scholarly journals Genetic Diversity Analysis of Cultivated Kappaphycus in Indonesian Seaweed Farms using COI Gene

2020 ◽  
Vol 15 (2) ◽  
pp. 65
Author(s):  
Pustika Ratnawati ◽  
Nova F Simatupang ◽  
Petrus R Pong-Masak ◽  
Nicholas A Paul ◽  
Giuseppe C Zuccarello
Keyword(s):  
Genetic Variation ◽  
Kappaphycus Alvarezii ◽  
Coi Gene ◽  
Morphological Examination ◽  
Bottom Line ◽  
Yield And Quality ◽  
Major Player ◽  
Coi Sequences ◽  
Trade Names ◽  
Prime End

Indonesia is a major player in the aquaculture of red algae, especially carrageenan producing ‘eucheumatoids’ such as Kappaphycus and Eucheuma. However, many current trade names do not reflect the evolutionary species and updated taxonomy, this is especially the case for eucheumatoid seaweeds that are highly variable in morphology and pigmentation. Genetic variation is also not known for the cultivated eucheumatoids in Indonesia. Therefore, this study aimed to determine the species and the level of genetic variation within species of cultivated eucheumatoids from various farms across Indonesia, spanning 150-1500 km, using the DNA barcoding method. Samples of seaweed were randomly collected at 14 farmed locations between April 2017 and May 2018. For this study the 5-prime end (~ 600 bp) of the mitochondrial-encoded cytochrome oxidase subunit one (COI) was amplified and sequenced. Morphological examination showed that the samples were quite variable in branching pattern and color. All samples collected from farms with floating line cultivation were identified based on COI sequences as Kappaphycus alvarezii and showed no variation in the COI gene. One farm sample with bottom-line cultivation was identified as K. striatus. The low genetic variation is in contrast to the phenotypic variation of samples, indicating that variation and phenotypic responses to environments is still found in samples with implications for growth rates and carrageenan yield and quality. Information about the genetic variation in stocks is important base knowledge for maintaining, expanding and continuing seaweed aquaculture.

scholarly journals Phylogeography of cliff racer (Platyceps rhodorachis Jan, 1865) from Punjab, Pakistan

2023 ◽  
Vol 83 ◽  
Author(s):  
S. Malik ◽  
A. Javid ◽  
Hamidullah ◽  
M. A. Iqbal ◽  
A. Hussain ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Species Identification ◽  
Dna Sequences ◽  
Large Scale ◽  
Coi Gene ◽  
Gene Sequences ◽  
Field Surveys ◽  
Coi Sequences

Abstract The present study reports the existence of cliff racer, Platyceps rhodorachis from the plains of Punjab, Pakistan. A total of 10 specimens were captured during the field surveys from June to September, 2018 from different sites of Punjab. Platyceps rhodorachis was identify on the basis of morphology and confirmed through COI gene sequences. The obtained DNA sequences have shown reliable and exact species identification. Newly produced DNA sequences of Platyceps rhodorachis were submitted to GenBank and accession numbers were obtained (MK936174.1, MK941839.1 and MT790210.1). N-J tree based on COI sequences of Platyceps rhodorachis clearly separated as out-group with other members of family Colubridae based on p-distance. The intra-specific genetic variation ranges from 12% to 18%. The DNA sequences of Platyceps rhodorachis kashmirensis, Platyceps rhodorachis ladacensis, Platyceps ventromaculatus, Platyceps ventromaculatus bengalensis and Platyceps ventromaculatus indusai are not available at NCBI to validate their taxonomic positions. In our recommendations, a large scale molecular based identification of Pakistan’s herpetofauna is required to report more new or subspecies from country.

scholarly journals Genetic variability and population structure of Leucinodes orbonalis (Guenée), a severe insect pest of brinjal in India

2022 ◽  
Vol 43 (1) ◽  
pp. 59-65
Author(s):  
K.G. Padwal ◽  
◽  
S. Chakravarty ◽  
C.P. Srivastava ◽  
◽  
...  
Keyword(s):  
Genetic Variation ◽  
Insect Pest ◽  
Geographical Location ◽  
Pcr Amplification ◽  
Haplotype Network ◽  
Coi Gene ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Leucinodes Orbonalis ◽  
Coi Sequences

