scholarly journals The genome of the Balearic shearwater (Puffinus mauretanicus), a Critically Endangered seabird: a valuable resource for evolutionary and conservation genomics

2021 ◽  
Author(s):  
Cristian Cuevas Caballe ◽  
Joan Ferrer Obiol ◽  
Joel Vizueta ◽  
Meritxell Genovart ◽  
Jacob Gonzalez-Solis ◽  
...  
Keyword(s):  
Reference Genome ◽  
Conservation Status ◽  
Sharp Decrease ◽  
Night Vision ◽  
Critically Endangered ◽  
Conservation Genomics ◽  
Critically Endangered Species ◽  
A Genome ◽  
Long Read ◽  
Longline Fisheries

The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the population size. Currently, populations continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, and some studies predict their extinction by 2070. We present the first high-quality reference genome for the species which was obtained by a combination of short and long-read sequencing. Our hybrid assembly includes 4,169 scaffolds, with a scaffold N50 of 2.1 Mbp, a genome length of 1.2 Gbp, and BUSCO completeness of 96%, which is amongst the highest across sequenced avian species. This reference genome allowed us to study critical aspects relevant to the conservation status of the species, such as an evaluation of overall heterozygosity levels and the reconstruction of its historical demography. Our phylogenetic analysis using whole-genome information resolves current uncertainties in the order Procellariiformes systematics. Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision and the development of natriuresis. This reference genome will be the keystone for future developments of genetic tools in conservation efforts for this Critically Endangered species.

scholarly journals Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 270 ◽  
Author(s):  
Yun Gyeong Lee ◽  
Sang Chul Choi ◽  
Yuna Kang ◽  
Kyeong Min Kim ◽  
Chon-Sik Kang ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Genome Structure ◽  
Plant Genome ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

scholarly journals Conservation status and management insights from tracking a cryptic and Critically Endangered species of Orchidaceae

Oryx ◽  
2016 ◽  
Vol 51 (3) ◽  
pp. 441-450
Author(s):  
T. Kraaij ◽  
J. A. Baard ◽  
B. J. Crain
Keyword(s):  
Population Biology ◽  
Habitat Management ◽  
Conservation Status ◽  
Management Strategies ◽  
Growing Season ◽  
Iucn Red List ◽  
Critically Endangered ◽  
Physical Damage ◽  
Beneficial Effects ◽  
Critically Endangered Species

AbstractNinety-five percent of orchid species associated with fynbos shrublands of South Africa's Cape Floristic Kingdom have been assessed for the IUCN Red List, yet aspects of their demography and population biology remain poorly understood. We conducted a 6-year demographic study of the Critically Endangered Disa procera, a cryptic, terrestrial species from South Africa with a global population of c. 50 individuals known from a single location. We aimed to provide management recommendations that would facilitate its persistence. Our findings indicate that the population of D. procera is larger than previously thought, and the species occurs at two distinct locations. These orchids exhibit high interannual variation in population size and turnover of individuals, potentially indicative of a species with a short life span, and still meet the criteria for Critically Endangered status. The species benefits from disturbances, such as brush cutting along trails, or fire, which open up clearances in the vegetation. However, physical damage to plants during their aboveground growing season (September–January) is particularly detrimental and should be avoided in habitat management for the species. Fire had beneficial effects at the population and individual levels and is recommended at 10–25-year intervals, outside the orchid's growing season. The species exhibited comparatively high rates of fruit set (68%), suggesting that pollination limitation does not currently constrain its performance. Its patchy distribution may, however, indicate constraints on dispersal or recruitment. We recommend that management strategies should include continued protection and monitoring of both populations, studies on pollination, habitat requirements and mycorrhizal associates, and a prescribed disturbance regime.

A new critically endangered species of Angraecum (Orchidaceae) endemic to the island of Mauritius, Indian Ocean

Phytotaxa ◽  
2015 ◽  
Vol 222 (3) ◽  
pp. 211 ◽  
Author(s):  
Jacques Fournel ◽  
Claire Micheneau ◽  
Claudia Baider
Keyword(s):  
Conservation Status ◽  
Small Population ◽  
Red List ◽  
Alien Plants ◽  
Critically Endangered ◽  
Invasive Alien Plants ◽  
International Union ◽  
Closely Related Species ◽  
Critically Endangered Species ◽  
A New Species

Angraecum jeannineanum, a new species endemic to Mauritius, is described and its ecology and conservation status are discussed. Angraecum jeannineanum differs from A. cadetii, which is the morphologically most closely related species, as follows: (i) leaves are smaller, thicker and darker green, (ii) inflorescences and flowers are thinner and smaller, (iii) flowers are more greenish and non-fleshy. Angraecum jeannineanum belongs to Angraecum section Hadrangis, endemic to the Mascarenes, which also includes A. bracteosum, A. cadetii and A. striatum. An updated key for the section is provided. The species should be considered as Critically Endangered (CR) according to the Red List Criteria of the International Union for the Conservation of Nature (IUCN). This assessment is based on the highly restricted species distribution, small population size, and habitat sustaining degradation by invasive alien plants and animals.

