scholarly journals Morphological and Molecular Identification of Three Ceriodaphnia Species (Cladocera: Daphniidae) from Australia

2014 ◽  
Vol 2014 ◽  
pp. 1-14
Author(s):  
Pranay Sharma
Keyword(s):  
Molecular Identification ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Species Discrimination ◽  
Morphological Attributes ◽  
Mitochondrial Markers ◽  
Coi Sequences ◽  
High Degree ◽  
One New Species

Australian Ceriodaphnia (Cladocera: Daphniidae) are examined using morphological attributes and two mitochondrial DNA (COI and 16s) and one nuclear DNA (28s) gene fragments to differentiate the species. The sequence data supports the existence of three species, that is, C. dubia, one reinstated species C. spinata Henry, 1919, and one new species C. sp. 1. Morphological characteristics were also able to accurately separate the three species. Furthermore, genetic analysis of COI sequences from Ceriodaphnia supported three clades. The high degree of correlation between morphological and molecular identification in this study indicates that mitochondrial markers, COI and 16s, are appropriate molecular markers for species discrimination and identification of Ceriodaphnia.

Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data

Zootaxa ◽  
2013 ◽  
Vol 3608 (1) ◽  
pp. 67-74 ◽  
Author(s):  
Chris J. LAW ◽  
KELLY M. DORGAN ◽  
GREG W. ROUSE
Keyword(s):  
Dna Sequence ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Hemoglobin Concentration ◽  
Sympatric Species ◽  
Sandy Beaches ◽  
Additional Species ◽  
Dna Sequence Data ◽  
C Subunit ◽  
Coi Sequences

Thoracophelia (Annelida, Opheliidae) are burrowing deposit feeders generally found in the mid- to upper intertidal areas of sandy beaches. Thoracophelia mucronata (Treadwell, 1914) is found along the west coast of North America, including at Dillon Beach, CA. Two additional species, Thoracophelia dillonensis (Hartman, 1938) and T. williamsi (Hartman, 1938) were also described from this beach. These three sympatric species have been primarily distinguished by branchial morphology, and efforts to determine the validity of the species have been based on morphological, reproductive and ecological studies. Here we demonstrate using mitochondrial and nuclear DNA sequence data that these three species are valid. Mitochondrial Cytochrome c subunit 1 (COI) sequences show uncorrected interspecific distances of ~9–13%. We found no inter—specific differences in body color or in hemoglobin concentration, but found that reproductive males were pinkish-red in color and had lower hemoglobin concentrations than purplish—red reproductive females.

scholarly journals Molecular identification of Auxis spp. larvae (Pisces: Scombridae) from the Gulf of California: Solving morphological identification limits

2018 ◽  
Vol 53 (2) ◽  
pp. 157 ◽  
Author(s):  
María J. Ochoa-Muñoz ◽  
Noé Díaz-Viloria ◽  
Laura Sánchez-Velasco ◽  
Sylvia P. A. Jiménez-Rosenberg ◽  
Ricardo Pérez-Enríquez
Keyword(s):  
Molecular Identification ◽  
Gulf Of California ◽  
Fish Larvae ◽  
Morphological Characteristics ◽  
Species Level ◽  
Morphological Identification ◽  
Larval Stages ◽  
Marine Fish Larvae ◽  
Coi Sequences ◽  
First Time

The larvae of the Auxis genus are abundant in the Gulf of California during summer; however, their identification to the species level by morphological methods is a challenge. The goal of this study was to identify A. thazard and A. rochei larvae for first time, through molecular markers using COI sequences of mtDNA, and look for distinctive morphological characteristics between species, mainly in pigmentation patterns. Larvae were obtained by zooplankton tows in 3 oceanographic cruises in the southern Gulf of California and adjacent waters. The presence of A. thazard and A. rochei larvae was genetically confirmed. The sequences of 7 larvae showed genetic divergences lower than 1% when were compared to sequences of A. thazard adults, while 15 larvae showed genetic divergences lower than 2% when where compared to sequences of A. rochei adults. Genetic divergences between both Auxis species were higher than 2%. These results suggest the spawning of both species in the Gulf of California. On the other hand, pigmentation patterns and morphometric characteristics, in all larval stages, did not permit the secure differentiation between species. Thus, the use of molecular identification by COI is recommended to identify Auxis larvae to the species level, as well as in other marine fish larvae collected in other regions of the world, that have identification troubles.

