scholarly journals Development and Characterization of Microsatellite Markers in The Small Indian Mongoose (Urva Auropunctata)

2021 ◽  
Author(s):  
Takuma Sato ◽  
Takamichi Jogahara
Keyword(s):  
Invasive Alien Species ◽  
Sex Identification ◽  
Individual Identification ◽  
The Novel ◽  
Genome Wide ◽  
Ssr Loci ◽  
Hardy Weinberg Equilibrium ◽  
Indian Mongoose ◽  
Small Indian Mongoose

Abstract The small Indian mongoose (Urva auropunctata) is listed among 100 of the World’s Worst Invasive Alien Species and eradication programs are ongoing worldwide. The development of individual and sex identification markers will improve their management. Therefore, we searched for novel mongoose short simple repeat (SSR) markers using genome-wide screening and identified 115,265 tetra-nucleotide repeat loci. Of 96 loci tested, 17 were genotyped in 28 mongooses from the Okinawa population. The genetic diversity analysis showed that the average expected and observed heterozygosity and number of alleles were 0.55, 0.56, and 2.94, respectively. Of 17 loci, one deviated from Hardy–Weinberg equilibrium and six loci pairs were likely linked to each other. However, we succeed in identifying all individuals using all of the SSR loci. The novel sex identification markers worked successfully in a test using six known sex samples. These novel SSR and sex identification markers should be useful in studies of individual identification and population genetics of the mongoose.

scholarly journals Genome-wide characterization of SPL family in Medicago truncatula reveals the novel roles of miR156/SPL module in spiky pod development

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Hongfeng Wang ◽  
Zhichao Lu ◽  
Yiteng Xu ◽  
Lingcui Kong ◽  
Jianjun Shi ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
The Novel ◽  
Genome Wide ◽  
Pod Development

scholarly journals Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0127812 ◽  
Author(s):  
Jing Xiao ◽  
Jin Zhao ◽  
Mengjun Liu ◽  
Ping Liu ◽  
Li Dai ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Chinese Jujube ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

scholarly journals Isolation And Characterization Of 45 SNP Markers In Triplophysa Tenuis

2021 ◽  
Author(s):  
Ya Liu ◽  
Yeyu Chen ◽  
Jiansheng Lai ◽  
Hongyu Ke ◽  
Zhongmeng Zhao ◽  
...  
Keyword(s):  
Polymorphic Information Content ◽  
Snp Markers ◽  
Gansu Province ◽  
The Novel ◽  
Genetic Management ◽  
Polymorphic Snps ◽  
Isolation And Characterization ◽  
Population Conservation ◽  
Hardy Weinberg Equilibrium

Abstract Triplophysa tenuis is an endemic species to China, which mainly distributed in Xinjiang and Gansu province. Effective conservation and management of this species is limited by insufficient molecular markers. In the present study, we reported the isolation and characterization of 45 SNP markers in T. tenuis. The minor allele frequency ranged from 0.046 to 0.500, and the observed and expected heterozygosities ranged from 0.061 to 0.667 and 0.088 to 0.508, respectively. Polymorphic information content ranged from 0.083 to 0.375. Among these SNPs, three loci showed significant departures from the Hardy–Weinberg equilibrium. The novel polymorphic SNPs will be helpful for the future study on genetic management and population conservation for this species.

scholarly journals Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose (Urva auropunctata): Identification of Novel Species

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1700
Author(s):  
Kerry Gainor ◽  
Anne A. M. J. Becker ◽  
Yashpal S. Malik ◽  
Souvik Ghosh
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Replicase Gene ◽  
High Genetic Diversity ◽  
Fecal Samples ◽  
Genome Wide ◽  
Putative Origin ◽  
Indian Mongoose ◽  
Complete Genome Analysis ◽  
Small Indian Mongoose

Fecal samples from 76 of 83 apparently healthy small Indian mongooses (Urva auropunctata) were PCR positive with circovirus/cyclovirus pan-rep (replicase gene) primers. In this case, 30 samples yielded high quality partial rep sequences (~400 bp), of which 26 sequences shared maximum homology with cycloviruses from an arthropod, bats, humans or a sheep. Three sequences exhibited maximum identities with a bat circovirus, whilst a single sequence could not be assigned to either genus. Using inverse nested PCRs, the complete genomes of mongoose associated circoviruses (Mon-1, -29 and -66) and cycloviruses (Mon-20, -24, -32, -58, -60 and -62) were determined. Mon-1, -20, -24, -29, -32 and -66 shared <80% maximum genome-wide pairwise nucleotide sequence identities with circoviruses/cycloviruses from other animals/sources, and were assigned to novel circovirus, or cyclovirus species. Mon-58, -60 and -62 shared maximum pairwise identities of 79.90–80.20% with human and bat cycloviruses, which were borderline to the cut-off identity value for assigning novel cycloviral species. Despite high genetic diversity, the mongoose associated circoviruses/cycloviruses retained the various features that are conserved among members of the family Circoviridae, such as presence of the putative origin of replication (ori) in the 5′-intergenic region, conserved motifs in the putative replication-associated protein and an arginine rich region in the amino terminus of the putative capsid protein. Since only fecal samples were tested, and mongooses are polyphagous predators, we could not determine whether the mongoose associated circoviruses/cycloviruses were of dietary origin, or actually infected the host. To our knowledge, this is the first report on detection and complete genome analysis of circoviruses/cycloviruses in the small Indian mongoose, warranting further studies in other species of mongooses.

