비만아 부모의 돌봄 경험: q 방법론

Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.

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Scallop genome provides insights into evolution of bilaterian karyotype and development

Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high-density single-nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction-site associated DNA sequencing (RAD-Seq) and subsequent variations have been extensively applied to generate population-level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD-Seq techniques have included generation of genetic linkage maps, performing genome-wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1111/raq.12193

Applications of genotyping by sequencing in aquaculture breeding and genetics.

Decapod crustaceans exhibit a wide range of osmoregulatory patterns and capabilities from marine osmoconformers to brackish and freshwater hyperregulators to terrestrial hyporegulators. The principal gill salt transport mechanisms proposed to underlie the ability of the better-known taxa to occupy these specific habitats are examined here. Traditional thinking suggests that a graduated series of successively stronger adaptive mechanisms may have driven the occupation of ever more dilute osmotic niches, culminating in the conquest of freshwater and dry land. However, when habitat and osmoregulatory parameters are analyzed quantitatively against the phylogenies of the taxa examined, as illustrated here using a palaemonid shrimp clade, their association becomes questionable and may hold true only in specific cases. We also propose a putative evolution for gill epithelial ion pump and transporter arrangement in a eubrachyuran crab clade whose lineages occupy distinct osmotic niches. By including the systematics of these selected groups, this review incorporates the notion of a protracted time scale, here termed ‘phylophysiology’, into decapod osmoregulation, allowing the examination of putative physiological transformations and their underlying evolutionary processes. This approach assumes that species are temporally linked, a factor that can impart phylogenetic structuring, which must be considered in comparative studies. Future experimental models in decapod osmoregulatory physiology should contemplate the phylogenetic relationships among the taxa chosen to better allow comprehension of the transformations arising during their evolution.

Evolution of osmoregulatory patterns and gill ion transport mechanisms in the decapod Crustacea: a review

/pdf/biomineralization-in-perforate-foraminifera-2f3ho10os9.pdf

Biomineralization in perforate foraminifera

Pearl oyster, Pinctada martensii, is a marine bivalve species widely distributed in tropic and subtropic marine coasts. Mantle is the special tissue of P. martensii that secretes biomineralization proteins inducing shell deposition as well as iridescent nacre both in the inner shell and artificial nucleus. The pearl oyster is very efficient for artificial pearl production and is therefore an ideal organism for studies into the processes of biomineralization. However, deficiency of transcriptome information limits the insight into biomineralization mechanisms and pearl formation. In this study, we sequenced and characterized the P. martensii mantle transcriptome using 454 pyrosequencing. A total of 25,723 unique transcripts were assembled from 220,824 quality reads, followed by annotation and Gene Ontology classification analysis. A total of 146 unique transcript segments homologous to 49 reference biomineralization genes were identified, including calcineurin-binding protein, amorphous calcium carbonate binding protein 1, calmodulin, calponin-like protein, carbonic anhydrase 1, glycine-rich shell matrix protein, lysine-rich matrix protein, mantle gene or protein, nacrein, pearlin, PIF, regucalcin, and shematrin. The sequence data enabled the identification of 10,285 potential single nucleotide polymorphism loci and 7,836 putative indels, providing a resource for molecular biomarker, population genetics, and functional genomic studies. A large number of candidate genes for biomineralization were identified, considerably enriching resources for the study of shell formation. These sequence data will notably advance biomineralization and transcriptome study in pearl oyster and other Pinctada species.

Characterization of the Pearl Oyster (Pinctada martensii) Mantle Transcriptome Unravels Biomineralization Genes

High-density single nucleotide polymorphisms linkage and quantitative trait locus mapping of the pearl oyster, Pinctada fucata martensii Dunker

A 16-microsatellite multiplex assay for parentage assignment in the eastern oyster (Crassostrea virginica Gmelin)

The pearl oyster, Pinctada martensii, is the primary species used for the aquaculture production of marine pearls in China and Japan. Genetic tools and resources are needed to study the genome of this species and to understand the molecular basis of development, growth, host defense, pearl formation, and other important traits. In this study, we developed a set of expressed sequence tags (ESTs) for P. martensii. We constructed cDNA libraries from adult tissues and sequenced 7,128 ESTs. Clustering analysis identified 788 contigs (covering 5,769 ESTs) and 1,351 singletons, yielding a total of 2,139 unique genes. Of these unique genes, only 935 had significant (E-value ≤ 0.005) hits in GenBank, and the remaining 1,204 (56.3%) were novel. Most of the known genes are related to cellular structure, protein binding, and metabolic processes. Putative host-defense genes (86) were identified including C-type lectin, ferritin, polyubiquitin, proteases, protease inhibitors, scavenger receptors, heat shock proteins, and RAS oncogenes. The EST sequences developed in this study provide a valuable resource for future efforts on gene identification, marker development, and studies on molecular mechanism of host defense in pearl oysters.

Development of Expressed Sequence Tags from the Pearl Oyster, Pinctada martensii Dunker

Cupped oysters are common and abundant along the coast of China, but their classification has been uncertain. In previous studies, we classified 2 of the cupped oysters into 2 subspecies: Crassostrea gigas gigas from the northern coast of China and Crassostrea gigas angulata from the southern coast of China. There is another small cupped oyster that seems different from these 2 species and resembles Crassostrea sikamea Amemiya 1928. To determine the taxonomic status of this oyster and its distribution, we collected wild oysters from 12 sites in China, identified putative C. sikamea with genetic markers, and compared them with known C. sikamea in both morphology and sequences of the mitochondrial 16S rRNA and cytochrome oxidase I gene fragments. Sequence analyses confirm classification based on genetic markers that this small cupped oyster from China is indeed C. sikamea. Our data show that C. sikamea not only occurs naturally in China, but also lives in abundance over a wide geographical distribution, ranging from Jiangsu to Guangxi, including Hainan Island. Our findings greatly extend the known distribution range of this species, and the extended distribution follows the Kuroshio and Tsushima currents, suggesting that ocean currents may play a role in shaping oyster distribution. Knowing the distribution range of C. sikamea is important to our understanding of its evolutionary history as well as fishery management and aquaculture breeding of this commercially important species.

https://bioone.org/journals/Journal-of-Shellfish-Research/volume-32/issue-2/035.032.0224/Occurrence-and-Distribution-of-iCrassostrea-sikamea-i-Amemiya-1928-in/10.2983/035.032.0224.pdf

Aimin Wang

Papers

Characterization of the Pearl Oyster (Pinctada martensii) Mantle Transcriptome Unravels Biomineralization Genes

High-density single nucleotide polymorphisms linkage and quantitative trait locus mapping of the pearl oyster, Pinctada fucata martensii Dunker

A 16-microsatellite multiplex assay for parentage assignment in the eastern oyster (Crassostrea virginica Gmelin)

Development of Expressed Sequence Tags from the Pearl Oyster, Pinctada martensii Dunker

Occurrence and Distribution of Crassostrea sikamea (Amemiya 1928) in China