scholarly journals Record of Copepod Parasite (Pennellidae) in Buccal Cavity and Gill Arch of Cultured Groupers, Epinephelus spp. in Batam, Indonesia

2021 ◽  
Vol 34 (4) ◽  
Author(s):  
ENDANG WIJAYANTI ◽  
◽  
INDAH ISTIQOMAH ◽  
MURWANTOKO MURWANTOKO
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Buccal Cavity ◽  
Gill Arch ◽  
Group Method ◽  
Local Alignment ◽  
Cox1 Gene ◽  
Copepod Parasite ◽  
Adult Copepod ◽  
Hybrid Grouper

The crustacean parasites are the most frequently encountered and cause significant economic loss in mariculture. These parasites infect fish fin, skin, gills, and buccal cavity. This study aims to describe copepod parasite in the buccal cavity of cultured groupers, Epinephelus spp., from Batam waters using morphological and molecular biology approaches. The tiger grouper, Epinephelus fuscoguttatus (Forsskal, 1775), and hybrid grouper, Epinephelus sp. showing lethargy and skin darkening were collected from sea cages. The parasite’s morphology was observed using light and scanning electron microscopes. The genomic DNA was isolated from the parasites and used as a template for amplification of cytochrome oxidase subunit-1 (Cox1) gene and followed by sequencing. The fish exhibited red nodules in the mouth cavity, on the lips, and gill arch in varying numbers and size of nodules. The copepodid, chalimus, and adult copepod stages were found from the nodule. Based on the presence of the oral cone, this parasite belonged to Siphonostomatoida order of copepods. Based on the structure of the caudal ramus with four long and four short setae, the first and second pair legs as biramous, and the third pair leg as uniramous, this parasite belonged to Pennellidae family of copepods. Basic local alignment search tool analysis of this Cox1 showed low homology within 80%, indicating that the DNA sequences of the parasite species were not reported in the GenBank. The unweighted pair group method using arithmetic average phylogenetic trees supported that this parasite belonged to the family Pennellidae. This is the first report on the pennellid parasite infection in the buccal cavity and gill arch of cultured groupers in Batam, Indonesia.

scholarly journals Morphological, phytochemical and molecular characterization of five common Jatropha species in the Niger Delta Region of Nigeria

2021 ◽  
Vol 25 (9) ◽  
pp. 1637-1644
Author(s):  
B.A. Odogwu ◽  
J. Ukomadu ◽  
I. Igwe
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Evolutionary Genetics ◽  
Morphological Data ◽  
Local Alignment ◽  
Phylogenetic Cluster ◽  
Niger Delta Region ◽  
Search Tool ◽  
Improvement Programs ◽  
Phylogenetic Cluster Analysis

The economic and medicinal important genus Jatropha contains many distinctly different species. To elucidate the genetic relationship of five common occurring Jatropha species namely J. multifida, J. podagrica, J.tanjorernsis, J. curcas, and J. gossypifolia, thirty-nine morphological, six phytochemical features and one arbitrary marker was used to screen and explore their similarity. Morphological data was obtained from the measurement of vegetative and reproductive parts while the presence of five phytochemicals was determined using differentphytochemical tests. The DNA of all five Jatropha species were amplified and sequenced using Ribolose 1, 5- biphosphate carboxylase molecular marker. The DNA sequences were then aligned using the Basic Local Alignment Search Tool for nucleotide 2.8.0 version of the National Center for Biotechnology Information database and phylogenetic trees were constructed using Paleontological Statistical software and Molecular Evolutionary Genetics Analysis version 7.0.26 software. From the results of the classical and phylogenetic cluster analysis, the five Jatropha species was separated into two major clusters. The highly distinctive J. gossypifolia was the only species that clustered separately from the other Jatropha species. Although, J. tanjorensis has been reported to be a hybrid from J. curcas and J. gossypifolia, the species did not segregate and cluster with these species, but segregated with J. multifida, and J.podagrica, indicating that this species is more closely related to J. multifida, and J. podagrica than J. curcas and J.gossypifolia. The result therefore provide information that would be useful in the plant improvement programs for the genus Jatropha.

Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences

2014 ◽  
Vol 80 ◽  
pp. 54-65 ◽  
Author(s):  
Xiaoyan Zheng ◽  
Danying Cai ◽  
Daniel Potter ◽  
Joseph Postman ◽  
Jing Liu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees

scholarly journals Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose
Keyword(s):  
Simple Sequence Repeats ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
High Level ◽  
Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

An integrated approach for synonymization of Rotylenchus rhomboides with R. goodeyi (Nematoda: Hoplolaimidae) reveals high intraspecific mitogenomic variation

2021 ◽  
Author(s):  
Phougeishangbam Rolish Singh ◽  
Bart van de Vossenberg ◽  
Katarzynar Rybarczyk-Mydłowska3 ◽  
Magdalena Kowalewska-Groszkowska ◽  
Wim Bert ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Integrated Approach ◽  
Morphological Characters ◽  
Molecular Data ◽  
Cox1 Gene ◽  
Protein Coding ◽  
Genome Shotgun Sequence ◽  
Important Character ◽  
Rna Genes ◽  
Level Identification

Rotylenchus is a widely-distributed economically important plant-parasitic nematode group whose species-level identification relies largely on limited morphological characters including character-based tabular keys and molecular data of ribosomal and mitochondrial genes. In this study, a combined morphological and molecular analysis of three populations of R. goodeyi from Belgium, Poland and the Netherlands revealed important character variations of this species leading to synonymisation of R. rhomboides with R. goodeyi, and a high nucleotide variation within cox1 gene sequences in these populations. Additional Illumina sequencing of DNA from individuals of the Dutch population revealed two variants of mitogenomes each of approximately 23 Kb in size, differing by about 9% and containing eleven protein coding genes, two ribosomal RNA genes and up to 29 transfer RNA genes. In addition to the first representative whole genome shotgun sequence datasets of the genus Rotylenchus, this study also provides the full length mitogenome and the ribosomal DNA sequences of R. goodeyi.

Higher-order Markov models for metagenomic sequence classification

2020 ◽  
Vol 36 (14) ◽  
pp. 4130-4136
Author(s):  
David J Burks ◽  
Rajeev K Azad
Keyword(s):  
Dna Sequences ◽  
Markov Models ◽  
Fragment Size ◽  
Higher Order ◽  
Training Data ◽  
Supplementary Information ◽  
Local Alignment ◽  
Metagenomic Sequence ◽  
Higher Order Models

Abstract Motivation Alignment-free, stochastic models derived from k-mer distributions representing reference genome sequences have a rich history in the classification of DNA sequences. In particular, the variants of Markov models have previously been used extensively. Higher-order Markov models have been used with caution, perhaps sparingly, primarily because of the lack of enough training data and computational power. Advances in sequencing technology and computation have enabled exploitation of the predictive power of higher-order models. We, therefore, revisited higher-order Markov models and assessed their performance in classifying metagenomic sequences. Results Comparative assessment of higher-order models (HOMs, 9th order or higher) with interpolated Markov model, interpolated context model and lower-order models (8th order or lower) was performed on metagenomic datasets constructed using sequenced prokaryotic genomes. Our results show that HOMs outperform other models in classifying metagenomic fragments as short as 100 nt at all taxonomic ranks, and at lower ranks when the fragment size was increased to 250 nt. HOMs were also found to be significantly more accurate than local alignment which is widely relied upon for taxonomic classification of metagenomic sequences. A novel software implementation written in C++ performs classification faster than the existing Markovian metagenomic classifiers and can therefore be used as a standalone classifier or in conjunction with existing taxonomic classifiers for more robust classification of metagenomic sequences. Availability and implementation The software has been made available at https://github.com/djburks/SMM. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Spatial distribution of the copepod parasite Lernanthropus kroyeri on the gills of bass, Dicentrarchus labrax (L.)

