scholarly journals Correction to: De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Jing Yang ◽  
Hafiz Muhammad Wariss ◽  
Lidan Tao ◽  
Rengang Zhang ◽  
Quanzheng Yun ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Assembly ◽  
Yunnan Province ◽  
De Novo ◽  
Small Populations ◽  
De Novo Genome Assembly

scholarly journals De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China

GigaScience ◽  
2019 ◽  
Vol 8 (7) ◽  
Author(s):  
Jing Yang ◽  
Hafiz Muhammad Wariss ◽  
Lidan Tao ◽  
Rengang Zhang ◽  
Quanzheng Yun ◽  
...  
Keyword(s):  
Plant Species ◽  
Single Molecule ◽  
Dna Sequences ◽  
Genome Assembly ◽  
Yunnan Province ◽  
De Novo ◽  
Small Populations ◽  
High Quality ◽  
Illumina Hiseq ◽  
De Novo Genome Assembly

Abstract Background Acer yangbiense is a newly described critically endangered endemic maple tree confined to Yangbi County in Yunnan Province in Southwest China. It was included in a programme for rescuing the most threatened species in China, focusing on “plant species with extremely small populations (PSESP)”. Findings We generated 64, 94, and 110 Gb of raw DNA sequences and obtained a chromosome-level genome assembly of A. yangbiense through a combination of Pacific Biosciences Single-molecule Real-time, Illumina HiSeq X, and Hi-C mapping, respectively. The final genome assembly is ∼666 Mb, with 13 chromosomes covering ∼97% of the genome and scaffold N50 sizes of 45 Mb. Further, BUSCO analysis recovered 95.5% complete BUSCO genes. The total number of repetitive elements account for 68.0% of the A. yangbiense genome. Genome annotation generated 28,320 protein-coding genes, assisted by a combination of prediction and transcriptome sequencing. In addition, a nearly 1:1 orthology ratio of dot plots of longer syntenic blocks revealed a similar evolutionary history between A. yangbiense and grape, indicating that the genome has not undergone a whole-genome duplication event after the core eudicot common hexaploidization. Conclusion Here, we report a high-quality de novo genome assembly of A. yangbiense, the first genome for the genus Acer and the family Aceraceae. This will provide fundamental conservation genomics resources, as well as representing a new high-quality reference genome for the economically important Acer lineage and the wider order of Sapindales.

scholarly journals The draft genome assembly of the critically endangered Nyssa yunnanensis, a plant species with extremely small populations endemic to Yunnan Province, China

Gigabyte ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Weixue Mu ◽  
Jinpu Wei ◽  
Ting Yang ◽  
Yannan Fan ◽  
Le Cheng ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Assembly ◽  
Tree Species ◽  
Yunnan Province ◽  
De Novo ◽  
Draft Genome ◽  
Deciduous Tree ◽  
Small Populations ◽  
Sequencing Data ◽  
Draft Genome Assembly

Nyssa yunnanensis is a deciduous tree species in the family Nyssaceae within the order Cornales. As only eight individual trees and two populations have been recorded in China’s Yunnan province, this species has been listed among China’s national Class I protection species since 1999 and also among 120 PSESP (Plant Species with Extremely Small Populations) in the Implementation Plan of Rescuing and Conserving China’s Plant Species with Extremely Small Populations (PSESP) (2011-2-15). 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 a scaffold N50 length of 985.59 kb. Within the assembled genome, 799.51 Mb was identified as repetitive elements, accounting for 54.24% of the sequenced genome, and a total of 39,803 protein-coding genes were predicted. With the genomic characteristics of N. yunnanensis available, our study might facilitate future conservation biology studies to help protect this extremely threatened tree species.

scholarly journals The Draft Genome Assembly of the Critically Endangered Nyssa yunnanensis, a Plant Species with Extremely Small Populations Endemic to Yunnan Province, China

2020 ◽  
Author(s):  
Weixue Mu ◽  
Jinpu Wei ◽  
Ting Yang ◽  
Yannan Fan ◽  
Le Cheng ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Assembly ◽  
Tree Species ◽  
Yunnan Province ◽  
De Novo ◽  
Draft Genome ◽  
Deciduous Tree ◽  
Small Populations ◽  
Sequencing Data ◽  
Draft Genome Assembly

