Morphological and Molecular Species Identification of Termites Attacking Ironwood Trees, Casuarina equisetifolia (Fagales: Casuarinaceae), in Guam

2019 ◽  
Vol 112 (4) ◽  
pp. 1902-1911 ◽  
Author(s):  
Jong-Seok Park ◽  
Claudia Husseneder ◽  
Robert L Schlub
Keyword(s):  
Dna Markers ◽  
Morphological Characters ◽  
Casuarina Equisetifolia ◽  
Molecular Species Identification ◽  
Dead Trees ◽  
Termite Attack ◽  
Coptotermes Gestroi ◽  
Reference Sequences ◽  
Close Sequence ◽  
Sequence Match

Abstract Ironwood trees (Casuarina equisetifolia subsp. equisetifolia L.) are ecologically and economically important trees in tropical and subtropical regions of the Indo-Pacific. Ironwood is one of the dominant tree species in Guam, but since 2002, this tree has been declining dramatically. A previous study showed that numerous sick or dead trees were under termite attack. However, the species of termites were not identified. As a first step to investigate causal relationships between termites and ironwood tree death, we assigned termites collected from ironwood trees to species using a combination of morphological characters and DNA barcoding of the 12S, 16S, COI, COII, and ITS2 regions. Based on morphology and comparisons to reference sequences in NCBI GenBank, the most likely species assignments were Nasutitermes takasagoensis (Nawa) (Blattodea: Termitidae) found to infest 45 trees, followed by Coptotermes gestroi (Wasmann) (Blattodea: Rhinotermitidae) (2 trees), Microcerotermes crassus Snyder (Blattodea: Termitidae) (2 trees), and an additional unidentified Microcerotermes species (1 tree) with no close sequence match to identified species in NCBI GenBank. However, taxonomic revisions and broader representation of DNA markers of well-curated specimen in public databases are clearly needed, especially for the N. takasagoensis species complex.

scholarly journals Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shan Shen ◽  
Shi-Liang Liu ◽  
Ji-Hang Jiang ◽  
Li-Wei Zhou
Keyword(s):  
Species Identification ◽  
Rolling Circle Amplification ◽  
Practical Method ◽  
Morphological Characters ◽  
Its Sequences ◽  
Commercial Development ◽  
Medicinal Mushrooms ◽  
Rolling Circle ◽  
Reference Sequences ◽  
Its Barcoding

Abstract“Sanghuang” refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of “Sanghuang” in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to “Sanghuang” in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.

scholarly journals Nothing in (sponge) biology makes sense – except when based on holotypes

2015 ◽  
Vol 96 (2) ◽  
pp. 305-311 ◽  
Author(s):  
Dirk Erpenbeck ◽  
Merrick Ekins ◽  
Nicole Enghuber ◽  
John N.A. Hooper ◽  
Helmut Lehnert ◽  
...  
Keyword(s):  
New Species ◽  
Reference Material ◽  
Species Identification ◽  
Dna Sequences ◽  
Morphological Plasticity ◽  
Morphological Characters ◽  
Molecular Techniques ◽  
Reference Sequences ◽  
Species Descriptions ◽  
Preservation History

Sponge species are infamously difficult to identify for non-experts due to their high morphological plasticity and the paucity of informative morphological characters. The use of molecular techniques certainly helps with species identification, but unfortunately it requires prior reference sequences. Holotypes constitute the best reference material for species identification, however their usage in molecular systematics and taxonomy is scarce and frequently not even attempted, mostly due to their antiquity and preservation history. Here we provide case studies in which we demonstrate the importance of using holotype material to answer phylogenetic and taxonomic questions. We also demonstrate the possibility of sequencing DNA fragments out of century-old holotypes. Furthermore we propose the deposition of DNA sequences in conjunction with new species descriptions.

scholarly journals Systematic Evaluation of Landrace Tea Populations in Northern Sichuan, China, Based on Morphology, DNA Markers, and Biochemistry Analyses

HortScience ◽  
2018 ◽  
Vol 53 (8) ◽  
pp. 1095-1101
Author(s):  
Li-Qiang Tan ◽  
Xin-Yu Wang ◽  
Hui Li ◽  
Guan-Qun Liu ◽  
Yao Zou ◽  
...  
Keyword(s):  
Dna Markers ◽  
Gene Diversity ◽  
Germplasm Conservation ◽  
Dry Weight ◽  
Morphological Characters ◽  
Systematic Evaluation ◽  
Total Amino Acid ◽  
Wide Range ◽  
High Level ◽  
Selection Of

