Development of EST-SSRs from the ark shell (Scapharca broughtonii) transcriptome and their application in genetic analysis of four populations

Wang, Wenjing; Wu, Biao; Liu, Zhihong; Zhou, Liqing; Sun, Xiujun; Tian, Jing; Yang, Aiguo

doi:10.1007/s13258-021-01090-3

Cited by 6 publications

(4 citation statements)

References 32 publications

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“…The regulatory ncRNAs are associated with various cellular processes and include: long-noncoding RNAs (lncRNAs), microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) (Frías-Lasserre and Villagra 2017; Bartel 2018; Kopp and Mendell 2018; Mattick et al 2023). A plethora of reports discuss the effects of regulatory ncRNA expression between the sexes on development, physiology, immunity and disease (Zhou et al 2014; Gershoni and Pietrokovski 2017; Zhang et al 2017; Gal-Oz et al 2019; Rosspopoff et al 2023; Wang et al 2023).…”

Section: Discussionmentioning

confidence: 99%

Sexual antagonism and sex determination in three syngnathid species alongside a male pregnancy gradient

Dubin,

Parker,

Böhne

et al. 2023

Preprint

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Teleost fish show an enormous diversity of sex determination systems, varying from environmental sex determination to full sex chromosomes. Traditionally sex chromosomes are considered within a framework of sexually antagonistic relationships and are viewed not only as sex determination systems but also as a means to resolve sexual conflict by confining conflicting genes to one sex. However, the relationship between emergence sexually-antagonistic loci, resolution of sexual conflict and sex determination is not fully understood. In this study we take a look at genomic and transcriptomic signatures of sexual antagonism, and relate them to putative sex determination systems in three species from the family Syngnathidae: Nerophis ophidion, Syngnathus typhle and Hippocampus erectus. The family is famous for their extreme form of parental care - male pregnancy. Male pregnancy forms a parental investment gradient among species of the family. We selected species alongside this gradient to investigate the effects male pregnancy has on sexual conflict in syngnathids. We found that both S.typhle and N.ophidion seem to have environmental sex determination and that sexual conflict is primarily resolved via differential gene and allele expression. On the other hand H.erectus possess an XY sex chromosome system. Strikingly, the identified homomorphic Y chromosome is not homologous to the Y chromosome of H.erectus identified in an independent study. We hypothesize that both sex-linked chromosomes evolved due to captive breeding and represent transition states between sex determination systems. Furthermore, we propose that the master sex determination gene is located outside of these sex-linked chromosomes.

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Section: Discussionmentioning

confidence: 99%

Sexual antagonism and sex determination in three syngnathid species alongside a male pregnancy gradient

Dubin,

Parker,

Böhne

et al. 2023

Preprint

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“…With the rapid development of molecular biology-related detection technologies such as high-throughput sequencing, the use of RNA-seq expressed sequences to develop molecular markers has obvious advantages, especially for non-model species without a reference genome [ 20 , 23 , 55 ]. The developed SSRs are tandem repeat sequences consisting of 1–6 nucleotides in the genome, distributed in both coding and non-coding regions of genes, and are the most suitable markers for constructing high-throughput genotyping with co-dominant inheritance, high polymorphism, good reproducibility, extensive genomic coverage, and cost-saving [ 20 ]. Moreover, because SSR originates from expressed gene regions and can directly reflect the diversity of related genes, it is widely used in plant genetic breeding, germplasm resource conservation and development, etc.…”

Section: Discussionmentioning

confidence: 99%

“…Although previous studies have confirmed the differences in the accumulation of secondary metabolites in different tissues of R. officinale and used RNA-seq to identify candidate genes involved in the biosynthesis of anthraquinones, etc. [ 16 , 19 , 20 , 21 , 22 ], the differences in the expression of the enzyme genes associated with the synthesis of these components are still indefinite in R. officinale .…”

Section: Introductionmentioning

confidence: 99%

Comparative Transcriptome Analyses of Different Rheum officinale Tissues Reveal Differentially Expressed Genes Associated with Anthraquinone, Catechin, and Gallic Acid Biosynthesis

