DNA Barcoding Of Species Research Articles

Barcoding of ornamental freshwater shrimp, Neocaridina denticulata (De Haan, 1844) from the aquatic ornamental market in Purbalingga, Central Java, Indonesia

Abstract. Kusmintarsih ES, Mahmoud HHA, Sastranegara MH, Syakuri H,Nuryanto A, Ambarningrum TB. 2023. Barcoding of ornamental freshwater shrimp, Neocaridina denticulata (De Haan, 1844) from the aquatic ornamental market in Purbalingga, Central Java, Indonesia. Biodiversitas 24: 3601-3608. Indonesia is one of the world’s leading aquatic ornamental shrimps producers and exports. One of the aquatic ornament shrimp species is a Neocaridina denticulate (De Haan, 1844). There is a wide range of colors including red, bright red, yellow, orange, green, blue, violet, black, and color combinations. It is a landlocked Atydiae family species comprising31 species and subspecies. Due to taxonomic difficulties, this species is continually under revision, and the validation of a few species is currently questionable and uncertain for the relationships among the various colors of N. denticulata. The Cytochrome Oxidase gene I (CO1) gene sequences of mitochondrial DNA were used for species DNA barcoding studies. This study aimed to validate the taxonomic status of different colors of N. denticulata species using the mitochondrial DNA or mtDNA Cytochrome oxidase (CO1) gene sequences. Neighbour Joining trees were constructed based on 545 bp of CO1 gene from white, black, red, yellow, blue colors, and their combination. Several sequences were derived from GenBank for relevant species from different countries and the outgroup. The result showed that all samples are homolog, even to N. denticulata from China NC_023823.1.

Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis

BackgroundCalanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae.ResultsThe complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius.ConclusionThis study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.

Let’s talk about the (lady)birds and the bees: how insects can whisper a multitude of stories

If you have watched A Bug’s Life, you would have seen that insects come in an assortment of colours, shapes, and sizes. They are the perfect organism that could be used to describe the myriad diversity of all life on earth. These six-legged creatures are one of the most diverse groups of species, accounting for more than 80% of all documented living animals Ødegaard 2008. This huge diversity also makes it extremely time- and labour-intensive to carry out large-scale monitoring of insects. High-throughput sequencing technologies and the use of DNA barcodes for species identification have paved the way for the rapid biomonitoring of insects Hebert et al. 2003. However, millions of insect species are not well-represented in DNA reference databases, making species-level identification challenging for molecular research. Projects such as the Darwin Tree of Life (DToL) aim to cover this gap and generate DNA barcodes for all eukaryotic species found in the UK Blaxter et al. 2022. At the Wellcome Sanger Institute, the BIOSCAN UK for Flying Insects project has two main aims; Documenting the diversity of UK flying insects Discovering insect-cobiont interactions Documenting the diversity of UK flying insects Discovering insect-cobiont interactions To meet these aims, we will be documenting the diversity of one million malaise-caught insects from 100 sites across the UK in the next five years. We will be using a non-destructive DNA extraction technique to preserve insect specimen integrity for museum collections or educational purposes Korlević et al. 2021. COI barcoding will be carried out using ONT and/or PacBio long-read technology to identify each insect specimen. To tease apart insect conbiont interactions, we will carry out mini barcoding using primers targeting microbes, parasites, vertebrates, invertebrates, and plants Fig. 1. Together, this molecular dataset consisting of one million specimens collected over space and time in the next five years will allow us to discover how insects interact with the ecosystem and advance insect biomonitoring research in the UK.