Landrace tea populations are important recourses for germplasm conservation and selection of elite tea clone cultivars. To understand their genetic diversity and use them effectively for breeding, two traditional landrace tea populations, Beichuan Taizicha (BCTZ) and Nanjiang Dayecha (NJDY), localized to northern Sichuan, were evaluated for morphological characters, simple sequence repeat (SSR)–based DNA markers and the contents of biochemical components. A wide range of morphological variation and a moderately high level of DNA polymorphism were observed from both BCTZ and NJDY. NJDY had on average, bigger leaves, larger flowers, higher total catechins (TCs), and greater gene diversity (GD) than BCTZ. Interestingly, samples from BCTZ had a wide range in the ratio of galloylated catechins to nongalloylated catechins (G/NG) (1.83–8.12, cv = 48.8%), whereas samples from NJDY were more variable in total amino acid (TAA) content (25.3–50.8 mg·g−1 dry weight) than those from BCTZ. We concluded that the two Camellia sinensis landrace populations are of great interest for both individual selection breeding and scientific studies.

A matrix-based revision of the genus Hypogena Dejean, 1834 (Coleoptera: Tenebrionidae)

Zootaxa ◽  
2020 ◽  
Vol 4780 (2) ◽  
pp. 201-258
Author(s):  
LUNA GREY ◽  
AARON D. SMITH
Keyword(s):  
Type Species ◽  
Morphological Characters ◽  
Species Relationships ◽  
Dominican Amber ◽  
Darkling Beetle ◽  
Dead Trees ◽  
Unidentified Species ◽  
Male Specific ◽  
Coleoptera Tenebrionidae

The darkling beetle genus Hypogena Dejean, 1834 (Tenebrionidae: Tenebrioninae) is revised. Hypogena is entirely composed of dorsoventrally flattened species that live subcortically in dead trees. This genus is generally identified by male specific characters, particularly the presence of cephalic horns. Hypogena is currently placed within the tribe Triboliini Gistel, 1848. However, several previously overlooked morphological characters call into question its placement within the tribe. A morphological matrix of 94 external adult characters was assembled to examine species relationships and boundaries. The resulting phylogeny is presented. Thirteen Hypogena species were previously recognized as valid, including Hypogena marginalis Doyen & Poinar from Dominican amber. Four previously unidentified species are described in this study: Hypogena akuma sp. nov. (Brazil), Hypogena cryptica sp. nov. (Mexico), Hypogena hirsuta sp. nov. (Ecuador), and Hypogena reburra sp. nov. (Colombia). Lectotypes are designated for Hypogena depressa (Champion, 1886), Hypogena dejeani (Champion, 1886), Hypogena canaliculata (Champion, 1886), and Hypogena vacca (Fabricius, 1801). A neotype is designated for Tenebrio biimpressus (Latreille, 1833) (type species of Hypogena, synonymized under Hypogena brasilica (Perty)) in order to maintain stability within the genus.  

scholarly journals Phylogenetic Analysis of Polyporous Fungi Collected from Batam Botanical Garden, Riau Province, Indonesia

2018 ◽  
Vol 10 (3) ◽  
pp. 510-518 ◽  
Author(s):  
Anis Sri Lestari ◽  
Deni Zulfiana ◽  
Apriwi Zulfitri ◽  
Ni Putu Ratna Ayu Krishanti ◽  
Titik Kartika
Keyword(s):  
Botanical Garden ◽  
Morphological Characters ◽  
Fungal Species ◽  
Vital Role ◽  
Pycnoporus Sanguineus ◽  
Dead Trees ◽  
Lenzites Betulina ◽  
Fungal Organisms ◽  
Advance Research ◽  
Fungal Tissue

Botanical gardens are areas that provide protection for trees and other organisms like polyporous fungi. Polyporous fungi are important fungi that degrade remaining lignocellulosic in leaf litter or dead trees. These mycobiota are also noted for their vital role in biorefinery, bioremediation, medicine and phytopathogen. The knowledge of the importance of the polyporous fungi to describe polyporous fungal species is fundamental for generating data base information of their occurrence and their functions. This research’s goal was to explore and characterize the polyporous fungi collected in Batam Botanical Garden in three sampling areas. Fungal samples were collected in May and July 2017. Subsequently, morphological characters were recorded, the fungal tissue was isolated to extract the DNA, then the data sequence was amplified and aligned to construct a phylogenetic tree. Five fungal families found belong to order Polyporales and were classified morphologically. They were Polyporaceae, Ganodermataceae, Fomitopsidaceae, Irpicaceae and Hymenochaetaceae. Three fungal species namely; Pycnoporus sanguineus, Trametes ijubarskii, and Antrodia wangii were identified based on phyllogenetic analysis whereas seven other fungal samples were identified as Earliella scabrosa, Hexagonia tenuis, Polyporus tenuiculus Lenzites betulina, Lentinus concavus, Phellinus rimosus and Hexagonia apiaria. This study classifies and adds fundamental databases on fungal taxonomy and diversity on the fungal organisms found in Batam Botanical Garden. This background data is vital to carry out an advance research in some areas such as bio-chemistry, bio-degradation, pharmacology and biotechnology.