Nyssa yunnanensis is a deciduous tree species in the family Nyssaceae within the order Cornales. As only eight individual trees and two populations have been recorded in China’s Yunnan province, this species has been listed among China’s national Class I protection species since 1999 and also among 120 PSESP (Plant Species with Extremely Small Populations) in the Implementation Plan of Rescuing and Conserving China’s Plant Species with Extremely Small Populations(PSESP) (2011-2-15). 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 a scaffold N50 length of 985.59 kb. Within the assembled genome, 799.51 Mb was identified as repetitive elements, accounting for 54.24% of the sequenced genome, and a total of 39,803 protein-coding genes were predicted. With the genomic characteristics of N. yunnanensis available, our study might facilitate future conservation biology studies to help protect this extremely threatened tree species.

scholarly journals The Draft Genome Assembly of the Critically Endangered Nyssa yunnanensis, a Plant Species with Extremely Small Populations Endemic to Yunnan Province, China

2020 ◽  
Author(s):  
Weixue Mu ◽  
Jinpu Wei ◽  
Ting Yang ◽  
Yannan Fan ◽  
Le Cheng ◽  
...  
Keyword(s):  
Plant Species ◽  
Tree Species ◽  
Yunnan Province ◽  
De Novo ◽  
Higher Plants ◽  
Draft Genome ◽  
Critically Endangered ◽  
Deciduous Tree ◽  
Conservation Strategies ◽  
Small Populations

Nyssa yunnanensis is a deciduous tree in family Nayssaceae within the order Cornales. As only 8 individuals in 2 sites recorded in Yunnan province of China, the species was listed as the China’s national grade-I protection species in 1999, and also as one of 120 PSESP(Plant Species with Extremely Small Populations) in Implementation Plan of Rescuing and Conserving China’s Plant Species with extremely Small Populations(PSESP) (2011-2-15). N. yunnanensis was also been evaluated as Critically Endangered in 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 sequenced and annotated the genome of N. yunnanensis using 10X genomics linked-reads sequencing data. The de novo assembled genome is 1474Mb in length with a scaffold N50 length of 985.59kb. We identified 823.51Mb of non-redundant sequence as repetitive elements and annotated 39,803 protein-coding genes in the assembly. Our result provided the genomic characteristics of N. yunnanensis, which will provide valuable resources for future genomic and evolutionary studies, especially for conservation biology studies of this extremely threatened tree species.

scholarly journals The Draft Genome Assembly of the Critically Endangered Nyssa yunnanensis, a Plant Species with Extremely Small Populations Endemic to Yunnan Province, China

2020 ◽  
Author(s):  
Weixue Mu ◽  
Jinpu Wei ◽  
Ting Yang ◽  
Yannan Fan ◽  
Le Cheng ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Assembly ◽  
Tree Species ◽  
Yunnan Province ◽  
Draft Genome ◽  
Critically Endangered ◽  
Deciduous Tree ◽  
Conservation Strategies ◽  
Small Populations ◽  
Draft Genome Assembly

Nyssa yunnanensis is a deciduous tree species in family Nyssaceae within the order Cornales. As owning only eight individuals in two sites recorded in Yunnan province of China, this species was listed as the China’s national grade-I protection species in 1999, and also as one of 120 PSESP (Plant Species with Extremely Small Populations) in Implementation Plan of Rescuing and Conserving China’s Plant Species with extremely Small Populations(PSESP) (2011-2-15). N. yunnanensis was also been evaluated as Critically Endangered in 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 a 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 annotated. 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 in future conservation biology studies to help protecting this extremely threatened tree species.

scholarly journals Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)

GigaScience ◽  
2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Xuewei Li ◽  
Ling Kui ◽  
Jing Zhang ◽  
Yinpeng Xie ◽  
Liping Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Malus X Domestica ◽  
De Novo Genome Assembly

scholarly journals Meraculous: De Novo Genome Assembly with Short Paired-End Reads

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e23501 ◽  
Author(s):  
Jarrod A. Chapman ◽  
Isaac Ho ◽  
Sirisha Sunkara ◽  
Shujun Luo ◽  
Gary P. Schroth ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly

Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing

2021 ◽  
Author(s):  
Minxuan Zhou ◽  
Lingxi Wu ◽  
Muzhou Li ◽  
Niema Moshiri ◽  
Kevin Skadron ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
De Novo Genome Assembly
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