scholarly journals Draft Genome of the Sea Cucumber Holothuria glaberrima, a Model for the Study of Regeneration

2021 ◽  
Vol 8 ◽  
Author(s):  
Joshua G. Medina-Feliciano ◽  
Stacy Pirro ◽  
Jose E. García-Arrarás ◽  
Vladimir Mashanov ◽  
Joseph F. Ryan
Keyword(s):  
Sea Cucumber ◽  
Draft Genome ◽  
Body Parts ◽  
Sea Cucumbers ◽  
Draft Genome Assembly ◽  
Life History Stages ◽  
Final Assembly ◽  
Molecular Events ◽  
High Conservation ◽  
Holothuria Glaberrima

Regeneration is one of the most fascinating and yet least understood biological processes. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Among echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The cellular and molecular events underlying these abilities in sea cucumbers have been most extensively studied in the species Holothuria glaberrima. However, research into the regenerative abilities of this species has been impeded due to the lack of adequate genomic resources. Here, we report the first draft genome assembly of H. glaberrima and demonstrate its value for future genetic studies. Using only short sequencing reads, we assembled the genome into 89,105 scaffolds totaling 1.1 gigabases with an N50 of 25 kilobases. Our BUSCO assessment of the genome resulted in 894 (91.4%) complete and partial genes from 978 genes queried. We incorporated transcriptomic data from several different life history stages to annotate 51,415 genes in our final assembly. To demonstrate the usefulness of the genome, we fully annotated the melanotransferrin (Mtf) gene family, which have a potential role in the regeneration of the sea cucumber intestine. Using these same data, we extracted the mitochondrial genome, which showed high conservation to that of other holothuroids. Thus, these data will be a critical resource for ongoing studies of regeneration and other studies in sea cucumbers.

scholarly journals Draft Genome of the Sea Cucumber Holothuria glaberrima, a model for the study of regeneration

2020 ◽  
Author(s):  
Joshua G. Medina-Feliciano ◽  
Stacy Pirro ◽  
Jose E. García-Arrarás ◽  
Vladimir Mashanov ◽  
Joseph F. Ryan
Keyword(s):  
Sea Cucumber ◽  
Draft Genome ◽  
Body Parts ◽  
Sea Cucumbers ◽  
Draft Genome Assembly ◽  
Life History Stages ◽  
Final Assembly ◽  
Molecular Events ◽  
High Conservation ◽  
Holothuria Glaberrima

AbstractRegeneration is one of the most fascinating and yet least understood processes of animals. Echinoderms, one of the closest related invertebrate groups to humans, can contribute to our understanding of the genetic basis of regenerative processes. Amongst echinoderms, sea cucumbers have the ability to grow back most of their body parts following injury, including the intestine and nervous tissue. The cellular and molecular events underlying these abilities in sea cucumbers have been most extensively studied in the species Holothuria glaberrima. However, research into the regenerative abilities of this species have been impeded due to the lack of adequate genomic resources. Here, we report the first draft genome assembly of H. glaberrima and demonstrate its value for future genetic studies. Using only short sequencing reads, we assembled the genome into 2,960,762 scaffolds totaling 1.5 gigabases with an N50 of 15 kilobases. Our BUSCO assessment of the genome resulted in 882 (90.2%) complete and partial genes from 978 genes queried. We incorporated transcriptomic data from several different life history stages to annotate 41,076 genes in our final assembly. To demonstrate the usefulness of the genome, we fully annotated the melanotransferrin (Mtf) gene family, which have a potential role in regeneration of the sea cucumber intestine. Using these same data, we extracted the mitochondrial genome, which showed high conservation to that of other holothuroids. Thus, these data will be a critical resource for ongoing studies of regeneration and other studies in sea cucumbers.

scholarly journals Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10260
Author(s):  
Yohei Yamazaki ◽  
Yuichi Sakai ◽  
Juanwen Yu ◽  
Sayaka Mino ◽  
Tomoo Sawabe
Keyword(s):  
Environmental Conditions ◽  
Gut Microbiome ◽  
Sea Cucumber ◽  
Apostichopus Japonicus ◽  
Fecal Microbiota ◽  
Experimental Models ◽  
Regeneration Process ◽  
Body Parts ◽  
Sea Cucumbers

Sea cucumbers possess the remarkable capacity to regenerate their body parts or organs. Regeneration of host organs and/or body parts involves reconstruction of the host associated microbiota, however, the dynamics and contribution of microbiota to the regeneration process are largely unknown due to a lack of experimental models. To track the dynamics of individual gut microbiomes during gut regeneration, both caged mariculture and laboratory isolator systems of sea cucumbers (Apostichopus japonicus) were developed and longitudinal meta16S analyses were performed. Under natural environmental conditions in the caged mariculture system, both bacterial and eukaryotic communities in sea cucumbers’ guts appeared to be reconstructed within 4 months after evisceration. Using the laboratory isolator, which can trace daily dynamics, we found that fecal microbiota collected before evisceration were clearly different from those collected after evisceration. We also identified eight key bacteria, belonging to Alteromonadaceae, Rhodobacteraceae, Oceanospirillaceae and family-unassigned Gammaproteobacteria, suggesting that these bacteria might interact with the host during the gut regeneration process. Six of the eight key bacteria were isolated for further bioassay using the isolator developed in this study to test whether these isolates affect gut regeneration.

