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Forests
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DNA Barcoding for Species Identification of Forest Organisms
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DNA Barcoding for Species Identification of Forest Organisms

A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (31 May 2024) | Viewed by 10374

Special Issue Editor

Dr. Dilnora E. Gouliamova

E-Mail Website
Guest Editor
Department of General Microbiology, Institute of Microbiology, Sofia, Bulgaria
Interests: biodiversity; yeast molecular systematics; yeast pathogens; DNA barcoding analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

About one-third of Earth’s land surface is covered by forests. Forest plants clean the atmosphere by absorbing carbon dioxide and releasing oxygen via photosynthesis, as well as providing humans with food and other valuable materials. Forests are the most biologically diverse ecosystem on our planet, home to 80 percent of terrestrial plants, animals, and insects; however, their biodiversity hotspots remain largely unexplored. With rapid deforestation caused by human activity and climate change, much of the forest's biodiversity fund is being lost. Hence, it is urgent to describe and protect forest organisms. This Special Issue aims to publish articles describing the forest biodiversity hotspots of poorly studied geographical areas and addressing nature-based solutions for their conservation. We welcome articles that analyze the biodiversity of forests using DNA barcoding analysis, currently considered a rapid and reliable tool for species identification, evolution, and biodiversity monitoring.

Dr. Dilnora E. Gouliamova
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Forests is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • forests
  • biodiversity
  • plants
  • animals
  • insects
  • DNA barcoding analysis

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Published Papers (5 papers)