1980 ◽  
Vol 60 (4) ◽  
pp. 1061-1067 ◽  
Author(s):  
J. T. Davey
Keyword(s):  
Spatial Distribution ◽  
Dicentrarchus Labrax ◽  
Gill Arch ◽  
Single Site ◽  
Copepod Parasite ◽  
Gill Parasites ◽  
External Face

Young estuarine bass of the 1976 and 1977 year classes were examined for gill parasites between February 1978 and June 1979. 344 specimens of the copepod Lernanthropus kroyeri were recovered from 177 of 289 fish. The distribution of the copepods on the gills showed clear preferences for site of attachment. With 48 such sites delineated per fish, 143 of 183 female copepods favoured a single site – the internal face of the medial sector of the posterior hemibranch of the second gill arch. 57 of 161 male copepods chose attachment to the external face of the medial sector of the anterior hemibranch of the second gill arch. Only seven copepods in all were found attached at any of the twelve possible sites on the first gill arch, and none at all at the six possible sites on the posterior hemibranch of the fourth gill arch. Explanations for the observed distribution are discussed in terms of the strength of the branchial ventilation currents over the different gills coupled with observations on the special respiratory adaptations of these parasites.

Localization of receptors causing hypoxic bradycardia in trout (Salmo gairdneri)

1978 ◽  
Vol 56 (6) ◽  
pp. 1260-1265 ◽  
Author(s):  
Frank M. Smith ◽  
David R. Jones
Keyword(s):  
Oxygen Tension ◽  
Buccal Cavity ◽  
Cranial Nerves ◽  
Gill Arch ◽  
Cardiac Response ◽  
Salmo Gairdneri ◽  
Acclimation Temperature ◽  
Tongue Depressor ◽  
Hypoxic Water ◽  
Biological Advantage

Receptors causing the cardiac response to environmental hypoxia have been located in rainbow trout (Salmo gairdneri). Intact, unrestrained trout, acclimated to7or 16 °C. showed a marked increase in ventilation and bradycardia when exposed to hypoxia at their acclimation temperature, In experiments designed to locate the site of receptors causing hypoxic bradycardia, the buccal cavity of a fish was divided into two chambers by a tongue depressor, allowing oxygen tension of water flowing over each set of gills lo be varied independently. Irrigating one set of gills with hypoxic water [Formula: see text] while flowing hyperoxic water [Formula: see text] over the other caused heart rate to fall from 42.2 ± 0.6 (± SEM) to 26.4 ± 0.5 (± SEM) beats/min after 1 min of hypoxic water flow. Dorsal aortic [Formula: see text] was always above that recorded when both sets of gills were flushed with normoxic water [Formula: see text]. Bilateral ligation of the efferent pseudobranch artery and the pseudobranch nerve (cranial nerve IX) had no effect on the cardiac response to irrigation of one set of gills by hypoxic water. Physical removal of, or section of the nerve supply (cranial nerves IX and X) to, the first gill arch eliminated hypoxic bradycardia. The biological advantage of hypoxic bradycardia is discussed and it is suggested that gill arch receptors may function to monitor and maintain oxygen tension of blood leaving the gills.

scholarly journals Jumping through the hoops: the challenges of daffodil (Narcissus) classification

2019 ◽  
Vol 190 (4) ◽  
pp. 389-404 ◽  
Author(s):  
Kálmán Könyves ◽  
John David ◽  
Alastair Culham
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Plastid Dna ◽  
Microsatellite Data ◽  
Population Sampling ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Nuclear Microsatellite ◽  
Congruent Group ◽  
First Time

Abstract Hoop-petticoat daffodils are a morphologically congruent group comprised of two distinct lineages in molecular phylogenetic trees of Narcissus. It is possible that the morphological similarity is a product of both historic and current low-level gene flow between these lineages. For the first time, we report population sampling from across the entire range of distribution covering the Iberian Peninsula and Morocco. In total, 455 samples were collected from 59 populations. Plastid DNA sequences of matK and ndhF were generated alongside 11 microsatellite loci to permit comparison between plastid and nuclear lineage histories. The plastid DNA phylogenetic tree was highly congruent with previous molecular studies and supported the recognition of these two lineages of hoop-petticoat daffodils as separate sections. Assignment of samples to sections sometimes differed between plastid DNA and (nuclear) microsatellite data. In these cases, the taxa had previously been the focus of dissent in taxonomic placement based on morphology. These discrepancies could be explained by hybridization and introgression among the two lineages during the evolution of hoop-petticoat daffodils, and shows that placement of species in sections is dependent on the source of data used. This study underlines the complex evolutionary history of Narcissus and highlights the discrepancies between floral morphology and phylogeny, which provides a continuing challenge for the systematics of Narcissus.