scholarly journals Antibiotics Modulate Intestinal Regeneration

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 236
Author(s):  
Lymarie M. Díaz-Díaz ◽  
Natalia Rosario-Meléndez ◽  
Andrea Rodríguez-Villafañe ◽  
Yariel Y. Figueroa-Vega ◽  
Omar A. Pérez-Villafañe ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Sea Cucumber ◽  
Regenerative Processes ◽  
Ecm Remodeling ◽  
Bacterial Cultures ◽  
Intestinal Regeneration ◽  
Negative Effect ◽  
Altered Cell ◽  
Holothuria Glaberrima ◽  
Mtt Assays

The increased antibiotics usage in biomedical and agricultural settings has been well documented. Antibiotics have now been shown to exert effects outside their purposive use, including effects on physiological and developmental processes. We explored the effect of various antibiotics on intestinal regeneration in the sea cucumber Holothuria glaberrima. For this, holothurians were eviscerated and left to regenerate for 10 days in seawater with different penicillin/streptomycin-based cocktails (100 µg/mL PS) including: 100 µg/mL kanamycin (KPS), 5 µg/mL vancomycin (VPS), and 4 µg/mL (E4PS) or 20 µg/mL (E20PS) erythromycin. Immunohistological and histochemical analyses were performed to analyze regenerative processes, including rudiment size, extracellular matrix (ECM) remodeling, cell proliferation, and muscle dedifferentiation. A reduction in muscle dedifferentiation was observed in all antibiotic-treated animals. ECM remodeling was decreased by VPS, E4PS, and E20PS treatments. In addition, organisms subjected to E20PS displayed a significant reduction in the size of their regenerating rudiments while VPS exposure altered cell proliferation. MTT assays were used to discard the possibility that the antibiotics directly affect holothurian metabolic activity while bacterial cultures were used to test antibiotic effects on holothurian enteric microbiota. Our results demonstrate a negative effect on intestinal regeneration and strongly suggest that these effects are due to alterations in the microbial community.

scholarly journals Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Bhavani Manivannan ◽  
Niranjana Mahalingam ◽  
Sudhir Jadhao ◽  
Amrita Mishra ◽  
Pravin Nilawe ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antibiotic Resistance ◽  
Genome Assembly ◽  
Biofilm Formation ◽  
Draft Genome ◽  
Drug Resistant ◽  
Draft Genome Assembly ◽  
Extensively Drug Resistant ◽  
History Of ◽  
Urinary Tuberculosis

We present the draft genome assembly of an extensively drug-resistant (XDR) Pseudomonas aeruginosa strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance.

scholarly journals Effect of thermal stimulation on gonad maturation in sea cucumber Phyllophorus sp. (Grube, 1840)

2018 ◽  
Vol 23 ◽  
pp. 39-46
Author(s):  
S Andriyono ◽  
N Masruroh ◽  
ED Masithah ◽  
J Triastuti ◽  
D Winarni
Keyword(s):  
Sea Cucumber ◽  
Histological Analysis ◽  
Temperature Treatment ◽  
Thermal Stimulation ◽  
Gonad Maturation ◽  
Marine Animals ◽  
Sea Cucumbers ◽  
Fishery Products ◽  
C 32 ◽  
The Ideal

Sea cucumbers, marine animals from the class Holothuroidea, have been widely known as fishery products for consumption in Indonesia. The Madura Strait is productive waters for sea cucumbers in eastern Indonesia, including sea cucumber species Phyllophorus sp. The exploitation of it mainly for consumption even though there are pharmaceutical beneficial of sea cucumber already known. The study of temperature effect is ideal inducement method for sea cucumber, but less research about this stimulation for Phyllophorus sp. for domestication purposes. The research showed that thermal stimulation treatment at the temperature of 30°C, 32°C and 34°C were in contrast to the that of control histological analysis proof that some of Phyllophorus sp. showed altered levels of gonadal maturation toward growth and advanced growth phase after thermal stimulation, respectively. The ideal stimulation treatment for gonad maturation was shown with stimulated temperature treatment of 32°C.J. bio-sci. 23: 39-46, 2015

scholarly journals Soft bodies make estimation hard: correlations among body dimensions and weights of multiple species of sea cucumbers

