scholarly journals Application of SNP in Genetic Sex Identification and Effect of Estradiol on Gene Expression of Sex-Related Genes in Strongylocentrotus intermedius

2021 ◽  
Vol 12 ◽  
Author(s):  
Ya-Lun Han ◽  
Zhi-Hui Sun ◽  
Shuai Chang ◽  
Bin Wen ◽  
Jian Song ◽  
...  
Keyword(s):  
Sea Urchins ◽  
Estrogen Metabolism ◽  
Marker Genes ◽  
Solid Base ◽  
Strongylocentrotus Intermedius ◽  
Genome Survey ◽  
Testis Differentiation ◽  
Conserved Genes ◽  
Breeding Efficiency ◽  
Sex Determination Mechanisms

Sea urchin (Strongylocentrotus intermedius) is an economically important mariculture species in Asia, and its gonads are the only edible part. The efficiency of genetic breeding in sea urchins is hampered due to the inability to distinguish gender by appearance. In this study, we first identified a sex-associated single nucleotide polymorphism (SNP) by combining type IIB endonuclease restriction site-associated DNA sequencing (2b-RAD-seq) and genome survey. Importantly, this SNP is located within spata4, a gene specifically expressed in male. Knocking down of spata4 by RNA interference (RNAi) in male individuals led to the downregulation of other conserved testis differentiation-related genes and germ cell marker genes. We also revealed that sex ratio in this validated culture population of S. intermedius is not 1:1. Moreover, after a 58-day feeding experiment with estradiol, the expression levels of several conserved genes that are related to testis differentiation, ovary differentiation, and estrogen metabolism were dynamically changed. Taken together, our results will contribute toward improving breeding efficiency, developing sex-controlled breeding, and providing a solid base for understanding sex determination mechanisms in sea urchins.

scholarly journals Light intensity regulates phototaxis, foraging and righting behaviors of the sea urchin Strongylocentrotus intermedius

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8001 ◽  
Author(s):  
Jiangnan Sun ◽  
Xiaomei Chi ◽  
Mingfang Yang ◽  
Jingyun Ding ◽  
Dongtao Shi ◽  
...  
Keyword(s):  
Light Intensity ◽  
Foraging Behavior ◽  
Sea Urchins ◽  
High Light Intensity ◽  
High Light ◽  
Strongylocentrotus Intermedius ◽  
Low Light ◽  
Low Light Intensity ◽  
Light Intensities ◽  
Significant Difference

Small sea urchins Strongylocentrotus intermedius (1–2 cm of test diameter) are exposed to different environments of light intensities after being reseeded to the sea bottom. With little information available about the behavioral responses of S. intermedius to different light intensities in the environment, we carried out an investigation on how S. intermedius is affected by three light intensity environments in terms of phototaxis, foraging and righting behaviors. They were no light (zero lx), low light intensity (24–209 lx) and high light intensity (252–2,280 lx). Light intensity had obvious different effects on phototaxis. In low light intensity, sea urchins moved more and spent significantly more time at the higher intensity (69–209 lx) (P = 0.046). S. intermedius in high light intensity, in contrast, spent significantly more time at lower intensity (252–690 lx) (P = 0.005). Unexpectedly, no significant difference of movement (average velocity and total distance covered) was found among the three light intensities (P > 0.05). Foraging behavior of S. intermedius was significantly different among the light intensities. In the no light environment, only three of ten S. intermedius found food within 7 min. In low light intensity, nine of 10 sea urchins showed successful foraging behavior to the food placed at 209 lx, which was significantly higher than the ratio of the number (two of 10) when food was placed at 24 lx (P = 0.005). In the high light intensity, in contrast, significantly less sea urchins (three of 10) found food placed at the higher light intensity (2,280 lx) compared with the lower light intensity (252 lx) (10/10, P = 0.003). Furthermore, S. intermedius showed significantly longer righting response time in the high light intensity compared with both no light (P = 0.001) and low light intensity (P = 0.031). No significant difference was found in righting behavior between no light and low light intensity (P = 0.892). The present study indicates that light intensity significantly affects phototaxis, foraging and righting behaviors of S. intermedius and that ~200 lx might be the appropriate light intensity for reseeding small S. intermedius.

scholarly journals A Fragment of21ORFs Around the Direct Repeat (DR) Region ofMycobacterium tuberculosisis Absent From the Other Sequenced Mycobacterial Genomes: Implications for the Evolution of the DR Region

2004 ◽  
Vol 5 (2) ◽  
pp. 116-122 ◽  
Author(s):  
Karina Caimi ◽  
Angel Cataldi
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Unknown Function ◽  
Repetitive Sequences ◽  
Direct Repeat ◽  
Singular Locus ◽  
The Other ◽  
Marker Genes ◽  
Complex Species ◽  
Conserved Genes ◽  
Complex Genome

