Phylogenetic study of living fossil Psilotum nudum L. from Himalayan range of Pakistan using DNA barcodes

The genus Psilotum belongs to Psilotaceae family, with about 133 to 189 species having outstanding social, economic and medically important relict plants. However, being living fossil plant, many hurdles come in way while trying to discern its phylogenetics reconstruction. The partial conserve nucleotide sequences of rbcLa, trnA, trnV, matK, ITS, ycF3 and rpoB genes were used to select the best suitable barcodes in Psilotum nudum L. The amplified fragments were subjected to Sanger sequencing and then Maximum likelihood, Maximum Parsimony and Neighbor Joining trees were generated using bioinformatics software. i.e., MUSCLE, BioEdit and Mega-7. Current population showed the best match between P. complanatum (KY099851.1), population reported from New Zealand and P. nudum (F384430.1) with identity value 100 and 99% having E-value 0.0 and 0.0 by rbcLa and trnA barcode region, respectively. The findings showed that P. nudum L. sequences are ever first reported from the Himalaya regions of Pakistan and could be utilized for further comparison among different populations of this relict plant species across the globe.

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Sex-linked photosynthetic physiologic research and the evolutionary ecological analysis in living fossil plant, Ginkgo biloba L.

Acta Ecologica Sinica ◽

10.1016/s1872-2032(08)60035-9 ◽

2008 ◽

Vol 28 (3) ◽

pp. 1128-1136 ◽

Cited By ~ 6

Author(s):

Jin Jing ◽

Jiang Hong ◽

Yu Shuquan ◽

Zhou Guomo

Keyword(s):

Ginkgo Biloba ◽

Fossil Plant ◽

Ecological Analysis ◽

Living Fossil

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Phyllocnistis podocarpa sp. nov. (Lepidoptera, Gracillariidae), a buddhist pine leaf-miner from Japan: taxonomy, DNA barcodes, damage and parasitoids

Zootaxa ◽

10.11646/zootaxa.4422.4.6 ◽

2018 ◽

Vol 4422 (4) ◽

pp. 558 ◽

Cited By ~ 2

Author(s):

TENGTENG LIU ◽

JIE SUN ◽

BO CAI ◽

YING WU

Keyword(s):

Economic Value ◽

Iucn Red List ◽

Red List ◽

Leaf Miner ◽

Dna Barcodes ◽

Neighbor Joining ◽

Parasitoid Species ◽

Frontal Process ◽

Podocarpus Macrophyllus ◽

Garden Plant

Phyllocnistis podocarpa sp. nov., is described from mines in Podocarpus macrophyllus (Family Podocarpaceae). The host plant P. macrophyllus, also known as buddhist pine on the IUCN Red List, is a noticeable garden plant and thus of high economic value. Buddhist pine has been introduced to many other countries from its native habitat in southern Japan. Special attention has been paid for it during the overseas import in China. The morphology of the pupae of P. podocarpa, particularly the frontal process of the head and the spine clusters on terga, ones of the most useful diagnostic characters for species identification of Phyllocnistis on morphology, is demonstrated using SEM. Two parasitoid species of Eulophidae (Hymenoptera) are identified and illustrated. COI barcode sequences are provided along with a Neighbor Joining Tree covering related species for aiding identification.

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A new species of Pima Hulst, 1888 from China (Lepidoptera, Pyralidae, Phycitinae), with a key to Holarctic species

ZooKeys ◽

10.3897/zookeys.975.56763 ◽

2020 ◽

Vol 975 ◽

pp. 111-124

Author(s):

Linlin Yang ◽

Yingdang Ren

Keyword(s):

New Species ◽

Species Delimitation ◽

Dna Barcodes ◽

Neighbor Joining ◽

Distribution Map ◽

Autonomous Region ◽

Ningxia Hui Autonomous Region ◽

Lepidoptera Pyralidae ◽

A New Species ◽

Holarctic Species

Pima tristriatasp. nov. is described as new to science based on specimens collected from the Ningxia Hui Autonomous Region, China, and P. boisduvaliella (Guenée, 1845) is also treated here for comparison. DNA barcodes of the two species are provided, together with a neighbor-joining tree for species delimitation. A key to the Holarctic species and a distribution map of the Chinese species are presented.

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Species delimitation and life stage association of Propsilocerus Kieffer, 1923 (Diptera, Chironomidae) using DNA barcodes

ZooKeys ◽

10.3897/zookeys.957.54668 ◽

2020 ◽

Vol 975 ◽

pp. 79-86

Author(s):

Hai-Jun Yu ◽

Xiao-Long Lin ◽

Rui-Lei Zhang ◽

Qian Wang ◽

Xin-Hua Wang

Keyword(s):

Species Delimitation ◽

Life Stage ◽

Dna Barcodes ◽

Neighbor Joining ◽

Index Numbers ◽

Nj Tree ◽

Barcode Gap

The utility of COI DNA barcodes in species delimitation is explored as well as life stage associations of five closely related Propsilocerus species: Propsilocerus akamusi (Tokunaga, 1938), Propsilocerus paradoxus (Lundström, 1915), Propsilocerus saetheri Wang, Liu et Paasivirta, 2007, Propsilocerus sinicus Sæther et Wang, 1996, and Propsilocerus taihuensis (Wen, Zhou et Rong, 1994). Results revealed distinctly larger interspecific than intraspecific divergences and indicated a clear “barcode gap”. In total, 42 COI barcode sequences including 16 newly generated DNA barcodes were applied to seven Barcode Index Numbers (BINs). A neighbor-joining (NJ) tree comprises five well-separated clusters representing five morphospecies. Comments on how to distinguish the larvae of P. akamusi and P. taihuensis are provided.