2015 ◽  
Vol 66 (10) ◽  
pp. 857 ◽  
Author(s):  
James Prescott ◽  
Shijie Zhou ◽  
Andhika P. Prasetyo
Keyword(s):  
Power Function ◽  
Body Length ◽  
Sea Cucumber ◽  
Dry Weight ◽  
Basic Knowledge ◽  
Small Scale ◽  
Body Width ◽  
Sea Cucumbers ◽  
Body Dimensions ◽  
Wet Weight

Tropical sea cucumbers are commonly exploited by small-scale, poorly managed fisheries. A fundamental problem in managing sea cucumber fisheries is the lack of basic knowledge of important life history characteristics for most species. As a result of plastic body dimensions, biological research on this group of animals becomes exceptionally challenging. To improve our understanding of essential biological parameters, we conducted a study to investigate correlations among various body measurements. We analysed a total of 18 sea cucumber species and more than 6600 individuals collected at Scott Reef in the Timor Sea, north-west Australia. We used hierarchical Bayesian errors-in-variables models to specifically take into account measurement errors that are obviously unavoidable. The measures included three types of weights (wet weight, gutted weight and dry weight) and two body dimensions (length and width). The modelling reveals that using both body length and width as independent variables, wet weight increases approximately linearly with body length, but is a power function (~1.6) of body width, although variability exists among species. Dry weight tends to increase more slowly with body length, but has a similar power function of body width. Linear relationships are established between the three types of weights. On average, ~11% of a live specimen and ~16% of a gutted specimen is processed to the commercially traded dry body wall. Our results can be applied to sea cucumbers in other areas and can be useful for data standardisation and size-based fisheries management.

scholarly journals Small-scale fishing income and fuel consumption: Fiji’s artisanal sea cucumber fishery

2018 ◽  
Vol 75 (5) ◽  
pp. 1758-1767 ◽  
Author(s):  
Steven W Purcell ◽  
Watisoni Lalavanua ◽  
Brian R Cullis ◽  
Nicole Cocks
Keyword(s):  
Gender Equity ◽  
Sea Cucumber ◽  
Large Scale ◽  
Small Scale ◽  
Breath Hold ◽  
Net Income ◽  
Fuel Use ◽  
Sea Cucumbers ◽  
Deep Water Species ◽  
And Gender

Abstract Understanding the income and costs of fishing is fundamental to managing fisheries and planning interventions to improve efficiency and gender equity. Few studies offer data on fisher incomes and fuel use in small-scale fisheries (SSFs), and fewer have assessed factors influencing variation among fishers and between genders. We interviewed 235 artisanal fishers among 34 island villages in an artisanal sea cucumber fishery in Fiji. Linear mixed models were used to determine the effect of geographic and socioeconomic variables on incomes and fuel use from fishing sea cucumbers. Net income of sea cucumbers to fishers, averaging FJ$8, 171 year−1 (US$4, 494 year−1) (range: FJ$0–52,008 year−1), varied among villages and was 47% lower for women than men. On an average, 60% of fishers’ gross annual income came from fishing and selling sea cucumbers, although this proportion varied greatly even within villages. Fishers who practised gleaning, fished less often, or possessing numerous livelihood income streams, were less economically dependent on sea cucumbers. Men tended to estimate higher incomes for an average day of fishing than women when compared with their recall of last sale. Fuel use varied greatly among regions in Fiji but, overall, averaged 428 L fisher−1 year−1, and represented 28% of gross income. More economical fishing strategies by women resulted in lower fuel use than men per fishing day. Breath-hold divers used less fuel (compared to fishers using scuba) and fishers targeting deep-water species used more fuel than other fishers. A best approximation of 8000 t CO2 year−1 for the carbon footprint of the whole fishery suggests that some SSFs, such as the one studied here, can be significant contributors to greenhouse gas emissions, even compared to many large-scale fisheries globally. Reforms to the management of SSFs should consider regulations that minimize carbon emissions and reduce economic dependency on vulnerable marine resources.

Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

2012 ◽  
Vol 71 (6) ◽  
pp. 895-906 ◽  
Author(s):  
Luming Yang ◽  
Dal-Hoe Koo ◽  
Yuhong Li ◽  
Xuejiao Zhang ◽  
Feishi Luan ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Genome Assembly ◽  
Draft Genome ◽  
High Density ◽  
Chromosome Rearrangements ◽  
Draft Genome Assembly

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 The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation

2016 ◽  
Author(s):  
Jian-Zhi Huang ◽  
Chih-Peng Lin ◽  
Ting-Chi Cheng ◽  
Ya-Wen Huang ◽  
Yi-Jung Tsai ◽  
...  
Keyword(s):  
Economic Value ◽  
Draft Genome ◽  
Floral Organ ◽  
Cool Temperature ◽  
Organ Development ◽  
Nucleotide Polymorphisms ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Genome Data ◽  
Expression Of Genes

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802’, a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

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