scholarly journals Prediction of the Sex-Associated Genomic Region in Tunas (Thunnus Fishes)

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Yoji Nakamura ◽  
Kentaro Higuchi ◽  
Kazunori Kumon ◽  
Motoshige Yasuike ◽  
Toshinori Takashi ◽  
...  
Keyword(s):  
Sex Determination ◽  
Bluefin Tuna ◽  
Pacific Bluefin Tuna ◽  
Estrogen Sulfotransferase ◽  
Unique Region ◽  
Genome Wide ◽  
A Genome ◽  
Southern Bluefin Tuna ◽  
Male Specific ◽  
Female Genome

Fish species have a variety of sex determination systems. Tunas (genus Thunnus) have an XY genetic sex determination system. However, the Y chromosome or responsible locus has not yet been identified in males. In a previous study, a female genome of Pacific bluefin tuna (T. orientalis) was sequenced, and candidates for sex-associated DNA polymorphisms were identified by a genome-wide association study using resequencing data. In the present study, we sequenced a male genome of Pacific bluefin tuna by long-read and linked-read sequencing technologies and explored male-specific loci through a comparison with the female genome. As a result, we found a unique region carrying the male-specific haplotype, where a homolog of estrogen sulfotransferase gene was predicted to be encoded. The genome-wide mapping of previously resequenced data indicated that, among the functionally annotated genes, only this gene, named sult1st6y, was paternally inherited in the males of Pacific bluefin tuna. We reviewed the RNA-seq data of southern bluefin tuna (T. maccoyii) in the public database and found that sult1st6y of southern bluefin tuna was expressed in all male testes, but absent or suppressed in the female ovary. Since estrogen sulfotransferase is responsible for the inactivation of estrogens, it is reasonable to assume that the expression of sult1st6y in gonad cells may inhibit female development, thereby inducing the individuals to become males. Thus, our results raise a promising hypothesis that sult1st6y is the sex determination gene in Thunnus fishes or at least functions at a crucial point in the sex-differentiation cascade.

scholarly journals A candidate for the sex-determination gene in tunas (Thunnus fishes)

2021 ◽  
Author(s):  
Yoji Nakamura ◽  
Kentaro Higuchi ◽  
Kazunori Kumon ◽  
Motoshige Yasuike ◽  
Toshinori Takashi ◽  
...  
Keyword(s):  
Sex Determination ◽  
Bluefin Tuna ◽  
Pacific Bluefin Tuna ◽  
Estrogen Sulfotransferase ◽  
Unique Region ◽  
Genome Wide ◽  
A Genome ◽  
Southern Bluefin Tuna ◽  
Male Specific ◽  
Female Genome

Fish species have a variety of sex determination systems. Tunas (genus Thunnus) have an XY genetic sex-determination system. However, the Y chromosome or responsible locus has not yet been identified in males. In a previous study, a female genome of Pacific bluefin tuna (T. orientalis) was sequenced, and candidates for sex-associated DNA polymorphisms were identified by a genome-wide association study using resequencing data. In the present study, we sequenced a male genome of Pacific bluefin tuna by long-read and linked-read sequencing technologies, and explored male-specific loci through a comparison with the female genome. As a result, we found a unique region carrying the male-specific haplotype, where a homolog of estrogen sulfotransferase gene was predicted to be encoded. The genome-wide mapping of previously resequenced data indicated that, among the functionally annotated genes, only this gene, named sult1st6y, was paternally inherited in the males of Pacific bluefin tuna. We reviewed the RNA-seq data of southern bluefin tuna (T. maccoyii) in the public database and found that sult1st6y of southern bluefin tuna was expressed in all male testes, but absent or suppressed in the female ovary. Since estrogen sulfotransferase is responsible for the inactivation of estrogens, it is reasonable to assume that the expression of sult1st6y in gonad cells may inhibit female development, thereby inducing the individuals to become males. Thus, our results raise a promising hypothesis that sult1st6y is the sex-determination gene in Thunnus fishes, or at least functions at a crucial point in the sex-differentiation cascade.

scholarly journals Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia (Oreochromis niloticus L.)

2019 ◽  
Vol 9 (10) ◽  
pp. 3213-3223 ◽  
Author(s):  
Giovanna Cáceres ◽  
María E. López ◽  
María I. Cádiz ◽  
Grazyella M. Yoshida ◽  
Ana Jedlicki ◽  
...  
Keyword(s):  
Sex Determination ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Major Gene ◽  
Whole Genome ◽  
Important Species ◽  
Genome Wide ◽  
A Genome

Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Müllerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.

scholarly journals Fine mapping using whole-genome sequencing confirms anti-Müllerian hormone as a major gene for sex determination in farmed Nile tilapia (Oreochromis niloticus L.)

2019 ◽  
Author(s):  
Giovanna Cáceres ◽  
María E. López ◽  
María I. Cadiz ◽  
Grazyella M. Yoshida ◽  
Ana Jedlicki ◽  
...  
Keyword(s):  
Sex Determination ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Oreochromis Niloticus ◽  
Nile Tilapia ◽  
Major Gene ◽  
Whole Genome ◽  
Important Species ◽  
Genome Wide ◽  
A Genome

ABSTRACTNile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Faster male development during grow-out phase is considered a major problem that generate heterogeneous sizes of fish at harvest. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sexual trait (males = 0; females = 1). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, located on chromosome 23 spanning a genomic region of 536 kb, was identified. Ten out of these 36 genetic variants, intercept the anti-Müllerian hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.

scholarly journals A general model to explain repeated turnovers of sex determination in the Salicaceae

