scholarly journals A multi-gene region targeted capture approach to detect plant DNA in environmental samples: A case study from coastal environments

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Van Dijk ◽  
Edward Biffin ◽  
Jennifer Young ◽  
Vicki Ann Thomson ◽  
...  

Metabarcoding of plant DNA recovered from environmental samples, termed environmental DNA (eDNA), has been used to detect invasive species, track biodiversity changes and reconstruct past ecosystems. The P6 loop of the trnL intron is the most widely utilized gene region for metabarcoding plants due to the short fragment length and subsequent ease of recovery from degraded DNA, which is characteristic of environmental samples. However, the taxonomic resolution for this gene region is limited, often precluding species level identification. Additionally, targeting gene regions using universal primers can bias results as some taxa will amplify more effectively than others. To increase the ability of DNA metabarcoding to better resolve flowering plant species (angiosperms) within environmental samples, and reduce bias in amplification, we developed a multi-gene targeted capture method that simultaneously targets 20 chloroplast gene regions in a single assay across all flowering plant species. Using this approach, we effectively recovered multiple chloroplast gene regions for three species within artificial DNA mixtures down to 0.001 ng/uL of DNA. We tested the detection level of this approach, successfully recovering target genes for 10 flowering plant species. Finally, we applied this approach to sediment samples containing unknown compositions of environmental DNA and confidently detected plant species that were later verified with observation data. Targeting multiple chloroplast gene regions in environmental samples enabled species-level information to be recovered from complex DNA mixtures. Thus, the method developed here, confers an improved level of data on community composition, which can be used to better understand flowering plant assemblages in environmental samples.

Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.


eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jered M Wendte ◽  
Yinwen Zhang ◽  
Lexiang Ji ◽  
Xiuling Shi ◽  
Rashmi R Hazarika ◽  
...  

In many plant species, a subset of transcribed genes are characterized by strictly CG-context DNA methylation, referred to as gene body methylation (gbM). The mechanisms that establish gbM are unclear, yet flowering plant species naturally without gbM lack the DNA methyltransferase, CMT3, which maintains CHG (H = A, C, or T) and not CG methylation at constitutive heterochromatin. Here, we identify the mechanistic basis for gbM establishment by expressing CMT3 in a species naturally lacking CMT3. CMT3 expression reconstituted gbM through a progression of de novo CHG methylation on expressed genes, followed by the accumulation of CG methylation that could be inherited even following loss of the CMT3 transgene. Thus, gbM likely originates from the simultaneous targeting of loci by pathways that promote euchromatin and heterochromatin, which primes genes for the formation of stably inherited epimutations in the form of CG DNA methylation.


Koedoe ◽  
1977 ◽  
Vol 20 (1) ◽  
Author(s):  
B.L. Penzhorn

Additions to the check list of flowering plants of the Mountain Zebra National Park. Thirteen additional flowering plant species are reported from the Mountain Zebra National Park, increasing the total reported to 371 species.


2018 ◽  
Vol 9 (1) ◽  
pp. 587-597
Author(s):  
Raúl Badillo‐Montaño ◽  
Armando Aguirre ◽  
Miguel A. Munguía‐Rosas

2006 ◽  
Vol 66 (2a) ◽  
pp. 463-471 ◽  
Author(s):  
Y. Antonini ◽  
R. G. Costa ◽  
R. P. Martins

Species of plants used by Melipona quadrifasciata Lepeletier for pollen and nectar gathering in an urban forest fragment were recorded in Belo Horizonte, Minas Gerais, Brazil. Melipona quadrifasciata visited 22 out of 103 flowering plant species. The plant species belonged mainly to Myrtaceae, Asteraceae, and Convolvulaceae (64% of the visits). Melipona quadrifasciata tended to collect pollen or nectar each time, except for Myrtaceae species, from which both pollen and nectar were collected. Bee abundance at flowers did not significantly correlate to food availability (expressed by flowering plant richness). We found a relatively high similarity (50%) between plant species used by M. quadrifasciata, which was also found in studies carried out in São Paulo State. However, low similarity (17%) was found between the results of this study and those of another done in Bahia State, Brazil.


Nature ◽  
1979 ◽  
Vol 281 (5733) ◽  
pp. 670-672 ◽  
Author(s):  
Nickolas M. Waser ◽  
Leslie A. Real

2020 ◽  
Vol 8 (2) ◽  
pp. 203
Author(s):  
Endro Setiawan ◽  
Dedy Darnaedi ◽  
Ismail Rachman ◽  
Teguh Triono ◽  
Campbell O. Webb

Indonesia is one of the world’s biodiversity hotspots. It is estimated to be the home of 9.5% flowering plant species, making it the seventh country with the highest biodiversity. Plant data collection is necessary to ascertain the level of plant biodiversity, as such data help in conservation efforts and long-term management. One of the methods applied is the collection of plants, with the purpose to acquire as much data about its biological resources. The collected specimen are then gathered and processed into a herbarium to be used as an information source in managing biological resources. Unfortunately, there are some difficulties related to the making and management of a herbarium. Digital herbarium are one of the potential solutions to the limitations of the traditional herbarium. It is a collection of plant pictures, replete with every step of productivity (leaf, flower, fruit) and the main characteristics of the plant species. It is an effective method for the identification and collection of plant biodiversity in Indonesia. About 2149 plants have been gathered from Borneo, Seram, Waigeo, Flores and Sulawesi which consisted of 152 family, 512 genus, and 1,832 species, with a total of 30391 pictures of plant parts. From the experiment conducted on 672 specimens, it achieved 98.8 % accuracy on the family level and 80.1 % accuracy on the genus level, while the species level reached 78.8%. The results showed that digital herbarium can be used to conduct identification and data collection of plant biodiversity. Furthermore, this method is simple, cheap and relatively easier to conduct. The output is a catalog of plant species in specific areas, which provides better understanding about plant identification and biodiversity, enhances conservation practices, and provides better long-term protection for Indonesian plant biodiversity.


2021 ◽  
Vol 11 (4) ◽  
pp. 109-121
Author(s):  
Yogita Solanki ◽  
Amit Kotiya

The Umari Dham is a sacred grove situated at the Jamwa Ramgarh Wildlife Sanctuary, Jaipur District of Rajasthan, India. It’s a beautiful arbour near the city of Jaipur. Umari Dham sacred grove has a temple, which has been visited by worshippers for approximately 450 years. During present field investigation, attempts were made to categorize the floral diversity of this sacred grove, and around 215 flowering plant species belonging to 159 genera under 52 families have been recorded according to Angiosperm Phylogeny Group III (APG III) classification. This grove serves as a vital pool for preservation of threatened, endemic and medicinal plant species.


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