Mission impossible completed: unlocking the nomenclature of the largest and most complicated subgenus of Cortinarius, Telamonia

So far approximately 144,000 species of fungi have been named but sequences of the majority of them do not exist in the public databases. Therefore, the quality and coverage of public barcode databases is a bottleneck that hinders the study of fungi. Cortinarius is the largest genus of Agaricales with thousands of species world-wide. The most diverse subgenus in Cortinarius is Telamonia and its species have been considered one of the most taxonomically challenging in the Agaricales. Its high diversity combined with convergent, similar appearing taxa have earned it a reputation of being an impossible group to study. In this study a total of 746 specimens, including 482 type specimens representing 184 species were sequenced. Also, a significant number of old types were successfully sequenced, 105 type specimens were over 50 years old and 18 type specimens over 100 years old. Altogether, 20 epi- or neotypes are proposed for recently commonly used older names. Our study doubles the number of reliable DNA-barcodes of species of C. subgenus Telamonia in the public sequence databases. This is also the first extensive phylogenetic study of the subgenus. A majority of the sections and species are shown in a phylogenetic context for the first time. Our study shows that nomenclatural problems, even in difficult groups like C. subgenus Telamonia, can be solved and consequently identification of species based on ITS barcodes becomes an easy task even for non-experts of the genus.

DNA barcoding of species of Bacopa coupled with high-resolution melting analysis.

In Thailand, there are three species of Bacopa, namely, B. monnieri, B. caroliniana, and B. floribunda. Among these species of Bacopa, B. monnieri is the only medicinal species, used for the treatment of cognitive impairment and improvement of cognitive abilities because of its bioactive constituents, bacoside A and B. However, because of the similar characteristics of these species, it is difficult to differentiate among related species, resulting in confusion during identification. For this reason, and to ensure therapeutic quality for consumers, authentication is important. In this study, the three abovementioned species of Bacopa were evaluated using barcoding coupled with high-resolution melting (Bar-HRM) analysis based on primers designed for the trnL-F sequences of the three species. The melting profiles of the trnL-F amplicons of B. caroliniana and B. floribunda were clearly different from the melting profile of the trnL-F amplicon from B. monnieri; thus, the species could be discriminated by Bar-HRM analysis. Bar-HRM was then used to authenticate commercial products in various forms. The melting curves of the six commercial samples indicated that all the tested products contained genuine B. monnieri species. This method provides an efficient and reliable authentication system for future commercial herbal products and offers a reference system for quality control.

Identification of Notoginseng powder based on similarity to “DNA Barcoding Core-genotype”

Notoginseng powder is a medicine form of Notoginseng radix et rhizoma in Chinese Pharmacopeia. Common adulterants of Notoginseng powder appeared in the market include powder of Panax ginseng and Panax quinquefolius. Here, “DNA Barcoding Core-Genotype (DBCG)” based on ITS sequences was developed for authenticating Notoginseng powder. DBCG was the genotype with the highest frequency of DNA barcoding in species. The DBCG was found as the reference sequence and minimal-similarity to identify species was calculated by large sample analysis. Then we could calculate similarity index between DBCG and sequences of the unidentified Notoginseng powder and compare it through minimal-similarity to identify the species. This method was simple, efficient, and might be a preferable tool for accurate authentication.

Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species: A Case Study in Taxus

Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues, we sampled 39 populations for nine Taxus species across their entire ranges, with two to three individuals per population randomly sampled. We sequenced one core DNA barcode (matK) and three supplementary regions (trnH-psbA, trnL-trnF and ITS) for all samples to test the effects of sampling design and the utility of indels. Our results suggested that increasing sampling within-population did not change the clustering of individuals, and that meant within-population P-distances were zero for most populations in all regions. Based on the markers tested here, comparison of methods either including or excluding indels indicated that discrimination and nodal support of monophyletic groups were significantly increased when indels were included. Thus we concluded that one individual per population was adequate to represent the within-population variation in these species for DNA barcoding, and that intra-specific sampling was best focused on representing the entire ranges of certain taxa. We also found that indels occurring in the chloroplast trnL-trnF and trnH-psbA regions were informative to differentiate among for closely related taxa barcoding, and we proposed that indel-coding methods should be considered for use in future for closed related plant species DNA barcoding projects on or below generic level.

Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification.

So-called DNA barcodes have recently been proposed to answer the problem of specimen identification and to quantify global biodiversity. We show that this proposition is wanting in terms of rationale, methodology and interpretation of results. In addition to falling short of all its stated goals, the method abandons the benefits of morphological studies in favor of a limited molecular identification system that would ultimately impede our understanding of biodiversity.