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Research

13 pages, 4520 KiB  
Article
Comparative Analyses of Acacia Plastomes to Detect Mutational Hotspots and Barcode Sites for the Identification of Important Timber Species
by Weixiong Li, Yongyao Li, Luke R. Tembrock, Zhiqiang Wu, Xuezhu Liao and Shuo Zhang
Forests 2024, 15(2), 306; https://doi.org/10.3390/f15020306 - 5 Feb 2024
Viewed by 1352
Abstract
The genus Acacia is a crucial source of industrial papermaking and timber, possessing significant economic value. Due to their nitrogen-fixing ability, rapid growth, and high tolerance to stress, Acacia species have become integral to short-term industrial timber forests, particularly in southern China and [...] Read more.
The genus Acacia is a crucial source of industrial papermaking and timber, possessing significant economic value. Due to their nitrogen-fixing ability, rapid growth, and high tolerance to stress, Acacia species have become integral to short-term industrial timber forests, particularly in southern China and various other regions worldwide. Nevertheless, comparative genomic analyses of Acacia species remain limited, impeding the development of molecular markers for identifying and distinguishing between distinct Acacia species as well as distinguishing their wood counterparts from other tree species. To address this gap, we generated plastomic sequences from eight species commonly cultivated in Chinese plantation forests and compared them with existing data. Our findings revealed a generally conserved structure and gene content within the plastid genomes of Acacia. Notably, the dN/dS ratio of genes from distinct functional groups varied, particularly between ribosomal proteins and photosynthesis genes. Furthermore, phylogenetic analyses and sequence comparisons suggest that the introduction of Acacia to China may have been less diverse than previously thought or that interspecies introgression has occurred more frequently than previously documented. This study offers a valuable starting point for future research in this area and for improving timber quality through marker-assisted breeding. Full article
(This article belongs to the Special Issue DNA Barcoding for Species Identification of Forest Organisms)
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14 pages, 1640 KiB  
Article
Study on the Extraction and Identification of DNA from Ten Dalbergia Species
by Changtao Gan, Haishan He and Jian Qiu
Forests 2023, 14(12), 2318; https://doi.org/10.3390/f14122318 - 26 Nov 2023
Viewed by 1563
Abstract
Most Dalbergia species are economically valuable and have been over-exploited, which has raised concerns. The regulation and protection of this genus require accurate and rapid authentication and identification processes. To address the issue of high residual inhibitors in extracted DNA from the Dalbergia [...] Read more.
Most Dalbergia species are economically valuable and have been over-exploited, which has raised concerns. The regulation and protection of this genus require accurate and rapid authentication and identification processes. To address the issue of high residual inhibitors in extracted DNA from the Dalbergia xylem, an optimized DNA extraction experiment was performed on 10 species of Dalbergia wood stored for 1–5 years; in particular, no gene sequence for D. tsoi can be found in the NCBI database. Additionally, universal primers ITS2 were used for PCR amplification and sequencing to confirm the effectiveness of DNA extraction. The results revealed that rinsing the wood with 0.25 M ammonium acetate buffer produced DNA with a high purity, without a significant decrease in the DNA yield. To achieve an optimal DNA yield, the wood DNA should be rinsed with ammonium acetate fewer than three times. All the wood DNA obtained using the kit method and treated with the ammonium acetate buffer rinsing solution one to four times was successfully amplified. The NJ phylogenetic tree constructed based on ITS2 can distinguish D. tsoi from other Dalbergia spp., and the predicted ITS2 secondary structure showed the difference between species. This experiment extracted high-quality DNA from wood, without the need for purification kits, thereby improving the efficiency of the extraction process. The extracted DNA was directly used for follow-up molecular experiments. Full article
(This article belongs to the Special Issue DNA Barcoding for Species Identification of Forest Organisms)
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13 pages, 2795 KiB  
Article
Comparative Study on Blowfly-Derived DNA and Camera Trapping in Assessing Mammalian Diversity in Subtropical Forests
by Pingshin Lee, Tianyi He, Minhui Dong, Qiang Huang, Xiang Zhou, Jun Liao, Xiaochun Chen, Xiaobing Wu, Suk-Ling Wee and Jinmin Chen
Forests 2023, 14(11), 2180; https://doi.org/10.3390/f14112180 - 1 Nov 2023
Viewed by 1908
Abstract
Mammalian DNA derived from invertebrates (iDNA), including blowfly iDNA, is an alternative tool to conventional camera trapping in assessing mammalian diversity. The method has been used in tropical mammal surveillance but no attempt has been made to compare the efficacy of blowfly iDNA [...] Read more.
Mammalian DNA derived from invertebrates (iDNA), including blowfly iDNA, is an alternative tool to conventional camera trapping in assessing mammalian diversity. The method has been used in tropical mammal surveillance but no attempt has been made to compare the efficacy of blowfly iDNA and camera trapping for monitoring mammal diversity in subtropical forests. We compared the blowfly iDNA monitoring with camera trapping to assess mammal diversity in the subtropical Jiulongfeng Nature Reserve (JLF), China, over a one-month period. The camera traps captured 2508 animal photos of 11 species belonging to four orders, eight genera, and eight families, whereas the blowfly iDNA method successfully detected ten species from six orders, eight genera, and eight families in JLF. Both methods were complementing each other instead of competing due to the low overlaps of mammal species detected. Of the total number of mammal species listed in JLF’s threatened list, 40% and 10% were detected through camera traps and blowfly iDNA methods, respectively. The estimated species richness curves indicated that combining camera traps and blowfly traps would increase the detection of mammal species. The strategy would significantly contribute to mammalian diversity surveillance and conservation programs in the tropical and subtropical forests. Full article
(This article belongs to the Special Issue DNA Barcoding for Species Identification of Forest Organisms)
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18 pages, 6358 KiB  
Article
Barcoding Hymenoptera: 11 Malaise Traps in Three Thai Forests: The First 68 Trap Weeks and 15,338 Parasitoid Wasp Sequences
by Donald L. J. Quicke, Paul D. N. Hebert, Mikko Pentinsaari and Buntika A. Butcher
Forests 2023, 14(10), 1991; https://doi.org/10.3390/f14101991 - 3 Oct 2023
Cited by 5 | Viewed by 3038
Abstract
We report the results of DNA barcoding week-long Malaise trap catches from 11 sites in three Thai conservation areas, concentrating on the parasitoid Hymenoptera, particularly the superfamily Ichneumonoidea. From a total of 15,338 parasitoid wasp sequences, 13,473 were barcode compliant and could be [...] Read more.
We report the results of DNA barcoding week-long Malaise trap catches from 11 sites in three Thai conservation areas, concentrating on the parasitoid Hymenoptera, particularly the superfamily Ichneumonoidea. From a total of 15,338 parasitoid wasp sequences, 13,473 were barcode compliant and could be assigned to a family based on morphology and sequence data. These collectively represented 4917 unique BINs (putative species) in 46 families, with the Scelionidae, Ichneumonidae, Eulophidae, Braconidae and Platygastridae being, by far, the most abundant. Spatial proximity had a strong positive effect on the numbers of BINs shared between traps. Full article
(This article belongs to the Special Issue DNA Barcoding for Species Identification of Forest Organisms)
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19 pages, 135525 KiB  
Article
Taxonomy, Phylogeny, and Life Cycle of Four Neophysopella Species on Meliosma myriantha and M. oldhamii in Korea
by Dong Hwan Na, Jae Sung Lee, Hyeon-Dong Shin and Young-Joon Choi
Forests 2023, 14(10), 1934; https://doi.org/10.3390/f14101934 - 22 Sep 2023
Cited by 2 | Viewed by 1630
Abstract
The present study performed an in-depth investigation of rust diseases affecting Meliosma myriantha and Meliosma oldhamii trees (Sabiaceae) in Korea. The analysis identified four distinct species of the genus Neophysopella (Pucciniales) as the causal agents. Among these, N. hornotina was found to infect [...] Read more.
The present study performed an in-depth investigation of rust diseases affecting Meliosma myriantha and Meliosma oldhamii trees (Sabiaceae) in Korea. The analysis identified four distinct species of the genus Neophysopella (Pucciniales) as the causal agents. Among these, N. hornotina was found to infect only M. oldhamii, whereas three Neophysopella species (N. meliosmae, N. meliosmae-myrianthae, and N. vitis) were parasitic on M. myriantha. To our knowledge, this is the first report of the former two species (N. hornotina and N. meliosmae) in Korea. In addition, we specified their alternate host plants for two heteroecious species (N. meliosmae-myrianthae and N. vitis) in Korea, completing the life cycles of the four rust species, and provided detailed morphological descriptions at each stage of their life cycles. Phylogenetic relationships of these rust species were uncovered using a comprehensive sample size, and we have constructed a phylogenetic tree for Neophysopella using the cytochrome c oxidase subunit III (cox3) gene sequences, demonstrating an effective approach for species delineation within this genus. The findings contribute to identifying and managing rust diseases affecting Meliosma species. Full article
(This article belongs to the Special Issue DNA Barcoding for Species Identification of Forest Organisms)
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