The direct repeat (DR) region is a singular locus of theMycobacterium tuberculosiscomplex genome. This region consists of 36 bp repetitive sequences separated by non-repetitive unique spacer sequences. Around this region there are several genes coding for proteins of unknown function. To determine whether theM. smegmatis, M. avium, M. marinumandM. lepraegenomes contain sequences and ORFs similar to those of the DR locus of theM. tuberculosiscomplex, we analysed the corresponding regions in these species. As a first step, some conserved genes that flank the DR genes [Rv2785c (rpsO), Rv2786c (ribF), Rv2790c (ltp1 ), Rv2793c (truB), Rv2800, Rv2825, Rv2828, Rv2831 (echA16 ), Rv2838 (rbfA)andRv2845 (proS )] were used as markers to locate the corresponding orthologues inM. smegmatis, M. avium, M. marinumandM. leprae in silico. Most of theseM. tuberculosismarker genes have highly similar orthologues located in the same order and orientation in the other mycobacteria. In contrast, no orthologues were found for ORFsRv2801–Rv2824, suggesting that these genes are unique toM. tuberculosiswithin the genusMycobacterium.We observed that inM. smegmatisandM. avium, Rv2800andRv2825are adjacent. This observation was experimentally confirmed by PCR. In conclusion, as the DR locus and the ORFs around it are absent inM. smegmatisandM. aviumand, as it is possible that these species are older thanM. tuberculosis, we postulated that the DR locus was acquired by theM. tuberculosiscomplex species or by an ancestor bacterium.

scholarly journals Transgenerational effects of UV-B radiation on egg size, fertilization, hatching and larval size of sea urchins Strongylocentrotus intermedius

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7598
Author(s):  
Jingyun Ding ◽  
Lingling Zhang ◽  
Jiangnan Sun ◽  
Dongtao Shi ◽  
Xiaomei Chi ◽  
...  
Keyword(s):  
Egg Size ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Marine Invertebrate ◽  
Ultraviolet B ◽  
Hatching Rate ◽  
Strongylocentrotus Intermedius ◽  
Transgenerational Effects ◽  
Larval Size ◽  
First Time

Transgenerational effects are important for phenotypic plasticity and adaptation of marine invertebrates in the changing ocean. Ultraviolet-B (UV-B) radiation is an increasing threat to marine invertebrates. For the first time, we reported positive and negative transgenerational effects of UV-B radiation on egg size, fertilization, hatchability and larval size of a marine invertebrate. Strongylocentrotus intermedius exposed to UV-B radiation showed positive transgenerational effects and adaptation on egg size, hatching rate and post-oral arm length of larvae. Negative transgenerational effects were found in body length, stomach length and stomach width of larvae whose parents were exposed to UV-B radiation. Sires probably play important roles in transgenerational effects of UV-B. The present study provides valuable information into transgenerational effects of UV-B radiation on fitness related traits of sea urchins (at least Strongylocentrotus intermedius).

scholarly journals The Structure and Function of Gut Microbiomes of Two Species of Sea Urchins, Mesocentrotus nudus and Strongylocentrotus intermedius, in Japan

2021 ◽  
Vol 8 ◽  
Author(s):  
Alfabetian Harjuno Condro Haditomo ◽  
Masanori Yonezawa ◽  
Juanwen Yu ◽  
Sayaka Mino ◽  
Yuichi Sakai ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Gut Microbiome ◽  
Environmental Changes ◽  
Growth Promotion ◽  
Sea Urchins ◽  
The Body ◽  
Sequence Variant ◽  
Strongylocentrotus Intermedius ◽  
Running Water ◽  
Mesocentrotus Nudus

Sea urchin is an indicator of coastal environmental changes in the global warming era, and is also a model organism in developmental biology and evolution. Due to the depletion of wild resources, new aquaculture techniques for improving stocks have been well studied. The gut microbiome shapes various aspects of a host’s physiology. However, these microbiome structures and functions on sea urchins, particularly Mesocentrotus nudus and Strongylocentrotus intermedius which are important marine bioresources commonly found in Japan, have not been fully investigated yet. Using metagenomic approaches including meta16S and shotgun metagenome sequencings, the structures, functions, and dynamics of the gut microbiome of M. nudus and S. intermedius, related to both habitat environment and host growth, were studied. Firstly, a broad meta16S analysis revealed that at the family level, Psychromonadaceae and Flavobacteriaceae reads (38–71%) dominated in these sea urchins, which is a unique feature observed in species in Japan. Flavobacteriaceae reads were more abundant in individuals after rearing in an aquarium with circulating compared to one with running water. Campylobacteraceae and Vibrionaceae abundances increased in both kinds of laboratory-reared sea urchins in both types of experiments. 2-weeks feeding experiments of M. nudus and S. intermedius transplanted from the farm to laboratory revealed that these gut microbial structures were affected by diet rather than rearing environments and host species. Secondly, further meta16S analysis of microbial reads related to M. nudus growth revealed that at least four Amplicon Sequence Variant (ASV) affiliated to Saccharicrinis fermentans, which is known to be a nitrogen (N2) fixing bacterium, showed a significant positive correlation to the body weight and test diameter. Interestingly, gut microbiome comparisons using shotgun metagenome sequencing of individuals showing higher and lower growth rates revealed a significant abundance of “Nitrate and nitrite ammonification” genes in the higher-grown individuals under the circulating water rearing. These findings provide new insights on the structure-function relationship of sea urchin gut microbiomes beyond previously reported nitrogen fixation function in sea urchin in 1950s; we discovered a nitrate reduction function into ammonium for the growth promotion of sea urchin.

Larval size and metamorphosis are significantly reduced in second generation of inbred sea urchins Strongylocentrotus intermedius

Aquaculture ◽  
2016 ◽  
Vol 452 ◽  
pp. 402-406 ◽  
Author(s):  
Chong Zhao ◽  
Ping Sun ◽  
Jing Wei ◽  
Lisheng Zhang ◽  
Weijie Zhang ◽  
...  
Keyword(s):  
Second Generation ◽  
Sea Urchins ◽  
Strongylocentrotus Intermedius ◽  
Larval Size
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