scholarly journals Elucidating the diet of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3176 ◽  
Author(s):  
Sheema Abdul Aziz ◽  
Gopalasamy Reuben Clements ◽  
Lee Yin Peng ◽  
Ahimsa Campos-Arceiz ◽  
Kim R. McConkey ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Plant Species ◽  
Peninsular Malaysia ◽  
Next Generation ◽  
Plant Parts ◽  
Reference Collection ◽  
Microhistological Analysis ◽  
Challenging Situation ◽  
Generation Sequencing ◽  
Flying Fox

There is an urgent need to identify and understand the ecosystem services of pollination and seed dispersal provided by threatened mammals such as flying foxes. The first step towards this is to obtain comprehensive data on their diet. However, the volant and nocturnal nature of bats presents a particularly challenging situation, and conventional microhistological approaches to studying their diet can be laborious and time-consuming, and provide incomplete information. We used Illumina Next-Generation Sequencing (NGS) as a novel, non-invasive method for analysing the diet of the island flying fox (Pteropus hypomelanus) on Tioman Island, Peninsular Malaysia. Through DNA metabarcoding of plants in flying fox droppings, using primers targeting therbcLgene, we identified at least 29 Operationally Taxonomic Units (OTUs) comprising the diet of this giant pteropodid. OTU sequences matched at least four genera and 14 plant families from online reference databases based on a conservative Least Common Ancestor approach, and eight species from our site-specific plant reference collection. NGS was just as successful as conventional microhistological analysis in detecting plant taxa from droppings, but also uncovered six additional plant taxa. The island flying fox’s diet appeared to be dominated by figs (Ficussp.), which was the most abundant plant taxon detected in the droppings every single month. Our study has shown that NGS can add value to the conventional microhistological approach in identifying food plant species from flying fox droppings. At this point in time, more accurate genus- and species-level identification of OTUs not only requires support from databases with more representative sequences of relevant plant DNA, but probably necessitatesin situcollection of plant specimens to create a reference collection. Although this method cannot be used to quantify true abundance or proportion of plant species, nor plant parts consumed, it ultimately provides a very important first step towards identifying plant taxa and spatio-temporal patterns in flying fox diets.

scholarly journals Elucidating the diet and foraging ecology of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing

2016 ◽  
Author(s):  
Sheema Abdul Aziz ◽  
Gopalasamy Reuben Clements ◽  
Lee Yin Peng ◽  
Ahimsa Campos-Arceiz ◽  
Kim R McConkey ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Plant Species ◽  
Foraging Ecology ◽  
Peninsular Malaysia ◽  
Next Generation ◽  
Flying Foxes ◽  
Plant Parts ◽  
New Family ◽  
Generation Sequencing ◽  
Flying Fox

There is an urgent need to identify and understand the ecosystem services provided by threatened animal species such as flying foxes. The first step towards this is to obtain comprehensive data on their diet. However, the volant and nocturnal nature of flying foxes presents a challenging situation, and conventional microhistological approaches to studying their diet can be laborious and time-consuming, and provide incomplete information. We used Illumina Next-Generation Sequencing (NGS) as a novel, non-invasive method for analysing the diet of the island flying fox (Pteropus hypomelanus) on Tioman Island, Peninsular Malaysia. Through NGS analysis of flying fox droppings over eight months, we identified at least 29 Operationally Taxonomic Units comprising the diet of this giant pteropodid, spanning 19 genera and 18 different plant families, including one new family not previously recorded for pteropodid diet. NGS was just as successful as conventional microhistological analysis in detecting plant taxa from droppings, but also uncovered six additional plant taxa. The island flying fox’s diet appeared to be dominated by figs (Ficus sp.), which was the most abundant plant taxon detected in the droppings every single month. Our study has shown that NGS can add value to the conventional microhistological approach in identifying food plant species from flying fox droppings. However, accurate and detailed identification requires a comprehensive database of the relevant plant DNA, which may require collection of botanical specimens from the study site. Although this method cannot be used to quantify true abundance or proportion of plant species, nor plant parts consumed, it ultimately provides a very important first step towards identifying plant taxa in pteropodid diet.

scholarly journals Elucidating the diet and foraging ecology of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing

2016 ◽  
Author(s):  
Sheema Abdul Aziz ◽  
Gopalasamy Reuben Clements ◽  
Lee Yin Peng ◽  
Ahimsa Campos-Arceiz ◽  
Kim R McConkey ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Plant Species ◽  
Foraging Ecology ◽  
Peninsular Malaysia ◽  
Next Generation ◽  
Flying Foxes ◽  
Plant Parts ◽  
New Family ◽  
Generation Sequencing ◽  
Flying Fox