Aim: The present study was undertaken to provide valuable insights regarding population genetic structure of Leucinodes orbonalis from diverse agro-ecologies of India. Methodology: Molecular characterization of L. orbonalis populations collected from five major agro-climatic zones of India was carried out using mitochondrial cytochrome oxidase I (COI) gene. Collected specimens were subjected to DNA extractions, partial PCR amplification and sequencing of the target gene, and multiple sequence alignments. Results: The results showed very less diversity in the nucleotide positions of the COI sequences of 79 studied specimens, with a low number of segregating sites (30), nucleotide diversity (0.00438) and overall mean genetic distance (0.004 ± 0.001). The significant negative values of neutrality tests and unimodal mismatch distribution supported the demographic expansion theory in Indian L. orbonalis. Analysis of the molecular variance revealed that 93.13% of the genetic variation was within populations, and the variation among populations was only 6.87%. The pairwise genetic differentiation was also found to be low to moderate between most of the populations. Multiple haplotypes were recorded from all the populations, and both neighbour-joining tree as well as the haplotype network showed that clustering of the haplotypes was independent of the geographical location. Interpretation: Thus, it can be inferred that Indian populations of L. orbonalis have very low genetic variation levels concerning the COI gene. There is a possible occurrence of stable inherited gene flow among populations, thereby reducing genetic variation in India.

scholarly journals Investigating the Parasitoid Community Associated with the Invasive Mealybug Phenacoccus solenopsis in Southern China

Insects ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 290
Author(s):  
Hua-Yan Chen ◽  
Hong-Liang Li ◽  
Hong Pang ◽  
Chao-Dong Zhu ◽  
Yan-Zhou Zhang
Keyword(s):  
Biological Control ◽  
Species Delimitation ◽  
Southern China ◽  
Insect Pest ◽  
Integrated Approach ◽  
Molecular Data ◽  
Coi Gene ◽  
Morphological Examination ◽  
Accurate Identification ◽  
Phenacoccus Solenopsis

The cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), is an emerging invasive insect pest in China. Hymenopteran parasitoids are the key organisms for suppressing populations of P. solenopsis in the field, and therefore could be used as biological agents. Accurate identification of the associated parasitoids is the critical step to assess their potential role in biological control. In this study, we facilitated the identification of the parasitoid composition of P. solenopsis using an integrated approach of species delimitation, combining morphology with molecular data. Eighteen Hymenoptera parasitoid species belonging to 11 genera of four families are recognized based on morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene and the 28S rDNA using the automatic barcode gap discovery (ABGD) and the Bayesian Poisson tree processes model (bPTP). Among these species, eight species are primary parasitoids with Aenasius arizonensis (Girault) (Hymenoptera: Encyrtidae) being the dominant taxon, while the other 10 species are probably hyperparasitoids, with a prevalence of Cheiloneurus nankingensis Li & Xu (Hymenoptera: Encyrtidae). These results indicate that parasitoid wasps associated with P. solenopsis from China are diverse and the integrated taxonomic approach applied in this study could enhance the accurate identification of these parasitoids that should be assessed in future biological control programs.

scholarly journals Markers of Genetic Variation in Blue Gourami (Trichogaster trichopterus) as a Model for Labyrinth Fish

Biology ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 228
Author(s):  
Gad Degani ◽  
Isana Veksler-Lublinsky ◽  
Ari Meerson
Keyword(s):  
Growth Hormone ◽  
Genetic Variation ◽  
Genetic Markers ◽  
Basic Research ◽  
Coi Gene ◽  
12S Rrna ◽  
Rrna Gene ◽  
Somatotropic Axis ◽  
Genes Encoding ◽  
Growth And Reproduction

Markers of genetic variation between species are important for both applied and basic research. Here, various genes of the blue gourami (Trichogaster trichopterus, suborder Anabantoidei, a model labyrinth fish), many of them involved in growth and reproduction, are reviewed as markers of genetic variation. The genes encoding the following hormones are described: kisspeptins 1 and 2, gonadotropin-releasing hormones 1, 2, and 3, growth hormone, somatolactin, prolactin, follicle- stimulating hormone and luteinizing hormone, as well as mitochondrial genes encoding cytochrome b and 12S rRNA. Genetic markers in blue gourami, representing the suborder Anabantoidei, differ from those in other bony fishes. The sequence of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene of blue gourami is often used to study the Anabantoidei suborder. Among the genes involved in controlling growth and reproduction, the most suitable genetic markers for distinguishing between species of the Anabantoidei have functions in the hypothalamic–pituitary–somatotropic axis: pituitary adenylate cyclase-activating polypeptide and growth hormone, and the 12S rRNA gene.

scholarly journals Genetic variation of COI gene of Hippa admirabilis in Northern Sulawesi

2021 ◽  
Vol 744 (1) ◽  
pp. 012060
Author(s):  
V W Putri ◽  
F Fahri ◽  
Y Wardiatno ◽  
A Farajallah
Keyword(s):  
Genetic Variation ◽  
Coi Gene

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav K Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

scholarly journals Genetic Variability for Yield and Nutritional Quality in Yam Bean (Pachyrhizus sp.)

