9种石斑鱼遗传多样性和系统发生关系的微卫星分析

利用实验室克隆的13个青石斑鱼微卫星分子标记, 对中国南海海域9种石斑鱼(青石斑鱼、蜂巢石斑鱼、鲑点石斑鱼、黑边石斑鱼、鞍带石斑鱼、赤点石斑鱼、七带石斑鱼、斜带石斑鱼和棕点石斑鱼)进行了遗传多样性和系统发生关系的分析。研究结果显示, 13个微卫星标记共检测到了84个等位基因, 9种石斑鱼中的平均等位基因数、平均多态信息含量(PIC)、平均观测杂合度(Ho)、平均期望杂合度(He)和平均Hardy-Weinberg遗传偏离指数(D)分别在2.69~5.38、0.1976~0.4267、0.4615~0.6239、0.3510~0.4754和0.1097~0.2836之间变动, 说明9种石斑鱼的遗传多样性都处于中等水平。用NJ法进行聚类分析的结果将9种石斑鱼分为3个支系：斜带石斑鱼、棕点石斑鱼和鞍带石斑鱼为第1支; 青石斑鱼、赤点石斑鱼和七带石斑鱼为第2支系; 蜂巢石斑鱼、黑边石斑鱼和鲑点石斑鱼为第3支系, 该支系与第2支系的关系较近。本研究支持将宽额鲈(鞍带石斑鱼)归入石斑鱼属。     

栲树微卫星分子标记的开发

采用基因组DNA富集法FIASCO对我国典型常绿阔叶林建群种栲树(Castanopsis fargesii Franch.)进行了微卫星分子标记的开发。从栲树基因组中分离和筛选了15个微卫星位点,并对江西九连山栲树自然分布居群的遗传多样性进行了分析。结果表明,栲树具有较高水平的遗传多样性,每个位点在28株栲树个体上的平均等位基因数(A)为6.7(4～8个),平均观察杂合度(HO)为0.690(0.250～1.000),平均预期杂合度(HE)为0.698(0.293～0.867)。每个位点的第一排除概率值Pr(Ex1)为0.043～0.527,位点综合值为0.9972。单个位点的第二排除概率Pr(EX2)为0.159～0.694,位点综合值为0.9999。这些微卫星标记可为研究栲树的遗传多样性及居群遗传结构提供有效的遗传工具。     

大鸨东方亚种遗传多样性的微卫星分析

为了探索东方亚种数量正在减少的原因和制定科学、有效的保护措施,利用微卫星DNA对大鸨东方亚种(Otistardadybowskii)的遗传多样性进行了研究。应用3个大鸨指名亚种的微卫星位点和13个波斑鸨的微卫星位点扩增了47个个体的基因组DNA,筛选出8个具有多态性的微卫星。其中有3个微卫星的多态性较低,其余5个微卫星的多态性较高。各位点的观察杂合度为0.0435-1.0000,平均杂合度(h)为0.6595;各位点多态信息含量(PIC)为0.0416-0.8520,平均为0.5497;有效等位基因数(E)为1.04-7.46,平均为3.61。4个位点符合HardyWeinberg平衡,4个位点偏离了HardyWeinberg平衡。多方面比较发现,大鸨东方亚种遗传多样性很低,且低于指名亚种,这可能由于其种群较小、历史遗传瓶颈作用、生境破碎化、分布地域紧缩等原因造成的。     

