzhen Municipal Government of China H Liu JCYJ20170817145512476
Shenzhen Municipal Government of China R Drmanac KQTD2015033017150531
Guangdong Provincial Key Laboratory of Genome Read and Write X Xu 2017B030301011
Date Action
August 4, 2020 Dataset publish
October 26, 2020 Manuscript Link added : 10.46471/gigabyte.4