HortScience ◽  
2016 ◽  
Vol 51 (9) ◽  
pp. 1079-1086 ◽  
Author(s):  
Rolland Agaba ◽  
Phinehas Tukamuhabwa ◽  
Patrick Rubaihayo ◽  
Silver Tumwegamire ◽  
Andrew Ssenyonjo ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Dry Matter ◽  
Dry Matter Content ◽  
Quality Traits ◽  
Storage Root ◽  
Storage Roots ◽  
High Dry Matter ◽  
Yield And Quality ◽  
Coefficients Of Variation

The amount of genotypic and phenotypic variability that exists in a species is important for selection and initiating breeding programs. Yam bean is grown locally in tropical countries of the Americas and Asia for their tasty storage roots, which usually have low dry matter content. The crop was recently introduced in Uganda and other East and Central African countries to supplement iron (Fe) and protein content in diets. This study aimed to estimate genetic variability for root yield and quality traits among 26 yam bean accessions in Uganda. A randomized complete block design was used with two replications across two ecogeographical locations and two seasons during 2012 and 2013. Near-infrared reflectance spectroscopy (NIRS) was used to determine quality of storage root samples. Significant differences among genotypes were observed for all traits except root protein, zinc (Zn), and phosphorus contents. Genotypic variance components () were significant for storage root fresh yield (SRFY), storage root dry matter (SRDM), storage root dry yield (SRDY), vine yield (VNY), fresh biomass yield (FBY), and storage root starch (STA) and Fe contents. For traits with significant the broad sense heritability estimates ranged from 58.4% for SRDY to 83.6% for FBY; and phenotypic coefficients of variation were high for SRFY (66%), SRDY (53.3%), VNY (60.5%), and FBY (59%), but low to medium for SRDM (22.6%), STA (15.1%), and Fe (21.3%). Similarly, the genotypic coefficients of variation were high for SRFY (56.7%), SRDY (53.3%), VNY (55%), and FBY (53.9%); and low for SRDM (20%), STA (12.4%), and Fe (17.8%). There were strong positive correlations between SRFY and both SRDY (r = 0.926) and FBY (r = 0.962), but low-to-moderate correlations among quality traits. It should be possible to breed for high dry matter yam beans by using low dry matter accessions due to the observed genetic variation ( = 9.3%2), which is important if the high dry matter Pachyrhizus tuberosus accessions (known as chuin) from Peru cannot be accessed. This study indicated substantial genetic variation for yield and quality traits in yam bean, demonstrating potential for adaptability to growing conditions and consumer needs in East and Central Africa and for genetic improvement through selection.

New species of Sargassum-boring Limnoria Leach, 1814 (Crustacea, Isopoda, Limnoriidae) from Japan

Zootaxa ◽  
2021 ◽  
Vol 4970 (1) ◽  
pp. 119-130
Author(s):  
HIROKI YOSHINO ◽  
YURIKO KAMBARA ◽  
SHOTA KAJIWARA ◽  
TAKESHI A. OHSAWA
Keyword(s):  
New Species ◽  
The Other ◽  
Coi Gene ◽  
Congeneric Species ◽  
Japanese Species ◽  
Mitochondrial Coi ◽  
Chiba Prefecture ◽  
Mitochondrial Coi Gene ◽  
Mandibular Palp ◽  
Coi Sequences

A new marine Sargassum-boring species of Limnoria (Limnoriidae) is described on the basis of specimens obtained at Kamogawa-shi, Chiba Prefecture, Japan. Limnoria aspera sp. nov. shares a reduced mandibular palp to a seta, algal-feeding, and the clavate shaped epipod of the maxilliped with the other species of non-mandibular-palp group. L. aspera sp. nov. differs morphologically from the congeneric species by secondary unguis of pereopods and unique carinae of pleonite 5 and pleotelson. We describe the sequences of the mitochondrial COI gene and the nuclear 28S rDNA gene. L. aspera sp. nov. differs by 14.2–18.0% in p-distance based on COI sequences from other Japanese species, L. furca and L. nagatai. 

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