湖栖鳍虾虎鱼微卫星DNA标记的 开发与群体遗传多样性分析

为研究雷州半岛湖栖鳍虾虎鱼(Gobiopterus lacustris)遗传多样性,对湖栖鳍虾虎鱼雌雄性腺进行转录组测序,采用MISA软件进行微卫星分析,共获得25 452个微卫星标记,其中包含14 708个单碱基重复类型,6 175个2碱基重复类型,3、4、5和6碱基重复类型数目分别为4 223、327、15和4。随机选取50个微卫星位点设计引物,能够扩增出清晰稳定条带的有39对,其中,11个位点表现出不同程度的多态,28个位点呈现单态。利用11个具有多态性的微卫星位点分析湖栖鳍虾虎鱼在廉江市高桥镇红树林保护区、湛江东海岛、雷州市附城镇和雷州市九龙山红树林国家湿地公园4个野生群体中的遗传多样性及遗传结构,11个微卫星位点呈现出不同程度的多态性,等位基因数(Na)2～15,平均等位基因为(6?3.9)个,有效等位基因数(Ne)、平均观测杂合度(Ho)和期望杂合度(He)分别在1.919～2.485、0.343～0.465和0.381～0.483之间,平均多态信息含量(PIC)为0.348～0.465。Hardy-Weinber平衡分析显示,4个群体的大部分位点未偏离平衡。在每个群体中进行连锁不平衡分析,有18对位点间显著(P 0.05)或者极显著(P 0.01)偏离连锁平衡。遗传分化系数在0.107～0.216之间,表明4个群体的遗传分化达到了中等水平以上。分子方差分析(AMOVA)显示,湖栖鳍虾虎鱼大部分的差异来自于群体内而非群体间。     

布氏罗非鱼微卫星位点筛选和群体遗传多样性分析

为阐明布氏罗非(Tilapia buttikoferi)群体遗传变异和遗传结构状况,采用50个尼罗罗非鱼特异性的微卫星分子标记对45个布氏罗非鱼个体进行遗传检测.结果有27对引物能获得稳定的特异性条带,占总数的54%,其中16个多态性微卫星座位共检测出52个等位基因.每个座位的等位基因数为2～6之间,平均每个座位为3.24;平均观测杂合度(Ho)为0.5266,平均期望杂合度(He)为0.5237,平均多态信息含量为0.4652,表明布氏罗非鱼群体遗传多样性较丰富,种群结构处于合理状态.     

梅花鹿3个种群遗传多样性的微卫星标记分析

利用16个微卫星标记对黑龙江省部分地区(兴凯湖农场、大庆市银浪牧场、五大连池大庆农场鹿苑)的3个梅花鹿(Cervus nippon)群体进行了遗传多样性检测.统计了3个鹿群的等位基因组成、平均有效等位基因数(Ne)、平均遗传杂合度(h)和多态信息含量(PIC).结果表明,除5个位点外,其余11个微卫星位点均表现出不同的多态信息含量,其中高度多态位点5个,中度多态位点4个.这说明本研究所选用的微卫星位点可较准确地评估3个梅花鹿群体的遗传多样性,并为今后相关研究筛选出了有价值的引物.3个梅花鹿群体的平均h在0.454～0.636之间变动,其中兴凯湖梅花鹿群体最高,为0.636,具有较大的遗传潜力.     

微卫星DNA标记及其在鱼类遗传多样性研究中的应用

微卫星DNA作为第二代分子遗传标记是高等真核生物基因组中种类多、分布广、具有高度的多态性和杂合度的分子标记,由于其具有多态性检出率高、信息含量大、共显性标记、实验操作简单、结果稳定可靠等优点,已经成为种群遗传学研究中被广泛应用的分子遗传标记。微卫星DNA标记技术在鱼类的群体遗传结构的分析、物种遗传多样性的鉴定以及遗传基因连锁图谱的构建等方面已初步得到应用。该文就微卫星技术的原理方法,在鱼类遗传多样性研究中的应用概况以及应用范围和注意事项等方面进行综述。为微卫星技术在鱼类遗传多样性研究中应用提供了理论参考。     

元江鲤种群遗传多样性

选择12对微卫星标记检测了于2011年采集自元江(红河上游中国江段)5个样点192尾鲤的群体遗传多样性.共检测到201个等位基因,每个位点等位基因2-27个.各群体各位点平均等位基因(NA)12.25-14.67个,平均有效等位基因(NE)8.28-9.73个,平均观察杂合度(Ho)o.7765-0.8037,平均期望杂合度(HE)0.7761-0.8080,平均多态信息含量(PIC)0.7534-0.7843.元江鲤种群192个个体各位点NA、NE、Ho、HE、PIC分别为16.50、11.26、0.7927、0.8049、0.7966,种群遗传多样性水平高.元江鲤群体之间遗传分化小,可作为一个种群管理单元进行管理.增殖放流要防止遗传多样性丧失.     

