2017年4月3日，中国海洋大学海洋生命学院包振民传授的研究团队在Nature子刊Nature Ecology & Evolution上颁发题为“Scallop genome provides insights into evolution of bilaterian karyotype and development”的研究文章。2017年11月23日，包教师团队又在Nature子刊Nature Communication上发文，题为“Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins” 。 把小扇贝研究到那种高度、一年发两篇Nature子刊，能够说很大佬了！
我深居此尝试室数月，认真研读文献，深切接触文献的做者们，找到了那两篇Nature子刊背后的故事。你确定不看看？
1.我可能并非实的认识扇贝
2
——“扇贝”？不就是“清蒸扇贝”和“蒜蓉扇贝”或者“辣炒扇贝肉”的阿谁扇贝嘛？！
——对呀！你还晓得扇贝的什么常识呢？
——扇贝属于软体动物门瓣鳃纲异形亚纲珍珠贝目扇贝科。我国是扇贝的主产国之一，沿海经济扇贝品种次要有4种，别离是栉孔扇贝（Chlamysfarreri）、海湾扇贝（Argopectenirradians）、虾夷扇贝（Patinopecten yessoensis）和华贵栉孔扇贝（Chlamys nobilis）。此中，虾夷扇贝和海湾扇贝由国外引进。
——那你晓得的实很多。
（啪！我就甩过来两张图）
常见扇贝（图片来自海大海洋生物遗传学与育种教育部重点尝试室）
栉孔扇贝内部构造（© 海生张）
栉孔扇贝就是咱们常见、常吃的扇贝啦，清蒸、蒜蓉…… 栉孔扇贝目前已成为我国海水养殖次要优势品种之一，在辽宁、河北和山东，尤其是山东沿海已构成相当大的养殖规模。在青岛的海鲜市场上很常见。11月那篇颁发于Nature Communication上的文章Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins研究的就是栉孔扇贝啦。
而虾夷扇贝原产于日本、俄罗斯千岛群岛南部等水域，1982年引入我国山东和辽宁，目前养殖散布在黄渤海，15℃为其最适生长温度。4月那篇颁发于Nature Ecology & Evolution上的文章Scallop genome provides insights into evolution of bilaterian karyotype and development讲的就是虾夷扇贝的故事。
虾夷扇贝哪里买？青岛台东海鲜市场早市有一家卖，新颖的34元/斤，不太新颖的也得30。（笔者连着两天看望过清晨五点半的青岛台东一路海鲜市场）
两种扇贝壳比照（上为虾夷扇贝，下为栉孔扇贝。© 海生张）
2.谁说研究扇贝的就只能讲扇贝的故事？
——通过扇贝来看生物的宏不雅进化
(1)扇贝的基因组是“化石基因组”？
做者们发现扇贝保留了近乎完美的古老染色体核型，是迄今为行发现的最接近双侧对称动物祖先的染色体核型。扇贝（单倍体染色体数为19）核型较为完美地与科学家们预言的双侧对称动物祖先（单倍体染色体数17）核型（Simakov, O. et al. Insights into bilaterian evolution from three spiralian genomes. Nature 493, 526–531 (2013)）相契合。而那个“化石基因组”关于研究双侧对称生物演化有着重要的意义。扇贝基因组，一把通向未知世界的奇异的钥匙🔑 。
The outstanding preservation of ancestral bilateriankaryotype in the scallop genome. Chromosome-based macrosynteny is shown in theform of dot plots with comparisons between the chromosomes of 12 bilateriangenomes (x axis) and the 17 presumed bilaterian ALGs (ALG1–17, y axis)that were previously reconstructed5.The scallop genome anchored in 19 chromosomes shows the highest level ofchromosome preservation (conservation index (CI) = 0.81) that far exceeds those of other bilaterians (CI = 0–0.42) withchromosome-level assemblies, suggesting that the scallop has a karyotypeclosely resembling that of a bilaterian ancestor. The haploid chromosome number(n) is shown for each species, and the CI measures the extent ofpreservation of bilaterian ALGs in each species. The chromosome-anchored genomeassemblies of Pacific oyster (C. gigas) and pearl oyster (P. fucata)were generated in this study by using two recently published high-densitylinkage maps
（2）Hox表达调控的新形式？
做者们发现扇贝基因组保留了最完好的Hox和ParaHox基因簇，提出了双侧对称动物Hox基因簇分段共线性（STC）表达新形式，阐了然动物体系体例发作决定基因Hox基因簇表达的起源和演化路子。
a, Chromosomal organization of Hox and ParaHox genesof scallop and other lophotrochozoans. Unlike other lophotrochozoans whose Hoxand ParaHox clusters are usually fragmented, both clusters arepresent as single, intact clusters in scallop, possibly representing theancestral state of these clusters in the lophotrochozoan ancestor (top).Horizontal arrows and triangles denote transcription orientation and externalgene insertion, respectively.