scholarly journals Investigation of Termite Attack on Cultural Heritage Buildings: A Case Study in Aceh Province, Indonesia

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 385
Author(s):  
Novita Novita ◽  
Hasbi Amiruddin ◽  
Husaini Ibrahim ◽  
Teuku Muhammad Jamil ◽  
Syaukani Syaukani ◽  
...  
Keyword(s):  
Land Use ◽  
Cultural Heritage ◽  
Traditional Knowledge ◽  
Daily Life ◽  
Termite Species ◽  
Aceh Province ◽  
Heritage Buildings ◽  
Termite Attack ◽  
Coptotermes Gestroi

Surveys of the conditions of termite attack were conducted in two regencies, Pidie and Greater Aceh, Aceh Province, Indonesia (40 houses in each location). Interviews were also conducted with home owners to collect data on the building history; culture, such as daily life in the house; the frequency and intensity of termite attacks; and traditional knowledge for avoiding and/or suppressing termite attacks. We found that 51% of traditional houses were infested by two termite species: Coptotermes gestroi and Nasutitermes matangensis. The lower parts of traditional houses were frequently attacked and severely damaged by termites. Previous land use and the ages of the traditional houses affected the intensity of the termite attacks. Several measures for avoiding and/or suppressing termite attacks on cultural heritage buildings are also proposed.

A complete species phylogeny of the marine midge Pontomyia (Diptera:Chironomidae) reveals a cosmopolitan species and a new synonym

2014 ◽  
Vol 28 (3) ◽  
pp. 277 ◽  
Author(s):  
Danwei Huang ◽  
Peter S. Cranston ◽  
Lanna Cheng
Keyword(s):  
Puerto Rican ◽  
Dna Markers ◽  
Morphological Characters ◽  
High Genetic Diversity ◽  
Larval Population ◽  
Western Atlantic ◽  
Species Phylogeny ◽  
New Synonym ◽  
History Of ◽  
Pacific Species

Pontomyia (Diptera : Chironomidae) is an exclusively marine and flightless insect genus with four described species from the Indo-Pacific and one undescribed taxon known only by its larvae, pupal skins and females from the western Atlantic. A previous study of relationships among three of the Indo-Pacific species reported each of them to be monophyletic, with high genetic diversity within P. natans Edwards, 1926, the type species, and P. pacifica Tokunaga, 1932. The evolutionary affinities of the Australian endemic P. cottoni Womersley, 1937, which resembles P. natans, as well as the putative Atlantic species are hitherto undetermined. A complete molecular phylogeny of the genus based on two nuclear and two mitochondrial DNA markers indicates that P. cottoni and a Puerto Rican (Atlantic) larval population are nested within the P. natans clade. Furthermore, P. natans and P. cottoni are inseparable in all morphological characters used previously to distinguish them. Therefore, we synonymise P. cottoni with P. natans, syn. nov., whose known range now encompasses all three ocean basins after including the Puerto Rican population. This distribution warrants further investigation into the life history of Pontomyia, a midge with one of the shortest known adult lifespans among insects.

scholarly journals IDENTIFIKASI VARIETAS KENTANG “SUPERJOHN” BERDASARKAN PENANDA RAPD (Random Amplified Polymorphic DNA)

EUGENIA ◽  
2011 ◽  
Vol 17 (1) ◽  
Author(s):  
David S. Runtunuwu ◽  
J. E.X. Rogi ◽  
J. H. Palendeng
Keyword(s):  
Molecular Markers ◽  
Molecular Marker ◽  
Potato Variety ◽  
Dna Markers ◽  
Random Amplified Polymorphic Dna ◽  
Field Research ◽  
Morphological Characters ◽  
North Sulawesi ◽  
Field Identification ◽  
Young Leaves