Additions to Karst Fungi 4: Botryosphaeria spp. associated with woody hosts in Guizhou province, China including B. guttulata sp. nov.

Phytotaxa ◽  
2020 ◽  
Vol 454 (3) ◽  
pp. 186-202
Author(s):  
YA-YA CHEN ◽  
ASHA J. DISSANAYAKE ◽  
ZUO-YI LIU ◽  
JIAN-KUI (JACK) LIU
Keyword(s):  
Plant Pathogens ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Abundant Species ◽  
Molecular Data ◽  
Nature Reserves ◽  
Guizhou Province ◽  
Botryosphaeria Dothidea ◽  
Wide Range ◽  
One New Species

Members of Botryosphaeria encompass important plant pathogens, saprobes and endophytes on a wide range of woody hosts worldwide. Botryosphaeria species are difficult to differentiate due to the overlapping morphological characteristics and the molecular data analyses are necessary recently when species identification is carried out. In this study, 28 Botryosphaeria isolates were obtained from decaying woody hosts in six nature reserves in Guizhou province, China. Based on both morphological characteristics and molecular analysis of combined ITS and tef1-α sequence data, four known species (Botryosphaeria dothidea, B. minutispermatia, B. sinensia and B. wangensis) are identified and one new species B. guttulata is introduced. Botryosphaeria sinensia (32% of the isolates obtained from various hosts) is the abundant species, followed by B. dothidea (28.5% of the isolates), B. guttulata (28.5% of the isolates), B. minutispermatia (7% of the isolates) and B. wangensis (4% of the isolates). These results represent the first study of Botryosphaeria species associated with woody hosts from nature reserves in Guizhou province, China. Our findings indicate that there is a potential of Botryosphaeria species remain to be discovered in this unique landform (Karst formations) in Guizhou province, China.

Revision and phylogeny of the subaptera-group of Phyllodromica (Blattoptera: Blattellidae: Ectobiinae), including a parthenogenetic species and the evaluation of COI sequences for species identification (DNA barcoding)

Zootaxa ◽  
2007 ◽  
Vol 1522 (1) ◽  
pp. 1-68 ◽  
Author(s):  
THOMAS KNEBELSBERGER ◽  
MICHAEL A. MILLER
Keyword(s):  
Species Identification ◽  
Dna Sequences ◽  
Sequence Data ◽  
Cladistic Analysis ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Coi Gene ◽  
Parthenogenetic Species ◽  
Mediterranean Countries ◽  
Coi Sequences

Until recently the subaptera-group of Phyllodromica contained only one species. The revision of the subaptera-group  herein consists of the two newly described bisexual species, P. iberica and P. quadracantha, endemic to the Iberian Peninsula and a parthenogenetic species, P. subaptera (Rambur, 1838), which is widely distributed over most of the Mediterranean countries and islands. Within P. iberica three conspecific morphotypes are distinguished. The morphological characteristics of the subaptera-group are described. The species and their distributions are described and depicted. A key for the morphological determination of P. quadracantha and the morphotypes of P. iberica is given. DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene are included in the species descriptions. The sequence data are suitable for species identification (DNA barcodes). A cladistic analysis of the morphological data and a phylogenetic analysis of the DNA sequences were performed to infer the phylogenetic relationships between the species of the subaptera-group.

scholarly journals A Customised Target Capture Sequencing Tool for Molecular Identification of Aloe Vera and Relatives

2021 ◽  
Author(s):  
Yannick Woudstra ◽  
Juan Viruel ◽  
Martin Fritzsche ◽  
Thomas Bleazard ◽  
Ryan Mate ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Sequence Data ◽  
Aloe Vera ◽  
Nuclear Genes ◽  
Degraded Dna ◽  
Species Discrimination ◽  
High Coverage ◽  
Target Capture ◽  
Target Capture Sequencing ◽  
Capture Sequencing

Abstract Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives (Asphodelaceae, subfamily Alooideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With >600 species and an origin of ±15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.