c, Temporal expression of scallop Hox and ParaHox clustergenes. Expression of ParaHox cluster follows temporal co-linearityduring embryonic and larval stages, whereas expression of Hox clusterexhibits an STC for four subclusters (S1: Hox1–Hox3, S2: Hox4–Hox5,S3: Lox5–Lox2, S4: Post2–Post1), with leading genesgenerally activated earlier than their followers in each subcluster. Verticalthick arrows indicate co-activation of leading genes of four subclusters,whereas thin arrows indicate gene activation order within each subcluster orthe whole cluster. 2-8cell, 2–8 cells; Bla, blastula; Gas, gastrula; Tro,trochophore; Dst, D-stage larva; Ped, pediveliger; Juv, juvenile.
d, Spatially co-linear expression of four leading genes (Hox1,Hox4, Lox5, Post2) of each subcluster at the gastrulastage. The expression regions of four leading genes almost span the entireanterior–posterior body axis, suggesting the prominent roles of these leadinggenes in early body plan determination. Expression of other Hox genes isnot detectable at this stage (see Supplementary Fig. 23) except Lox4,which is less likely to be a candidate leading gene as its expression does notconform to the characteristic pattern of leading genes (stronger expression atearly developmental stages than latter stages). A, anterior; P, posterior; V,ventral; D, dorsal. Scale bar, 50 μm.
Schematic illustration ofvarious types of Hox temporal expression andtheir possible evolutionary origins. The phenomenon of STC exists in an intact Hoxcluster of scallop and fragmented clusters of different lophotrochozoanlineages (bivalves and annelids)9,29 anddistantly related bilaterian groups (ecdysozoan and deuterostome)30,31, suggesting that STC could be ancestral. Thebasal bilaterian acoels33 have only threeunlinked Hox genes (corresponding to Hox1, Hox4/5 and Postparalogous group46), and it has beenproposed that these acoel Hox genes may belong to the ancient Hox clusterof Urbilateria or proto-Urbilateria, duplication of which gives rise to presentprotostome/deuterostome Hox clusters46.In the acoel Convolutriloba longifissura, all three Hox genesshow contemporaneous expression after gastrulation32,which is consistent with the co-activation of subclusters in scallop and otherbilaterians, and suggests STC might be established along with the stepwiseduplication of primordial Hox genes. Interestingly, the Hox expressionof the annelid C. teleta exhibits an unusual mode of WTC that issubcluster-based35 (called S-WTC here),probably representing an intermediate state in evolutionary transition betweenSTC and WTC. STC may be central to the bilaterian body plan evolution and, ifindeed ancestral, would provide bilaterian ancestors great potential ingenerating diverse body plans.
3.做扇贝，仍是要探究一些扇贝的生物学问题的
——看看扇贝的微不雅进化
3
（1）扇贝眼睛的遗传调控及进化起源
Summary of opsins and Pax genes used in cephalic andnoncephalic bilaterian eyes or light sensors from this and previous studies.The observation of cephalic and noncephalic bilaterian eyes controlled by different Pax regulators (Pax6 for the former and Pax2/5/8 for the latter) across majorbilaterian clades, supporting their different evolutionary origins.
研究发现扇贝眼睛的发作是由Pax2/5/8主导，向之前遍及认为眼睛起源单源论(以Pax6基因主导)提出了挑战。头眼（人类、果蝇等）由Pax6主导，而扇贝、线虫的躯干眼由Pax2/5/8主导。
Diversity of opsins andphototransduction cascades in scallop eyes.
a, Scallop has numerous noncephalic eyes scattered along mantlemargins, with two distinct retinal layers consisted of rhabdomeric and ciliaryPRCs, respectively (scale bars on the upper and lower images represent 5 cm and100 μm, respectively). Diverse opsin types (r-opsin, Go-opsin and c-opsin) are identified in the scallopgenome, with r-opsins showing the highest expression and probably playing aprominent role in scallop eye function. The finding of c-opsin expression inscallop eyes is intriguing, as c-opsin has not been identified in scallopsbefore and was once considered a vertebrate-type opsin for ciliaryphototranduction. Eye samples from three individuals were used in expressionevaluation with standard errors shown for eye and mantle groups.
b, Key components of different phototransduction cascades(mediated by r-opsin, Go-opsin and c-opsin)identified in the scallop genome with their gene expression in eyes relative tomantle colour-coded. The coexistence of multiple phototransduction cascades inscallop eyes is unusual and intriguing, as these cascades have been selectivelypreserved for visual function in invertebrates (r-opsin) and vertebrates(c-opsin). FC, fold change.