鲮鱼的微卫星位点筛选和群体遗传多样性初步分析

利用鲤科鱼类微卫星引物在鲮鱼中进行扩增,结果在24对引物中,13对引物能成功扩增,且在鲮鱼中的扩增产物表现稳定,其中11对有较高多态性,等位基因数在2—7个之间,扩增的条带符合孟德尔遗传规律。随后利用筛选的微卫星座位对鲮鱼野生和养殖群体遗传多样性进行了初步分析。分析结果显示鲮鱼野生群体的平均等位基因数5.2个;观测杂合度在0.25与0.8之间,平均观测杂合度(Ho)是0.61±0.2 ,平均期望杂合度(He)是0.8±0.09 ;群体座位平均多态信息含量(PIC)为0.72±0.1。相比之下,养殖群体的平均观测杂合度(Ho)和平均期望杂合度(He)都低于野生群体,分别是0.59±0.2、0.75±0.1。两群体间的遗传相似度为0.7774、遗传距离为0.2518。研究表明用其他鱼类分离出的微卫星引物可以快速筛选到适用于鲮鱼遗传分析的微卫星座位。     

墨西哥湾扇贝与“中科红”海湾扇贝群体遗传多样性SSR分析

利用微卫星(SSR)分子标记技术,对墨西哥湾扇贝和"中科红"海湾扇贝2个群体共80个个体的遗传结构和遗传多样性进行分析。结果显示:6个微卫星位点共扩增出31个等位基因,各位点的等位基因数为4~8个,平均等位基因数为5.2个;墨西哥湾扇贝与"中科红"海湾扇贝群体平均有效等位基因数(Ne)分别为2.890、2.753;平均观测杂合度(Ho)分别为0.415、0.353;平均期望杂合度(He)分别为0.604、0.479;多态信息含量(PIC)分别为0.554、0.444;两群体具有相同的等位基因数(Na)(4.333)。Hardy-Weinberg平衡检验发现,2个群体各有3个位点(50%)偏离平衡(p0.05),且均表现为杂合子缺失。两群体的遗传分化指数(Fst)为0.109 7,遗传距离(Dxy)为0.316 4,遗传相似性系数为0.728 8。研究结果说明:两个群体均保持较高的遗传多样性,但经过多年的定向选育,"中科红"海湾扇贝群体的遗传多样性低于墨西哥湾扇贝群体且两个群体具有中等程度的遗传分化,存在一定的遗传差异。     

Assessment of genetic diversity and phylogenetic relationship among grouper species Epinephelus spp. from the Saudi waters of the Arabian Gulf

Understanding of fish genetic characterization plays a vital role in the conservation and utilization of fish genetic resources of grouper species. The present study was carried out to assess the genetic diversity and phylogenetic relationships in five grouper species, Epinephelus spp. from eastern Saudi Arabian coast using two molecular marker systems, inter simple sequence repeat (ISSR) and microsatellite (SSR) markers. In total, 219 individuals grouper specimens (Epinephelus tauvina, E. coioides, E. bleekeri, E. malabaricus, and E. areolatus) were genotyped with 10 ISSR and 11 SSR selected primers. The ISSR produced 94 DNA fragments, of which 44 were polymorphic with an average of 2.13 fragment per primer. While SSR primers generated 107 alleles, all of them were polymorphic with an average 9.72 per primer. ISSR and SSR techniques demonstrated a high level of gene diversity and genetic distances illustrated by UPGMA dendrograms among the grouper species. The results proved that the SSR markers were highly informative and efficient in detecting genetic variability and relationships of the Epinephelus spp.     