ABSTRACT Identification using morphological characters has time consuming. Currently, identification using molecular markers has now been popular due to rapid, saving time and more precisely. Superjohn potato variety has been cultivated in North Sulawesi. However, the Superjohn potato variety has not been characterized using molecular markers. This research was aiming to identify “Superjohn” potato based on RAPD (Random Amplified Polymorphic DNA) markers. The research was conducted in field and laboratory. Field research was performed by taking some young leaves from “Superjohn”, Granola, and Atlantic variety from the field. Identification using molecular marker was conducted at laboratory.  Nine RAPD primers were used to identify the superjohn variety. The nine primers were OPA-1, OPA-2, OPA-3, OPA-4, OPA-5, OPA-7, OPA-9,  OPA-10, and  OPO-1.  The molecular identification revealed that “Superjohn” variety was different with Granola and Atlantic. OPA-9700 primer could be used for identification  “Superjohn” variety while OPA-101000 primer was suitable  for identification  Granola variety. Keywords:  Potatoes, variety, “Superjohn”, Granola, Atlantic, and RAPD ABSTRAK Penelitian ini dilakukan untuk mengidentikasi kentang “Superjohn” berdasarkan penanda RAPD (Random Amplified Polymorphic DNA).  Penelitian dilakukan di lapangan dan laboratorium. Penelitian lapangan dilakukan dengan mengambil beberapa daun muda dari varietas kentang “Superjohn”, Atlantik dan Granola. Kemudian  analisis DNA dilakukan di laboratorium menggunakan analisis RAPD. Berdasarkan penanda RAPD ternyata kentang “Superjohn” berbeda dari kentang Granola dan kentang Atlantik. Penanda RAPD OPA-9700 dapat digunakan untuk mengidentifikasi kentang“Superjohn” dan penanda RAPD  OPA-101000 dapat digunakan  untuk mengidentifikasi kentang Granola. Kata kunci:  Kentang,  varietas, Superjohn, Granola, Granola, RAPD

scholarly journals IDENTIFIKASI VARIETAS KENTANG SUPERJOHN BERDASARKAN PENANDA RAPD (Random Amplified Polymorphic DNA)

EUGENIA ◽  
2011 ◽  
Vol 17 (1) ◽  
pp. 52
Author(s):  
Runtunuwu D. S. ◽  
J. E. X. Rogi ◽  
J. H. Palendeng
Keyword(s):  
Molecular Markers ◽  
Molecular Marker ◽  
Potato Variety ◽  
Dna Markers ◽  
Random Amplified Polymorphic Dna ◽  
Field Research ◽  
Morphological Characters ◽  
North Sulawesi ◽  
Field Identification ◽  
Young Leaves

Identification using morphological characters has time consuming. Currently, identification usingmolecular markers has now been popular due to rapid, saving time and more precisely. Superjohnpotato variety has been cultivated in North Sulawesi. However, the Superjohn potato variety has notbeen characterized using molecular markers. This research was aiming to identify ―Superjohn‖ potatobased on RAPD (Random Amplified Polymorphic DNA) markers. The research was conducted in fieldand laboratory. Field research was performed by taking some young leaves from ―Superjohn‖, Granola,and Atlantic variety from the field. Identification using molecular marker was conducted at laboratory.Nine RAPD primers were used to identify the superjohn variety. The nine primers were OPA-1, OPA-2,OPA-3, OPA-4, OPA-5, OPA-7, OPA-9, OPA-10, and OPO-1. The molecular identification revealedthat ―Superjohn‖ variety was different with Granola and Atlantic. OPA-9700 primer could be used foridentification ―Superjohn‖ variety while OPA-101000 primer was suitable for identification Granolavariety.Keywords: Potatoes, variety, “Superjohn”, Granola, Atlantic, and RAPD ABSTRAKPenelitian ini dilakukan untuk mengidentikasi kentang ―Superjohn‖ berdasarkan penanda RAPD(Random Amplified Polymorphic DNA). Penelitian dilakukan di lapangan dan laboratorium. Penelitianlapangan dilakukan dengan mengambil beberapa daun muda dari varietas kentang ―Superjohn‖,Atlantik dan Granola. Kemudian analisis DNA dilakukan di laboratorium menggunakan analisis RAPD.Berdasarkan penanda RAPD ternyata kentang ―Superjohn‖ berbeda dari kentang Granola dan kentangAtlantik. Penanda RAPD OPA-9700 dapat digunakan untuk mengidentifikasi kentang―Superjohn‖ danpenanda RAPD OPA-101000 dapat digunakan untuk mengidentifikasi kentang Granola.

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