There is an urgent need to identify and understand the ecosystem services provided by threatened animal species such as flying foxes. The first step towards this is to obtain comprehensive data on their diet. However, the volant and nocturnal nature of flying foxes presents a challenging situation, and conventional microhistological approaches to studying their diet can be laborious and time-consuming, and provide incomplete information. We used Illumina Next-Generation Sequencing (NGS) as a novel, non-invasive method for analysing the diet of the island flying fox (Pteropus hypomelanus) on Tioman Island, Peninsular Malaysia. Through NGS analysis of flying fox droppings over eight months, we identified at least 29 Operationally Taxonomic Units comprising the diet of this giant pteropodid, spanning 19 genera and 18 different plant families, including one new family not previously recorded for pteropodid diet. NGS was just as successful as conventional microhistological analysis in detecting plant taxa from droppings, but also uncovered six additional plant taxa. The island flying fox’s diet appeared to be dominated by figs (Ficus sp.), which was the most abundant plant taxon detected in the droppings every single month. Our study has shown that NGS can add value to the conventional microhistological approach in identifying food plant species from flying fox droppings. However, accurate and detailed identification requires a comprehensive database of the relevant plant DNA, which may require collection of botanical specimens from the study site. Although this method cannot be used to quantify true abundance or proportion of plant species, nor plant parts consumed, it ultimately provides a very important first step towards identifying plant taxa in pteropodid diet.

Promiscuous Cryptic Rearrangements of the MYC Locus Cis-Dysregulate MYC Expression and Are Present in the Majority of Patients with Hyperdiploid Myeloma

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 724-724
Author(s):  
P Leif Bergsagel ◽  
Maurizio Affer ◽  
Oleg K Glebov ◽  
Wei-Dong D Chen ◽  
Jonathan J Keats ◽  
...  
Keyword(s):  
Gene Expression ◽  
Next Generation Sequencing ◽  
Copy Number ◽  
Genetic Mutation ◽  
Monoallelic Expression ◽  
Next Generation ◽  
Activating Mutations ◽  
Reference Collection ◽  
In Cis ◽  
Generation Sequencing

Abstract Abstract 724 Background: Chromosome content identifies two pathogenic pathways, each occurring in about half of patients with MGUS and multiple myeloma (MM). Hyperdiploid MM (HRD) has 48–75 chromosomes with multiple trisomies selectively involving chromosomes 3, 5, 7, 9, 11, 15, 19 and 21; only 10% of these HRD tumors have primary IgH translocations and no frequent focal genetic mutations have been identified. In contrast primary IgH translocations are identified in over 70% of non-hyperdiploid MM (NHRD). Rearrangements of MYC have been detected by FISH in only 16% of untreated MM, but over 90% of MM cell lines, identifying a late role for MYC in the progression of MM. The introduction of a MYC transgene into a mouse strain predisposed to MGUS results in mice that uniformly develop MM, suggesting a distinct early role of MYC in the progression of MGUS to MM. We report here that rearrangements in a 4Mb region surrounding MYC are present in 70% of HRD, representing the most frequent focal genetic mutation in this genetic subtype of MM. Results: We analyzed the MMRC reference collection of gene expression (Affymetrix Hu133Plus2) and copy number (Agilent 244k CGH) data and performed FISH to identify MYC rearrangements with IgH or IgL loci in 218 patients with untreated and relapsed MM. We found MYC rearrangements in 48% of MM (identified only by FISH in 5%, only by aCGH in 33%, and by both FISH and aCGH in 10%), including 43% of untreated, and 51% of relapsed MM. Using a hyperdiploid index calculated from the median copy number of the chromosomes involved in trisomies we determined that rearrangements of MYC were present in 70% of the top third, 35% of the middle third, and 25% of the bottom third. Using the paired gene expression data we found that the expression of MYC was approximately two-fold higher in the samples with rearrangements compared to those without rearrangements (p<0.001) and about three-fold higher in MM tumors without rearrangements compared to MGUS (p<0001). Using paired RNA and DNA from the MMRC reference collection we determined in 22 informative patients that MYC rearrangements are associated with monoallelic expression of MYC (p<0.01), consistent with cis-dysregulation of MYC. Analysis of the various changes on aCGH, and fine mapping of the genetic architecture of the rearrangements using next generation sequencing identifies a promiscuous array of rearrangements that often result in the introduction of an enhancer within the MYC locus, resulting in its cis-dysregulation. Since they cannot be comprehensively identified by either CGH or FISH alone, more sensitive techniques, such as next generation sequencing approaches, will be required to comprehensively identify all MYC rearrangements in MM. Conclusions: Rearrangements of MYC are the most frequent focal genetic mutation in untreated MM and are particularly prevalent in hyperdiploid MM. While only one third involve an immunoglobulin locus, they all result in cis-dysregulated expression of MYC, and may be one mechanism responsible for the progression of MGUS to MM. Tumors lacking MYC rearrangements bi-allelically over-express MYC by a trans mechanism including potentially inactivating mutations of BLIMP1/PRDM1, or activating mutations of IRF4. We propose two largely non-overlapping pathogenic pathways in MM: HRD associated with frequent MYC rearrangements, and NHRD associated with frequent primary IgH translocations. The prevalence of MYC rearrangements increases with tumor progression, identifying a role for MYC both early and late in tumorigenesis. As therapies that have been reported to target MYC (e.g., IMiDs®, bortezomib, bromodomain inhibitors) are used in the clinic, it will be important to associate their effect with the presence or absence of MYC rearrangements. Disclosures: Bergsagel: Constellation Pharmaceuticals: Consultancy. Keats:Tgen: Employment.

Sign in / Sign up

Export Citation Format

Share Document