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 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 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 distribution and population of Seychelles Black Paradise-flycatcher Terpsiphone corvina on La Digue: implications for conservation and translocation

2003 ◽  
Vol 13 (4) ◽  
pp. 307-318 ◽  
Author(s):  
Dave Currie ◽  
Rachel Bristol ◽  
James Millett ◽  
Nirmal Jivan Shah
Keyword(s):  
Indian Ocean ◽  
Tree Species ◽  
Western Indian Ocean ◽  
Critically Endangered ◽  
Native Forest ◽  
World Population ◽  
Small Populations ◽  
Freshwater Bodies ◽  
Viable Population ◽  
Equivalent Reduction

The 10 km2 island of La Digue, Republic of Seychelles, western Indian Ocean supports the last viable population of the Critically Endangered Seychelles Black Paradise-flycatcher Terpsiphone corvina. Small populations recorded on adjacent islands since the 1980s appear to be ephemeral and not self-sustaining. We document the results of the first island-wide survey of the flycatcher on La Digue using the playback of conspecific calls at random points. Previous surveys were based largely on counting the number of singing males. The survey was conducted between April and August 2001 and confirmed (i) the current world population is at least 200 individuals (109-145 territories, 218-290 individuals) in a c. 4.4 km2 range, thus accurately quantifying the documented increase in flycatcher numbers since the late 1970s; (ii) territories were more widely distributed than previously recorded and not exclusively associated with coastal plateaux or freshwater bodies, contrary to previous descriptions; and (iii) distribution was determined largely by the presence of high canopy (native) broad-leaved tree species. The importance of canopy height to flycatchers was highlighted by the fact that localized loss of high canopy (native) forest (4%), in a 161 ha study area on the large western plateau, resulted in an equivalent reduction (4%) in the number of territories. In light of our findings we discuss the implications for conservation of the flycatcher on La Digue and its possible translocation.

scholarly journals Diet of the critically endangered brown-headed spider monkey (Ateles fusciceps fusciceps) in the Ecuadorian Chocó: Conflict between primates and loggers over fruiting tree species

2015 ◽  
Author(s):  
Citlalli Morelos-Juárez ◽  
Andrea Tapia ◽  
Galo Conde ◽  
Mika Peck
Keyword(s):  
Tree Species ◽  
Spider Monkey ◽  
Critically Endangered ◽  
Conservation Strategies ◽  
Primary Forest ◽  
Healthy Population ◽  
Term Survival ◽  
Forest Remnant ◽  
The Impact ◽  
Effective Conservation

Identifying key food resources for critically endangered species is vital in the design of effective conservation strategies, particularly if these resources are also targeted by anthropogenic activities such as logging. The province of Esmeraldas in NW Ecuador is heavily dependent on commercial logging. It also maintains the only healthy population of the critically endangered brown-headed spider monkey (Ateles fusciceps fusciceps). The unprotected forest remnant of Tesoro Escondido, in the buffer zone of the Cotacachi Cayapas Ecological Reserve, is home to an estimated 130 individuals of a global population of approximately 250. There is an urgent need for information to develop effective conservation action plans for the species, in particular the impact of logging activity on key feeding resources. We characterised the floristic composition of the habitat of A. f. fusciceps and estimated the availability of fruit resources for the annual cycle of 2012-2013 in sixteen 0.1 hectare vegetation plots. We determined feeding preferences for A. f. fusciceps using behavioural observations applying the Chesson ε index to identify key feeding tree species. We reviewed regional logging permits to identify species targeted for extraction by the timber industry and calculated extraction volumes in primary forest for key feeding tree species to identify potential conflict between logging and primate diet. We identified 65 fruiting tree species from 34 families that formed the diet of A. f. fusciceps. The Chesson ε index identified twelve species as preferred species with further phenological observations identifying seven species as staple foods and two palms as potential fall back fruits. Additionally, high densities of the lipid rich fruits of Brosimum utile make this an important resource for this primate throughout the year. Of 65 feeding tree species identified for A. f. fusciceps, 35 species are also targeted as sources of timber. Five key feeding species would be depleted under current sustainable management extraction protocols while two other species would be significantly impacted in terms of local abundance.Given the critically endangered status of A. f. fusciceps, remaining primary forest in NW Ecuador requires urgent protection, including thorough revision of current logging protocols to ensure long term survival of the species.

scholarly journals Diet of the critically endangered brown-headed spider monkey (Ateles fusciceps fusciceps) in the Ecuadorian Chocó: Conflict between primates and loggers over fruiting tree species

2015 ◽  
Author(s):  
Citlalli Morelos-Juárez ◽  
Andrea Tapia ◽  
Galo Conde ◽  
Mika Peck
Keyword(s):  
Tree Species ◽  
Spider Monkey ◽  
Critically Endangered ◽  
Conservation Strategies ◽  
Primary Forest ◽  
Healthy Population ◽  
Term Survival ◽  
Forest Remnant ◽  
The Impact ◽  
Effective Conservation

Identifying key food resources for critically endangered species is vital in the design of effective conservation strategies, particularly if these resources are also targeted by anthropogenic activities such as logging. The province of Esmeraldas in NW Ecuador is heavily dependent on commercial logging. It also maintains the only healthy population of the critically endangered brown-headed spider monkey (Ateles fusciceps fusciceps). The unprotected forest remnant of Tesoro Escondido, in the buffer zone of the Cotacachi Cayapas Ecological Reserve, is home to an estimated 130 individuals of a global population of approximately 250. There is an urgent need for information to develop effective conservation action plans for the species, in particular the impact of logging activity on key feeding resources. We characterised the floristic composition of the habitat of A. f. fusciceps and estimated the availability of fruit resources for the annual cycle of 2012-2013 in sixteen 0.1 hectare vegetation plots. We determined feeding preferences for A. f. fusciceps using behavioural observations applying the Chesson ε index to identify key feeding tree species. We reviewed regional logging permits to identify species targeted for extraction by the timber industry and calculated extraction volumes in primary forest for key feeding tree species to identify potential conflict between logging and primate diet. We identified 65 fruiting tree species from 34 families that formed the diet of A. f. fusciceps. The Chesson ε index identified twelve species as preferred species with further phenological observations identifying seven species as staple foods and two palms as potential fall back fruits. Additionally, high densities of the lipid rich fruits of Brosimum utile make this an important resource for this primate throughout the year. Of 65 feeding tree species identified for A. f. fusciceps, 35 species are also targeted as sources of timber. Five key feeding species would be depleted under current sustainable management extraction protocols while two other species would be significantly impacted in terms of local abundance.Given the critically endangered status of A. f. fusciceps, remaining primary forest in NW Ecuador requires urgent protection, including thorough revision of current logging protocols to ensure long term survival of the species.

scholarly journals Genome Report: A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

2021 ◽  
Author(s):  
Nikolay Alabi ◽  
Yihan Wu ◽  
Oliver Bossdorf ◽  
Loren H Rieseberg ◽  
Robert I Colautti
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Genome Mapping ◽  
Draft Genome ◽  
Alliaria Petiolata ◽  
Conservation Strategies ◽  
Ecological Knowledge ◽  
Garlic Mustard ◽  
A Genome ◽  
Invasion Genetics

Abstract The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC3-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ∼70 × coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7% of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99% of plant BUSCO genes and 98% of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite < 2% genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.

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