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Molecular Phylogenetic Analysis of the Orthoptera (Arthropoda, Insecta) based on Hexamerin Sequences

Zootaxa ◽

10.11646/zootaxa.4232.4.4 ◽

2017 ◽

Vol 4232 (4) ◽

pp. 523 ◽

Cited By ~ 2

Author(s):

XIAOHONG ZHANG ◽

JINFENG HAO ◽

YU XIA ◽

YAGE CHANG ◽

DAOCHUAN ZHANG ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Bayesian Inference ◽

Phylogenetic Reconstruction ◽

Phylogenetic Study ◽

Neighbor Joining ◽

Morphological Classification ◽

Good Marker ◽

Insect Order ◽

Higher Taxa ◽

Molecular Phylogenetic

The higher taxa classification and phylogeny of the insect order Orthoptera have long been controversial. Hexamerin, as a member of the highly conserved arthropod hemocyanin superfamily, has been shown to be a good marker for the phylogenetic study of insects. However, few studies have used hexamerins on the phylogeny of Orthoptera. In this study, we determined twenty-seven different hexamerin subunit type sequences in seventeen speices of Orthoptera. In order to infer the phylogenetic relationships among the superfamilies within Orthoptera and test the monophyly of Orthoptera, phylogenic trees were reconstructed using Neighbor-Joining (NJ) and Bayesian inference (BI) methods with two dipluran and three hymenopteran hexamerin sequences as outgroups. The result supported the monophyly of Orthoptera, which includes two monophyletic suborders Caelifera and Ensifera. The Caelifera includes Acridoidea, Eumastacoidea, Tetrigoidea and Tridactyloidea, and the Ensifera includes Tettigonioidea, Grylloidea and Gryllotalpoidea. Our study is basically consistent with the study of morphological classification. In addition, our study indicates that a relatively comprehensive taxa sampling is essential to solve some problems in phylogenetic reconstruction.

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

Fungal Diversity ◽

10.1007/s13225-020-00459-1 ◽

2020 ◽

Vol 104 (1) ◽

pp. 291-331

Author(s):

Kare Liimatainen ◽

Tuula Niskanen ◽

Bálint Dima ◽

Joseph F. Ammirati ◽

Paul M. Kirk ◽

...

Keyword(s):

World Wide ◽

Phylogenetic Study ◽

Dna Barcodes ◽

Type Specimens ◽

Easy Task ◽

The Public ◽

Identification Of Species ◽

Sequence Databases ◽

First Time ◽

High Diversity

AbstractSo 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.

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A new species of Manoa Fittkau (Diptera: Chironomidae), with DNA barcodes from Xianju National Park, Oriental China

Zootaxa ◽

10.11646/zootaxa.4231.3.6 ◽

2017 ◽

Vol 4231 (3) ◽

pp. 398 ◽

Cited By ~ 1

Author(s):

XIN QI ◽

XIN-HUA WANG ◽

TROND ANDERSEN ◽

XIAO-LONG LIN

Keyword(s):

New Species ◽

Adult Male ◽

National Park ◽

Dna Barcodes ◽

Neighbor Joining ◽

Male And Female ◽

Oriental Region ◽

First Time ◽

A New Species

The genus Manoa and the tribe Pseudochironomini are recorded from the Oriental region for the first time. Manoa xianjuensis Qi & Lin sp. n. from Xianju National Park, Zhejiang, China is described and illustrated as adult male and female, the latter associated with the male by standard DNA barcodes. A neighbor joining tree based on available Pseudochironomini DNA barcodes and keys to the adults in Manoa are given.

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An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210858 ◽

2020 ◽

Vol 21 (8) ◽

Author(s):

Viet The Ho ◽

MINH PHUONG NGUYEN

Keyword(s):

Dna Barcoding ◽

In Silico ◽

Genetic Relatedness ◽

Dna Barcode ◽

Species Level ◽

Resolving Power ◽

Phylogenetic Study ◽

Dna Barcodes ◽

Sequence Parameters ◽

Cucurbitaceae Family

Abstract. Ho VT, Nguyen MP. 2020. An in silico approach for evaluation of rbcL and matK loci for DNA barcoding of Cucurbitaceae family. Biodiversitas 21: 3879-3885. DNA barcodes have been used intensively to discriminate different species in Cucurbitaceae family. The main of this study is to evaluate the effectiveness of rbcL and matK loci for 16 species of Cucurbitaceae family by using in silico approach. For analysis, sequences were firstly retrieved from NCBI and then calculated for sequence parameters. Sequences were then aligned and constructed phylogenetic try and examined for species resolution ability. The obtained data show the variability of resolving capacity among species. rbcL region is suitable for distinguishing five species namely S. edule, M. cochinchinensis, L. aegyptiaca, C. melo, and C. pepo, whereas matK locus is more proper for different five species consisting of M. balsamina, M. cochinchinensis, M. charantia, S. edule, and C. sativus. The resolving power is improved sharply by analyzing the rbcL + matK combination with up to nine species consisting of C. lanatus, B. hispida, C. melo, C. sativus, C. pepo, C. agryrosperma, L. aegyptiaca, S. edule, and M. cochinchinensis. Therefore, the integration of rbcL and matK loci may improve the competence of assessing genetic relatedness at species level of members in Cucurbitaceae family. The obtained information could be important for choosing proper DNA barcode loci for phylogenetic study of this crop family.

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