Application of Next Generation Semiconductor-Based Sequencing for the Identification of Apis mellifera Complementary Sex Determiner (csd) Alleles from Honey DNA

The complementary sex determiner (csd) gene plays an essential role in the sex determination of Apis mellifera L. Females develop only if fertilized eggs have functional heterozygous genotypes at this gene whereas males, being haploids, are hemizygous. Two identical csd alleles produce non vital males. In light of the recent decline in honey bee populations, it is therefore important to monitor the allele variability at this gene. In this study, we tested the application of next generation semiconductor-based sequencing technology (Ion Torrent) coupled with environmental honey DNA as a source of honey bee genome information to retrieve massive sequencing data for the analysis of variability at the hypervariable region (HVR) of the csd gene. DNA was extracted from 12 honey samples collected from honeycombs directly retrieved from 12 different colonies. A specifically designed bioinformatic pipeline, applied to analyze a total of about 1.5 million reads, identified a total of 160 different csd alleles, 55% of which were novel. The average number of alleles per sample was compatible with the number of expected patrilines per colony, according to the mating behavior of the queens. Allele diversity at the csd could also provide information useful to reconstruct the history of the honey.

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The Ability of Honey Bee Drones to Ejaculate

Journal of Apicultural Science ◽

10.1515/jas-2015-0027 ◽

2015 ◽

Vol 59 (2) ◽

pp. 127-133 ◽

Cited By ~ 2

Author(s):

Krystyna Czekońska ◽

Bożena Chuda-Mickiewicz

Keyword(s):

Apis Mellifera ◽

Honey Bee ◽

Reproductive Organs ◽

Seminal Vesicles ◽

Analysis And Evaluation ◽

Anatomical Changes ◽

Manual Method ◽

Delayed Development

Abstract The effectiveness of two methods of collecting semen from honeybee Apis mellifera drones was compared, and the reasons for problems with ejaculating semen were analysed. Among 275 drones, 100 were stimulated to release semen using a manual method, 100 with the use of chloroform, and from 75 drones the reproductive organs were dissected for analysis and evaluation. It was found that the principal causes of problems that drones had with ejaculating their semen were anatomical changes or a delay in the development of the mucus glands. It was also found that the method employing chloroform was less efficient in the first phase of eversion of the endophallus, compared with the manual method. The method with the use of chloroform allows the determination of the proportion of drones, which do not evert the endophallus because of poor or delayed development of mucus glands, as well as the proportion of drones which evert the organ, but do not ejaculate semen because of the absence of semen in the seminal vesicles.

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A Benchmark of Structural Variant Analysis Tools for Next Generation Sequencing Data

International Journal of Systems Biology and Biomedical Technologies ◽

10.4018/ijsbbt.2013100106 ◽

2013 ◽

Vol 2 (4) ◽

pp. 86-98

Author(s):

Chatzinikolaou Panagiotis ◽

Makris Christos ◽

Dimitrios Vlachakis ◽

Sophia Kossida

Keyword(s):

Next Generation Sequencing ◽

Level Structure ◽

Atomic Level ◽

Protein Sequencing ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Variant Analysis ◽

Generation Sequencing

In language of genetics and biochemistry, sequencing is the determination of an unbranched biopolymer's primary structure. A sequence is a symbolic linear depiction, result of sequencing. This sequence is a succinct summary of the most of the sequenced molecule's atomic-level structure. (Most known is DNA-sequencing, RNA-sequencing, Protein-sequencing and Next-Generation-sequencing)

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Targeted Next-Generation Sequencing in Patients with Suggestive X-Linked Intellectual Disability

Genes ◽

10.3390/genes11010051 ◽

2020 ◽

Vol 11 (1) ◽

pp. 51

Author(s):

Nekane Ibarluzea ◽

Ana Belén de la Hoz ◽

Olatz Villate ◽

Isabel Llano ◽

Intzane Ocio ◽

...

Keyword(s):

Intellectual Disability ◽

Next Generation Sequencing ◽

Fragile X ◽

Next Generation ◽

Sequencing Data ◽

Targeted Next Generation Sequencing ◽

Biochemical Assays ◽

History Of ◽

Male Patients ◽

Generation Sequencing

X-linked intellectual disability (XLID) is known to contribute up to 10% of intellectual disability (ID) in males and could explain the increased ratio of affected males observed in patients with ID. Over the past decade, next-generation sequencing has clearly stimulated the gene discovery process and has become part of the diagnostic procedure. We have performed targeted next-generation sequencing of 82 XLID genes on 61 non-related male patients with suggestive non-syndromic XLID. These patients were initially referred to the molecular genetics laboratory to exclude Fragile X Syndrome. The cohort includes 47 male patients with suggestive X-linked family history of ID meaning that they had half-brothers or maternal cousins or uncles affected; and 14 male patients with ID and affected brothers whose mothers show skewed X-inactivation. Sequencing data analysis identified 17 candidate variants in 16 patients. Seven families could be re-contacted and variant segregation analysis of the respective eight candidate variants was performed: HUWE1, IQSEC2, MAOA, MED12, PHF8, SLC6A8, SLC9A6, and SYN1. Our results show the utility of targeted next-generation sequencing in unravelling the genetic origin of XLID, especially in retrospective cases. Variant segregation and additional studies like RNA sequencing and biochemical assays also helped in re-evaluating and further classifying the genetic variants found.

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