2020 ◽  
Author(s):  
Wenlu Yang ◽  
Zhiyang Zhang ◽  
Deyan Wang ◽  
Yiling Li ◽  
Shaofei Tong ◽  
...  
Keyword(s):  
Sex Determination ◽  
General Model ◽  
Genome Wide Association Study ◽  
Sex Chromosome ◽  
Response Regulator ◽  
Single Gene ◽  
Entire Family ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
A Genome

AbstractDioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms through which sex systems evolve and their commonalities among plant species remain poorly understood. With both XY and ZW sex systems, the family Salicaceae provides a system to uncover the evolutionary forces driving sex chromosome turnovers. In this study, we performed a genome-wide association study to characterize sex determination in two Populus species, P. euphratica and P. alba. Our results reveal an XY system of sex determination on chromosome 14 of P. euphratica, and a ZW system on chromosome 19 of P. alba. We further assembled the corresponding sex determination regions, and found that their sex chromosome turnovers may be driven by the repeated translocations of a Helitron-like transposon. During the translocation, this factor may have captured partial or intact sequences that are orthologous to a type-A cytokinin response regulator gene. Based on results from this and other recently published studies, we hypothesize that this gene may act as a master regulator of sex determination for the entire family. We propose a general model to explain how the XY and ZW sex systems in this family can be determined by the same RR gene. Our study provides new insights into the diversification of incipient sex chromosome in flowering plants by showing how transposition and rearrangement of a single gene can control sex in both XY and ZW systems.

scholarly journals The placenta and neurodevelopment: sex differences in prenatal vulnerability

2016 ◽  
Vol 18 (4) ◽  
pp. 459-464 ◽  
Keyword(s):  
Sex Differences ◽  
Molecular Mechanisms ◽  
Maternal Stress ◽  
Disease Risk ◽  
Risk And Resilience ◽  
Hyperactivity Disorder ◽  
Neurodevelopmental Disease ◽  
Genome Wide ◽  
A Genome ◽  
Male Specific

Prenatal insults, such as maternal stress, are associated with an increased neurodevelopmental disease risk and impact males significantly more than females, including increased rates of autism, mental retardation, stuttering, dyslexia, and attention deficit/hyperactivity disorder (ADHD). Sex differences in the placenta, which begin with sex chromosomes, are likely to produce sex-specific transplacental signals to the developing brain. Our studies and others have identified X-linked genes that are expressed at higher levels in the female placenta. Through a genome-wide screen after maternal stress in mice, we identified the X-linked gene O-linked N-acetylglucosamine transferase (OGT) and demonstrated its causality in neurodevelopmental programming producing a male-specific stress phenotype. Elucidating the sex-specific molecular mechanisms involved in transplacental signals that impact brain development is key to understanding the sex bias in neurodevelopmental disorders and is expected to yield novel insight into disease risk and resilience.

scholarly journals Improvement of the Pacific bluefin tuna (Thunnus orientalis) reference genome and development of male-specific DNA markers

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ayako Suda ◽  
Issei Nishiki ◽  
Yuki Iwasaki ◽  
Aiko Matsuura ◽  
Tetsuya Akita ◽  
...  
Keyword(s):  
Dna Markers ◽  
Sequence Data ◽  
Draft Genome ◽  
Linkage Disequilibrium Block ◽  
Bluefin Tuna ◽  
Sex Identification ◽  
Pacific Bluefin Tuna ◽  
Thunnus Orientalis ◽  
The Pacific ◽  
Male Specific

Abstract The Pacific bluefin tuna, Thunnus orientalis, is a highly migratory species that is widely distributed in the North Pacific Ocean. Like other marine species, T. orientalis has no external sexual dimorphism; thus, identifying sex-specific variants from whole genome sequence data is a useful approach to develop an effective sex identification method. Here, we report an improved draft genome of T. orientalis and male-specific DNA markers. Combining PacBio long reads and Illumina short reads sufficiently improved genome assembly, with a 38-fold increase in scaffold contiguity (to 444 scaffolds) compared to the first published draft genome. Through analysing re-sequence data of 15 males and 16 females, 250 male-specific SNPs were identified from more than 30 million polymorphisms. All male-specific variants were male-heterozygous, suggesting that T. orientalis has a male heterogametic sex-determination system. The largest linkage disequilibrium block (3,174 bp on scaffold_064) contained 51 male-specific variants. PCR primers and a PCR-based sex identification assay were developed using these male-specific variants. The sex of 115 individuals (56 males and 59 females; sex was diagnosed by visual examination of the gonads) was identified with high accuracy using the assay. This easy, accurate, and practical technique facilitates the control of sex ratios in tuna farms. Furthermore, this method could be used to estimate the sex ratio and/or the sex-specific growth rate of natural populations.

scholarly journals Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate

2017 ◽  
Author(s):  
Gemma B. Danks ◽  
Pavla Navratilova ◽  
Boris Lenhard ◽  
Eric Thompson
Keyword(s):  
Transcription Initiation ◽  
Core Promoter ◽  
Ribosomal Protein Genes ◽  
Oikopleura Dioica ◽  
Transcription Start Sites ◽  
Spliced Leader ◽  
Genome Wide ◽  
A Genome ◽  
Cap Analysis ◽  
Male Specific

AbstractDevelopment is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of transcription in the testis, including the male-specific use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. During oogenesis the cell cycle regulator, E2F1, has been co-opted in regulating maternal transcription in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in vertebrates and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box, which indicates that this ancient promoter motif may play a role in selecting DNA for transcription-associated methylation in invertebrate genomes.

Establishment of a genome-wide RNAi screen; Identification of novel genes involved in clonal maintenance of ALL

2014 ◽  
Vol 226 (03) ◽  
Author(s):  
F Ponthan ◽  
D Pal ◽  
J Vormoor ◽  
O Heidenreich
Keyword(s):  
Rnai Screen ◽  
Novel Genes ◽  
Genome Wide ◽  
A Genome
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