Phylogeny and systematics of the Crocidura suaveolens species group: corroboration and controversy between nuclear and mitochondrial DNA markers / Phylogénie et systématique du groupe d'espèces Crocidura suaveolens: coordination et contradiction des marqueurs nucléaire et mitochondriaux de l'ADN

Mammalia ◽  
2006 ◽  
Vol 70 (1-2) ◽  
Author(s):  
Anna A. Bannikova ◽  
Vladimir S. Lebedev ◽  
Dmitri A. Kramerov ◽  
Mikhail V. Zaitsev
Keyword(s):  
Phylogenetic Relationships ◽  
Western Europe ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Distinct Species ◽  
Species Group ◽  
Systematic Research ◽  
Cyt B ◽  
Cyt B Gene

AbstractDespite obvious advances in systematic research on Palaearctic white-toothed shrews ( Crocidura ), phylogenetic relationships and species diagnosis of 40-chromosome species ( suaveolens sp. group) remain poorly understood. Phylogenetic relationships of these shrews were analyzed on the basis of two independent molecular markers: interspersed repeat PCR fingerprints (inter-SINE-PCR) and complete (1140 bp) or partial (∼400 bp) sequences of the mtDNA cyt b gene. According to these data, C. suaveolens from Western Europe (Italy) appeared distinct from samples of C. suaveolens from Eastern Europe and Mongolia, as well as a Siberian sample. mtDNA introgression of Eastern European C. suaveolens with C. gueldenstaedtii in their contact zone in the Tuapse region was revealed. Hybrydization between C. gueldenstaedtii and C. suaveolens resulted in the formation of a population, nuclear DNA and morphological characteristics typical for C. gueldenstaedtii , while the mitochondrial genome is assimilated from C. suaveolens . The population of the Talysh region of the Caucasus ( C. caspica ) represents a separate entity that is clearly distinguished from the populations of Georgia and Tuapse ( C. gueldenstaedtii ) and C. suaveolens . Therefore, the position of C. caspica as a full species is supported. The present analysis of both inter-SINE-PCR and cyt b sequence data revealed two major clades in Palaearctic 40-chromosome Crocidura . The eastern clade is formed by true C. suaveolens/C. sibirica , together with C. caspica , and the western clade is formed by Western European C. suaveolens , which should be treated as a distinct species, C. mimula and the closely related C. gueldenstaedtii.

scholarly journals A customised target capture sequencing tool for molecular identification of Aloe vera and relatives

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yannick Woudstra ◽  
Juan Viruel ◽  
Martin Fritzsche ◽  
Thomas Bleazard ◽  
Ryan Mate ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Sequence Data ◽  
Aloe Vera ◽  
Nuclear Genes ◽  
Degraded Dna ◽  
Species Discrimination ◽  
High Coverage ◽  
Target Capture ◽  
Target Capture Sequencing ◽  
Capture Sequencing

AbstractPlant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.

Phylogeny and systematics of the Crocidura suaveolens species group: corroboration and controversy between nuclear and mitochondrial DNA markers / Phylogénie et systématique du groupe d'espèces Crocidura suaveolens: coordination et contradiction des marqueurs nucléaire et mitochondriaux de l'ADN

Mammalia ◽  
2006 ◽  
Vol 70 (1-2) ◽  
Author(s):  
Anna A. Bannikova ◽  
Vladimir S. Lebedev ◽  
Dmitri A. Kramerov ◽  
Mikhail V. Zaitsev
Keyword(s):  
Phylogenetic Relationships ◽  
Western Europe ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Distinct Species ◽  
Species Group ◽  
Systematic Research ◽  
Cyt B ◽  
Cyt B Gene

AbstractDespite obvious advances in systematic research on Palaearctic white-toothed shrews ( Crocidura ), phylogenetic relationships and species diagnosis of 40-chromosome species ( suaveolens sp. group) remain poorly understood. Phylogenetic relationships of these shrews were analyzed on the basis of two independent molecular markers: interspersed repeat PCR fingerprints (inter-SINE-PCR) and complete (1140 bp) or partial (∼400 bp) sequences of the mtDNA cyt b gene. According to these data, C. suaveolens from Western Europe (Italy) appeared distinct from samples of C. suaveolens from Eastern Europe and Mongolia, as well as a Siberian sample. mtDNA introgression of Eastern European C. suaveolens with C. gueldenstaedtii in their contact zone in the Tuapse region was revealed. Hybrydization between C. gueldenstaedtii and C. suaveolens resulted in the formation of a population, nuclear DNA and morphological characteristics typical for C. gueldenstaedtii , while the mitochondrial genome is assimilated from C. suaveolens . The population of the Talysh region of the Caucasus ( C. caspica ) represents a separate entity that is clearly distinguished from the populations of Georgia and Tuapse ( C. gueldenstaedtii ) and C. suaveolens . Therefore, the position of C. caspica as a full species is supported. The present analysis of both inter-SINE-PCR and cyt b sequence data revealed two major clades in Palaearctic 40-chromosome Crocidura . The eastern clade is formed by true C. suaveolens/C. sibirica , together with C. caspica , and the western clade is formed by Western European C. suaveolens , which should be treated as a distinct species, C. mimula and the closely related C. gueldenstaedtii.