Phylogeny and higher classification of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea)*

Zootaxa ◽  
2007 ◽  
Vol 1668 (1) ◽  
pp. 413-425 ◽  
Author(s):  
P. J. GULLAN ◽  
L. G. COOK
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nuclear Dna ◽  
Sister Group ◽  
Scale Insect ◽  
Scale Insects ◽  
Morphological Data ◽  
Adult Males ◽  
Plant Feeding ◽  
Phylogenetic Studies

The superfamily Coccoidea contains nearly 8000 species of plant-feeding hemipterans comprising up to 32 families divided traditionally into two informal groups, the archaeococcoids and the neococcoids. The neococcoids form a monophyletic group supported by both morphological and genetic data. In contrast, the monophyly of the archaeococcoids is uncertain and the higher level ranks within it have been controversial, particularly since the late Professor Jan Koteja introduced his multi-family classification for scale insects in 1974. Recent phylogenetic studies using molecular and morphological data support the recognition of up to 15 extant families of archaeococcoids, including 11 families for the former Margarodidae sensu lato, vindicating Koteja’s views. Archaeococcoids are represented better in the fossil record than neococcoids, and have an adequate record through the Tertiary and Cretaceous but almost no putative coccoid fossils are known from earlier. In contrast, the sister group of the scale insects (Aphidoidea) has a more informative Jurassic and Triassic record. Relationships among most scale insect families are unresolved in phylogenetic trees based on nuclear DNA sequences, and most nodes in trees based on morphological data, including those from adult males, are poorly supported. Within the neococcoids, the Eriococcidae is not monophyletic and the monophyly of the Coccidae and Diaspididae may be compromised by the current family-level recognition of a few species-poor autapomorphic groups.

scholarly journals A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini)

Zootaxa ◽  
2020 ◽  
Vol 4748 (1) ◽  
pp. 182-194 ◽  
Author(s):  
JING ZHANG ◽  
ERNST BROCKMANN ◽  
QIAN CONG ◽  
JINHUI SHEN ◽  
NICK V. GRISHIN
Keyword(s):  
Dna Sequences ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Type Specimens ◽  
African Species ◽  
Protein Coding ◽  
Coding Regions ◽  
As Species ◽  
Close Relatives ◽  
Genomic Regions

We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe, 1912, Gomalia Moore, 1879, Carcharodus Hübner, [1819] and Muschampia Tutt, 1906) form a monophyletic group that we call a subtribe Carcharodina Verity, 1940. In the phylogenetic trees built from various genomic regions, these species form 7 (not 4) groups that we treat as genera. We find that Muschampia Tutt, 1906 is not monophyletic, and the 5th group is formed by currently monotypic genus Favria Tutt, 1906 new status (type species Hesperia cribrellum Eversmann, 1841), which is sister to Gomalia. The 6th and 7th groups are composed of mostly African species presently placed in Spialia. These groups do not have names and are described here as Ernsta Grishin, gen. n. (type species Pyrgus colotes Druce, 1875) and Agyllia Grishin, gen. n. (type species Pyrgus agylla Trimen, 1889). Two subgroups are recognized in Ernsta: the nominal subgenus and a new one: Delaga Grishin, subgen. n. (type species Pyrgus delagoae Trimen, 1898). Next, we observe that Carcharodus is not monophyletic, and species formerly placed in subgenera Reverdinus Ragusa, 1919 and Lavatheria Verity, 1940 are here transferred to Muschampia. Furthermore, due to differences in male genitalia or DNA sequences, we reinstate Gomalia albofasciata Moore, 1879 and Gomalia jeanneli (Picard, 1949) as species, not subspecies or synonyms of Gomalia elma (Trimen, 1862), and Spialia bifida (Higgins, 1924) as a species, not subspecies of Spialia zebra (Butler, 1888). Sequencing of the type specimens reveals 2.2-3.2% difference in COI barcodes, the evidence that combined with wing pattern differences suggests a new status of a species for Spialia lugens (Staudinger, 1886) and Spialia carnea (Reverdin, 1927), formerly subspecies of Spialia orbifer (Hübner, [1823]). 

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