上图示研究发现的扇贝眼睛的多套光传导通路（别离由r-opsin、Go-opsin和c-opsin主导）及视卵白进化阐发。
（2）贝类毒素积累及耐受机造
Toxinresistance and response regulatory networks in the scallop kidney andhepatopancreas.
a Aminoacids conferring PST or TTX resistance on sodium channel Nav1 (highlighted inred) identified inthis and other studies. Skull signs indicate toxin-producing and -resistantspecies.
b Expressionof sodium channels Nav1 and Nav2, and PST concentration and toxicity levels inmajor organs of C. farreri. Toxicity (μgSTX eq. per 100 g) was determined by converting total concentration of PSTs tomicrograms of STX equivalents per 100 g of tissue.
c Temporalvariations in abundance of different PSTs and gene networks in the kidney andhepatopancreas after exposure to the toxic alga Alexandrium minutum. Toxin response modules were identified by enrichment analysis of DEGs duringexposure to A. minutum and eachmodule was annotated with the two most significantly enriched GO term(s). The green moduleis the largest kidney-specificresponse module, where cytosolic sulfotransferase (Sult) genes are enriched andhighly expressed on day 5 after A. minutum exposure (as indicated in the heatmap).
d Aschematic diagram showing different roles of the scallop hepatopancreas andkidney in toxin metabolism, with the hepatopancreas primarily responsible forPST accumulation, whereas the kidney primarily for PST transformation mediatedby SULTs.
做者们探究了扇贝对麻木性贝毒（PST）积累、转化及耐受的组学根底，确定肾脏是扇贝毒素转化的次要器官，解析了PST攻毒过程中扇贝的基因收集调控及表达形式，提出了扇贝贝毒耐受及转化的遗传机造。
所以以后吃扇贝的时候，请先把毒素含量更高的肝胰腺（黑色一坨）和肾脏（两颗小黄豆状）剔除再吃吧！
（3）扇贝足丝构成及黏附机造
The evolution of opsin diversity and photoreceptiontuning in C. farreri.
a. Morphology of scallop eyes scattered along the edge ofmantles (left, scale bar: 1 cm), schematic structure of a typical scallop eye(middle), and expression of diverse opsin genes in scallop eyes (right). Eyesamples from three individuals were used in expression evaluation with standarderror shown for eye and mantle groups. The asterisks indicate genes showingsignificantly higher expression in eyes than in the mantle (p-value< 0.05, the exact test by edgeR).
b. R-opsin gene structures of Mollusca and Branchiopoda.Exons rather than introns were plotted in proportion, with scale barrepresenting 500 bp. NETR (neurotrypsin) and FPV246 (putative ankyrin repeatprotein) are the conserved neighboring genes.
c. Sequence similarity and Ka/Ks values of all opsingenes between the scallops of C. farreri (CF)and P. yessoensis (PY). These datawere calculated based on full protein sequences. The black line insides the boxindicates the median value, and the whiskers extend from the first or third quartiles to the minimum or maximum values.
d. Bivalve opsin phylogeny and variation at keyfunctional sites sensitive to various light ranges. Species abbreviations: Chlamys farreri (CF), Pinctada fucata (PF), Crassostrea gigas (CG), Argopecten irradians (AI), Patinopecten caurinus (PC) and Argopecten purpuratus (AP). Sitecombinations of “SFA” “GFA” and “AFA” above the major branches are the putativeancestral bivalve types deduced from extant species. Colors of the sitescorrespond to the colors or wavelengths of opsin sensitivity in human opsins
研究查了然扇贝足丝显微构造及卵白关键组分，确定了酪氨酸酶、磷酸化酶等酶类参与的催化反响对足丝粘附起重要感化。海洋生物黏附质料？听起来就很有应用前景呢！
4.文章背后的故事？我们学到了什么样的科研精神？
4
4
合做。那两篇文章都不是以一人之力、一尝试室之力完成。霸占一个科学难题，可能需要来自差别学校/科研机构、差别研究标的目的的科研工做者们的群策群力。
自信。“我一个做水产育种的为啥不克不及颁发最顶级的文章？！” 那种自信不是自觉自卑，而是在尝试室教师们履历屡次失败后生长
起来的。
勤奋。看起来是包教师团队在一年内颁发了那两篇文章，可是那两篇文章的工做花了整个科研团队好几年的时间，可谓厚积薄发！
向研究人员们致敬！
此外，海生张比来正在烟台市某育苗场处置扇贝育种工做，请看他从消费一线发来的照片。
那么大的虾夷扇贝我可是第一次见
斑斓的海湾扇贝
扇贝销魂的泳姿
后续会推出《小师弟下场日志》，我们一路走进扇贝育种场，去看看我们餐桌上营养而甘旨的扇贝是怎么长大的。敬请等待!
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