Redescription of Orthopristis ruber and Orthopristis scapularis (Haemulidae: Perciformes), with a hybridization zone off the Atlantic coast of South America

Zootaxa ◽  
2019 ◽  
Vol 4576 (1) ◽  
pp. 109 ◽  
Author(s):  
ALEXANDRE PIRES MARCENIUK ◽  
RODRIGO ANTUNES CAIRES ◽  
LEONARDO MACHADO ◽  
NAJILA NOLIE CATARINE DANTAS CERQUEIRA ◽  
RAYLA ROBERTA M. DE S. SERRA ◽  
...  
Keyword(s):  
South America ◽  
Nuclear Dna ◽  
Atlantic Coast ◽  
Morphological Characteristics ◽  
Distinct Species ◽  
Valid Species ◽  
Brazilian Coast ◽  
Northern Coast ◽  
Western Atlantic ◽  
Coloration Patterns

The genus Orthopristis includes seven valid species, three from the western Atlantic and five from eastern Pacific, while the available identification guides and taxonomic keys incorrectly recognize Orthopristis ruber as the only valid species found on the Atlantic coast of South America. Efforts to expand the inventory of fish species from the northern coast of Brazil led to the identification of two distinct species of Orthopristis from Atlantic South America, based on the analysis of coloration patterns and meristic data, as well as DNA. In the present study, the limits of Orthopristis ruber are reviewed, while Orthopristis scapularis is recognized as a valid species for the northern and northeastern coasts of South America. Based on intermediate morphological characteristics and nuclear DNA markers, a hybrid zone was identified off the state of Espírito Santo, on the eastern Brazilian coast. Additionally, considerations are made on the diversity and biogeography of the coastal marine and estuarine fishes found on the Brazilian coast. 

scholarly journals Phylogeny and Taxonomical Investigation ofTrichodermaspp. from Indian Region of Indo-Burma Biodiversity Hot Spot Region with Special Reference to Manipur

2015 ◽  
Vol 2015 ◽  
pp. 1-21 ◽  
Author(s):  
Th. Kamala ◽  
S. Indira Devi ◽  
K. Chandradev Sharma ◽  
K. Kennedy
Keyword(s):  
Sequence Data ◽  
Hot Spot ◽  
Morphological Characteristics ◽  
Indian Region ◽  
Agricultural Practice ◽  
Phenotypic Data ◽  
Unique Region ◽  
Seedborne Pathogens ◽  
Fungal Phytopathogens ◽  
Agroclimatic Zones

Towards assessing the genetic diversity and occurrence ofTrichodermaspecies from the Indian region of Indo-Burma Biodiversity hotspot, a total of 193Trichodermastrains were isolated from cultivated soils of nine different districts of Manipur comprising 4 different agroclimatic zones. The isolates were grouped based on the morphological characteristics. ITS-RFLP of the rDNA region using three restriction digestion enzymes: Mob1, Taq1, and Hinf1, showed interspecific variations among 65 isolates ofTrichoderma. Based on ITS sequence data, a total of 22 different types of representativeTrichodermaspecies were reported and phylogenetic analysis showed 4 well-separated main clades in whichT. harzianumwas found to be the most prevalent spp. among all theTrichodermaspp. Combined molecular and phenotypic data leads to the development of a taxonomy of all the 22 differentTrichodermaspp., which was reported for the first time from this unique region. All these species were found to produce different extrolites and enzymes responsible for the biocontrol activities against the harmful fungal phytopathogens that hamper in food production. This potential indigenousTrichodermaspp. can be targeted for the development of suitable bioformulation against soil and seedborne pathogens in sustainable agricultural practice.

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