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 ◽  
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 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 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 First draft genome of loach (Orenectus shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish

2021 ◽  
Author(s):  
Zhijin Liu ◽  
Xuekun Qian ◽  
Ziming Wang ◽  
Huamei Wen ◽  
Ling Han ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Eye Development ◽  
Draft Genome ◽  
Evolutionary Process ◽  
Integrated Approach ◽  
Sequencing Data ◽  
Retina Development ◽  
Draft Genome Assembly ◽  
Surface Dwelling

Abstract BcakgroundLoaches of the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth. The genus Oreonectes with 18 currently recognized species contains representatives for all three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwelling-related traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable resource for research into the evolution of cavefishes.ResultsHere we assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. Based on in total 50.9 Gb of sequencing data, our genome assembly from Canu and Pilon spans approximately 515.64 Mb (estimated coverage of 100 ×), containing 803 contigs with N50 values of 5.58 Mb. 25,247 protein-coding genes were predicted, of which 95.65% have been functionally annotated. We also performed genome re-sequencing of three additional cave-dwelling Oreonectes fishes. Twenty-nine pseudogenes annotated using DAVID showed significant enrichment for the GO terms of “eye development” and “retina development in camera-type eye”. It is presumed that these pseudogenes might lead to eye degeneration of semi/complete cave-dwelling Oreonectes species. Furthermore, Mc1r (melanocortin-1 receptor) is a pseudogenization by a deletion in O. daqikongensis, likely blocking biosynthesis of melanin and leading to the albino phenotype.ConclusionsWe here report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. Pseudogenization of genes related to body color and eye development may be responsible for loss of pigmentation and vision deterioration in cave-dwelling species. This genome assembly will contribute to the study of the evolution and adaptation of fishes within Oreonectes and beyond (Cobitidea).

scholarly journals Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

2020 ◽  
Vol 12 (2) ◽  
pp. 3917-3925
Author(s):  
Greer A Dolby ◽  
Matheo Morales ◽  
Timothy H Webster ◽  
Dale F DeNardo ◽  
Melissa A Wilson ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Mojave Desert ◽  
De Novo ◽  
Stop Codon ◽  
Draft Genome ◽  
Gene Families ◽  
Sea Turtle ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Gene Expansion

Abstract Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.

scholarly journals Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

2018 ◽  
Vol 6 (16) ◽  
pp. e00265-18 ◽  
Author(s):  
Stewart T. G. Burgess ◽  
Kathryn Bartley ◽  
Edward J. Marr ◽  
Harry W. Wright ◽  
Robert J. Weaver ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Psoroptes Ovis ◽  
Protein Coding ◽  
Content Type ◽  
Sheep Scab ◽  
Draft Genome Assembly ◽  
Intense Pruritus

ABSTRACT Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious, results in intense pruritus, and represents a major welfare and economic concern. Here, we report the first draft genome assembly and gene prediction of P. ovis based on PacBio de novo sequencing. The ∼63.2-Mb genome encodes 12,041 protein-coding genes.

scholarly journals First draft genome assembly of the Argane tree (Argania spinosa)

F1000Research ◽  
2020 ◽  
Vol 7 ◽  
pp. 1310
Author(s):  
Slimane Khayi ◽  
Nour Elhouda Azza ◽  
Fatima Gaboun ◽  
Stacy Pirro ◽  
Oussama Badad ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Environmental Changes ◽  
De Novo ◽  
Arid Zone ◽  
Draft Genome ◽  
Illumina Hiseq ◽  
Argania Spinosa ◽  
Draft Genome Assembly ◽  
Food And Feed ◽  
Tree Genetics

Background: The Argane tree ( Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of  A. spinosa was created using a hybrid  de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.6 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological.

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