scholarly journals Effects of human disturbance on the mongoose lemur Eulemur mongoz in Comoros: implications and potential for the conservation of a Critically Endangered species

Oryx ◽  
2015 ◽  
Vol 51 (1) ◽  
pp. 60-67 ◽  
Author(s):  
Bakri Nadhurou ◽  
Roberta Righini ◽  
Marco Gamba ◽  
Paola Laiolo ◽  
Ahmed Ouledi ◽  
...  
Keyword(s):  
Group Size ◽  
Negative Impact ◽  
Human Impacts ◽  
Conservation Status ◽  
Environmental Parameters ◽  
Critically Endangered ◽  
Anthropogenic Pressure ◽  
Critically Endangered Species ◽  
The Impact ◽  
Group Size And Composition

AbstractThe decline of the mongoose lemur Eulemur mongoz has resulted in a change of its conservation status from Vulnerable to Critically Endangered. Assessing the current threats to the species and the attitudes of the people coexisting with it is fundamental to understanding whether and how human impacts may affect populations. A questionnaire-based analysis was used to study the impact of agriculture and other subsistence activities, and local educational initiatives, on lemur abundance, group size and composition in the Comoros. On the islands of Mohéli and Anjouan we recorded 214 lemurs in 63 groups, the size and composition of which depended both on environmental parameters and the magnitude and type of anthropogenic pressure. There was no evidence of an impact of anthropogenic disturbance on abundance. In contrast, group size and composition were sensitive to human impacts. The most important threats were conflicts related to crop raiding, as well as illegal capture and hunting. The promotion of educational activities reduced the negative impact of hunting and illegal activities. These results highlight a need for urgent conservation measures to protect the species.

scholarly journals QAlign: Aligning nanopore reads accurately using current-level modeling

2019 ◽  
Author(s):  
Dhaivat Joshi ◽  
Shunfu Mao ◽  
Sreeram Kannan ◽  
Suhas Diggavi
Keyword(s):  
Reference Genome ◽  
Genomic Analysis ◽  
Vital Role ◽  
High Error Rate ◽  
Sequencing Technology ◽  
Long Reads ◽  
A Genome ◽  
Long Read ◽  
Nanopore Sequencer ◽  
Sequencing Process

AbstractMotivationEfficient and accurate alignment of DNA / RNA sequence reads to each other or to a reference genome / transcriptome is an important problem in genomic analysis. Nanopore sequencing has emerged as a major sequencing technology and many long-read aligners have been designed for aligning nanopore reads. However, the high error rate makes accurate and efficient alignment difficult. Utilizing the noise and error characteristics inherent in the sequencing process properly can play a vital role in constructing a robust aligner. In this paper, we design QAlign, a pre-processor that can be used with any long-read aligner for aligning long reads to a genome / transcriptome or to other long reads. The key idea in QAlign is to convert the nucleotide reads into discretized current levels that capture the error modes of the nanopore sequencer before running it through a sequence aligner.ResultsWe show that QAlign is able to improve alignment rates from around 80% up to 90% with nanopore reads when aligning to the genome. We also show that QAlign improves the average overlap quality by 9.2%, 2.5% and 10.8% in three real datasets for read-to-read alignment. Read-to-transcriptome alignment rates are improved from 51.6% to 75.4% and 82.6% to 90% in two real datasets.Availabilityhttps://github.com/joshidhaivat/QAlign.git

scholarly journals A new record of critically endangered Saussurea bogedaensis (Asteraceae) from Dzungarian Gobi, Mongolia

PhytoKeys ◽  
2020 ◽  
Vol 160 ◽  
pp. 109-121
Author(s):  
Shukherdorj Baasanmunkh ◽  
Nudkhuu Nyamgerel ◽  
Gun-Aajav Bayarmaa ◽  
Batlai Oyuntsetseg ◽  
Khurelpurev Oyundelger ◽  
...  
Keyword(s):  
Endangered Species ◽  
New Record ◽  
Conservation Status ◽  
Critically Endangered ◽  
Genetic Characteristics ◽  
Critically Endangered Species ◽  
The Family

A species in the family Asteraceae, Saussurea bogedaensis, was newly described from Bogeda Mountain in Xinjiang, China and is a critically endangered species in China. Morphological and genetic characteristics confirm the presence of this species in Mongolia, as it was found in Baitag Bogd Mountain (in the Dzungarian Gobi). In addition, the distribution and conservation status of S. bogedaensis are provided.