Zhou

Sun

Zhang

et al. 2022

Genes

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Rheum officinale Baill. is an important traditional Chinese medicinal herb, its dried roots and rhizomes being widely utilized to cure diverse diseases. However, previous studies mainly focused on the active compounds and their pharmacological effects, and the molecular mechanism underlying the biosynthesis of these ingredients in R. officinale is still elusive. Here, we performed comparative transcriptome analyses to elucidate the differentially expressed genes (DEGs) in the root, stem, and leaf of R. officinale. A total of 236,031 unigenes with N50 of 769 bp was generated, 136,329 (57.76%) of which were annotated. A total of 5884 DEGs was identified after the comparative analyses of different tissues; 175 and 126 key enzyme genes with tissue-specific expression were found in the anthraquinone, catechin/gallic acid biosynthetic pathway, respectively, and some of these key enzyme genes were verified by qRT-PCR. The phylogeny of the PKS III family in Polygonaceae indicated that probably only PL_741 PKSIII1, PL_11549 PKSIII5, and PL_101745 PKSIII6 encoded PKSIII in the polyketide pathway. These results will shed light on the molecular basis of the tissue-specific accumulation and regulation of secondary metabolites in R. officinale, and lay a foundation for the future genetic diversity, molecular assisted breeding, and germplasm resource improvement of this essential medicinal plant.

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“…Compared to the screening of polymorphic SSR loci by silver staining, the use of uorescence has many advantages, including simple experimental operation; automatic identi cation and collection of data through software to improve e ciency; and the ability to identify alleles that are only 1-2 bp apart to improve data accuracy(Li et al, 2009;Pan et al, 2014). PIC is an important indicator for measuring the polymorphism information of SSR loci(Wang et al, 2021).…”

mentioning

confidence: 99%

Inferring the impact of large-scale aquaculture of Haliotis discus hannai in northern and southern China using EST-SSR markers

杨,

Zhou,

et al. 2024

Preprint

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The Pacific abalone Haliotis discus hannai originated in cold waters, but as an economically important aquaculture shellfish in China, there has been a large-scale transfer of fish to Fujian Province in southern China for culture. Our goal was to clarify the current status of the genetic structure of Pacific abalone in China. In this study, eighteen polymorphic EST-SSR loci were successfully developed based on the hemolymph transcriptome data of Pacific abalone, and thirteen highly polymorphic EST-SSR loci were selected for the genetic variation analysis of six populations collected from Zhangzhou in Fujian Province (ZZ), Dalian in Liaoning Province (DL), Rongcheng in Shandong Province (RC), and the Changshan Archipelago, including Nanhuangcheng Island (NH), Daqin Island (DQ), and Tuoji Island (TJ). The results showed that the average number of observed alleles was 8.0769 (RC)-11.3848 (DQ) in each population. The number of observed alleles in the DQ, NH, and TJ populations was significantly higher than that in the RC population. If the NH and TJ cultured populations of the Changshan Archipelago were excluded, then compared with the DQ wild population, the number of alleles in the cultured population decreased by 22.79%. The pairwise Fst values and analysis of molecular variance (AMOVA) revealed significant population differentiation among most populations, with the RC and ZZ cultured populations exhibiting the largest population differentiation (Fst = 0.1334). The UPGMA phylogenetic tree and structural analysis divided the six populations into two groups (group 1: NH, DQ, and ZZ; group 2: DL, TJ, and RC), and there was no relationship between geographical distance and genetic distance. These results may reflect the large-scale culture from north to south in China and the exchange of juveniles between hatcheries. Different breeding conditions have led to a higher degree of genetic differentiation between the RC and ZZ populations. In conclusion, this study provides valuable information on the genetic structure of Pacific abalone populations in China and contributes to the management and restoration of Pacific abalone.

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Development of EST-SSRs from the ark shell (Scapharca broughtonii) transcriptome and their application in genetic analysis of four populations

Cited by 6 publications

References 32 publications

Sexual antagonism and sex determination in three syngnathid species alongside a male pregnancy gradient

Sexual antagonism and sex determination in three syngnathid species alongside a male pregnancy gradient

Comparative Transcriptome Analyses of Different Rheum officinale Tissues Reveal Differentially Expressed Genes Associated with Anthraquinone, Catechin, and Gallic Acid Biosynthesis

Inferring the impact of large-scale aquaculture of Haliotis discus hannai in northern and southern China using EST-SSR markers

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