scholarly journals Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze)

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Rajni Parmar ◽  
Romit Seth ◽  
Ram Kumar Sharma
Keyword(s):  
Transcription Factor ◽  
Stress Tolerance ◽  
Ssr Markers ◽  
Single Amino Acid ◽  
Large Set ◽  
Genome Wide ◽  
Transcription Factor Genes ◽  
Ssr Loci ◽  
Transcriptome Resource

AbstractTea, being one of the most popular beverages requires large set of molecular markers for genetic improvement of quality, yield and stress tolerance. Identification of functionally relevant microsatellite or simple sequence repeat (SSR) marker resources from regulatory “Transcription factor (TF) genes” can be potential targets to expedite molecular breeding efforts. In current study, 2776 transcripts encoding TFs harbouring 3687 SSR loci yielding 1843 flanking markers were identified from traits specific transcriptome resource of 20 popular tea cultivars. Of these, 689 functionally relevant SSR markers were successfully validated and assigned to 15 chromosomes (Chr) of CSS genome. Interestingly, 589 polymorphic markers including 403 core-set of TF-SSR markers amplified 2864 alleles in key TF families (bHLH, WRKY, MYB-related, C2H2, ERF, C3H, NAC, FAR1, MYB and G2-like). Their significant network interactions with key genes corresponding to aroma, quality and stress tolerance suggests their potential implications in traits dissection. Furthermore, single amino acid repeat reiteration in CDS revealed presence of favoured and hydrophobic amino acids. Successful deployment of markers for genetic diversity characterization of 135 popular tea cultivars and segregation in bi-parental population suggests their wider utility in high-throughput genotyping studies in tea.

Development and introduction of detection dogs in surveying for scats of small Indian mongoose as invasive alien species

2010 ◽  
Vol 5 (2) ◽  
pp. 101-111 ◽  
Author(s):  
Ryoji Fukuhara ◽  
Takako Yamaguchi ◽  
Hiromi Ukuta ◽  
Sugot Roy ◽  
Junichi Tanaka ◽  
...  
Keyword(s):  
Alien Species ◽  
Invasive Alien Species ◽  
Indian Mongoose ◽  
Small Indian Mongoose

scholarly journals Isolation and Characterization of Microsatellites Markers in Centaurium Grandiflorum ssp. Boissieri

2021 ◽  
Author(s):  
Vania Jiménez-Lobato ◽  
Marcial Escudero ◽  
Zoila Díaz Lifante ◽  
Cristina Andrés Camacho ◽  
Alejandra de Castro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mating System ◽  
Flower Morphology ◽  
System Parameters ◽  
Microsatellites Markers ◽  
Isolation And Characterization ◽  
Ssr Loci ◽  
Hardy Weinberg Equilibrium ◽  
Two Populations

Abstract Estimation of outcrossing/selfing rates and characterization of genetic diversity with microsatellite markers are crucial to understand the evolution of mating system in plant species. We developed, optimized and characterized eight new primers pairs for Centaurium grandiflorum ssp. boissieri and transferred them to three subspecies of Centaurium quadrifolium. Two SSR loci were transferred from Sabatia campestris to the four mentioned taxa of Centaurium. Polymorphisms, He, Ho and H-W deviations were estimated in two populations of C. grandiflorum ssp. boissieri, and in seven individuals of C. quadrifolium ssp. barrelieri, C. quadrifolium ssp. parviflorum and C. quadrifolium ssp. quadrifolium. A total of 80 individuals were used in these experiments. The number of polymorphic loci varied among species from one to ten. A total number of 127 alleles were scored. The average number of alleles per locus was 12.7. He was higher than Ho in all sampled populations. Hardy-Weinberg equilibrium was found for some loci in different species. This is the first report of microsatellites successfully amplified in the whole Centaurium genus. They will be valuable for estimation of mating system parameters, genetic diversity and explore its relationship with the wide flower morphology, especially anther-stigma separation, found along the genus.

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