A new species of Rudgea (Palicoureeae, Rubiaceae) from Espírito Santo state, Brazil

Phytotaxa ◽  
2018 ◽  
Vol 379 (2) ◽  
pp. 180
Author(s):  
FILIPE TORRES-LEITE ◽  
CARLA P. BRUNIERA ◽  
DANIELA C. ZAPPI ◽  
TATIANA T. CARRIJO
Keyword(s):  
New Species ◽  
Endangered Species ◽  
Conservation Status ◽  
Critically Endangered ◽  
Southeastern Brazil ◽  
Espírito Santo ◽  
Critically Endangered Species ◽  
Forest Remnant ◽  
Espirito Santo ◽  
A New Species

A new endemic and critically endangered species of Rudgea (Rubiaceae) from Southeastern Brazil is described and illustrated. Rudgea minutifolia Bruniera & Torres-Leite is distinguished by its small leaves, a character found in only a handful of species in this genus. The indumentum of the branches, leaves and stipules, low number of secondary veins, corniculate corolla lobes, and vinaceous to almost black mature fruits are also characteristic of this species. Discovered in a forest remnant within the Atlantic Rainforest domain in the south of Espírito Santo state, this species is found only in the municipality of Castelo, an area that has been recognized as prioritary for conservation. Besides the description, taxonomic comments, conservation status, images and illustrations are provided.

scholarly journals Distribution, status and conservation of a Critically Endangered, extremely narrow endemic: Lamyropsis microcephala (Asteraceae) in Sardinia

Oryx ◽  
2011 ◽  
Vol 45 (2) ◽  
pp. 180-186 ◽  
Author(s):  
Giuseppe Fenu ◽  
Efisio Mattana ◽  
Gianluigi Bacchetta
Keyword(s):  
Population Size ◽  
Conservation Status ◽  
Integrated Approach ◽  
Critically Endangered ◽  
Ex Situ ◽  
Endemic Plant ◽  
Critically Endangered Species ◽  
Narrow Endemic ◽  
Conservation Measures ◽  
Endangered Status

AbstractThe aims of this work were to verify the distribution and population size of Lamyropsis microcephala (Asteraceae), characterize its habitat, assess its conservation status and initiate conservation measures for this Critically Endangered species. Distribution was determined by field surveys and mapping. To estimate population size and density 81 permanent monitoring plots were randomly established. Ex situ conservation measures were activated by harvesting and appropriate storage of seed. We confirmed the presence of L. microcephala at two previously known sites and found it in two previously unknown localities. The areas in which the species occur vary from 200 to 240,000 m2, at altitudes of 1,450–1,820 m, on slopes of 15–45° with aspects from north to west. The estimated number of ramets per population varied from c. 2,000 to c. 2,000,000, with a mean density of 8.29 ± SD 14.3 to 10.33 ± SD 10.05 ramets m-2. Our findings confirmed the Critically Endangered status of this species, although with different criteria. This study is an example of an integrated approach for the conservation of an extremely narrow endemic plant species and may be useful for other little-known threatened species for which urgent conservation measures are needed.

scholarly journals State of Shark and Ray Genomics in an Era of Extinction

2021 ◽  
Vol 8 ◽  
Author(s):  
Jessica Pearce ◽  
Matthew W. Fraser ◽  
Ana M. M. Sequeira ◽  
Parwinder Kaur
Keyword(s):  
Conservation Status ◽  
Marine Species ◽  
Chromosome Length ◽  
Cultural Significance ◽  
Conservation Genomics ◽  
Genomic Resources ◽  
A Genome ◽  
Sampling Protocols ◽  
Threatened Taxa ◽  
Data Deficient

Chondrichthyan species (sharks, rays, skates, and chimeras) are a class of high ecological, economic, and cultural significance, and yet they are the most threatened taxa in the marine environment. The creation of reference chromosome-length genome assemblies allows for conservation genomics methods, such as population and ecological genomics, to be utilized. Despite being greatly threatened and of great importance in maintaining ecosystem function, chondrichthyan species have been repeatedly absent from conservation-based genome sequencing projects. Less than 1% of these species have a genome sequence, despite their almost 50% either threatened or Data Deficient conservation status. Most notably, there are seven orders within this class without any genome representation. In this review, we identify gaps in chondrichthyan genomic resources and demonstrate how the lack of genomic resources for this major taxonomic class is limiting the conservation of these already difficult to conserve species. We highlight other applications for chondrichthyans genomics, such as evolutionary and developmental biology. Likely, the mismatching sampling protocols and limited computational skills and communication between fields have been preventing the integration of marine and molecular sciences. Here, we propose that this field is in dire need to move forward quickly to increase protection for marine species and ecosystems through improved collaboration between marine, molecular, and computer sciences.

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