Isolation and characterization of polymorphic microsatellites from red coral grouper (Plectropomus maculatus)

The red coral grouper, Plectropomus maculatus, is a high value marine food fish species. We isolated the first set of 10 polymorphic microsatellites and examined their polymorphism in two related species: the Malabar grouper Epinephelus malabaricus and the brown‐marbled grouper Epinephelus fuscoguttatus. The average allele number of these 10 microsatellite DNA loci is 9.1/locus with a range of four to 17, whereas the expected heterozygosity ranged from 0.18 to 0.94, averaging 0.76. Five of the 10 markers amplified polymorphic and specific products in E. malabaricus, whereas only four were amplified in E. fuscoguttatus. These microsatellites could be applicable to captive breeding and to the studies on genetic diversity and population structure of grouper wild stocks.     

Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) × Epinephelus polyphekadion (male)

Hybridization is one of the primary methods used to cultivate farmed grouper species. The hybrid grouper derived from crossing Epinephelus fuscoguttatus (♀) and E. polyphekadion (♂) exhibits growth superiority over its parents. The genetic characteristics and growth patterns of the hybrid grouper have not yet been defined. This study confirms the ploidy level of the hybrid grouper (2n = 48) using chromosome count analysis and flow cytometry. The 5S rDNA family was used to evaluate genetic diversity. Only one 5S class (~400 bp) was detected in the hybrid grouper, which could be used to distinguish between two different types based on nucleotide sequences, likely representing homologous unit classes from the female and male parental species. Growth patterns of 5–8-month-old hybrid groupers were also monitored. In this phase, a positive allometric growth pattern in body mass with total length was found. Body height and body mass were significantly correlated based on correlation and path coefficient, suggesting that body height could serve as an excellent index to increase body mass. These results aid our understanding of the genetic evolution of the hybrid grouper and inform the development of improved rearing techniques.     

Molecular phylogeography of western Mediterranean dusky grouper Epinephelus marginatus

Intraspecific sequence variation in a portion of the gene coding for cytochrome b in the dusky grouper (Epinephelus marginatus Lowe 1834), an endangered fish species in various regions of the Mediterranean sea, was examined in 29 individuals from the western Mediterranean sea. Sixty-four phylogenetically informative nucleotide positions were present in a 353-base pair cytochrome b sequence, amplified using the polymerase chain reaction. Statistical analysis of the sequence data using a variety of tree-building algorithms separated the taxa into one group of dusky groupers corresponding to some of the Algerian individuals and another regrouped set of fishes originating in France, Tunisia and the remaining Algerian specimens. Although, on the basis of their morphology, E. marginatus are now considered as a single species, our results suggest that a subgroup of the Algerian dusky grouper constitutes a cryptic (undescribed) species. These results suggest that morphological and genetic evolution may be uncoupled in dusky grouper, resulting in morphological similarity between species despite extensive genetic divergence. In addition, we cannot rule out the possibility of gene introgression with other species of grouper. A more in depth phylogenetic analysis (i.e. between and within the different Epinephelus species) would likely affect many conservation management decisions about this assemblage of groupers.     

De novo assembly of a chromosome‐level reference genome of red‐spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi‐C

The red‐spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and South‐East Asia and is a threatened species. The species is also considered a good model for studies of sex inversion, development, genetic diversity and immunity. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a chromosome‐level reference genome of E. akaara by taking advantage of long‐read single‐molecule sequencing and de novo assembly by Oxford Nanopore Technology (ONT) and Hi‐C. A red‐spotted grouper genome of 1.135 Gb was assembled from a total of 106.29 Gb polished Nanopore sequence (GridION, ONT), equivalent to 96‐fold genome coverage. The assembled genome represents 96.8% completeness (BUSCO) with a contig N50 length of 5.25 Mb and a longest contig of 25.75 Mb. The contigs were clustered and ordered onto 24 pseudochromosomes covering approximately 95.55% of the genome assembly with Hi‐C data, with a scaffold N50 length of 46.03 Mb. The genome contained 43.02% repeat sequences and 5,480 noncoding RNAs. Furthermore, combined with several RNA‐seq data sets, 23,808 (99.5%) genes were functionally annotated from a total of 23,923 predicted protein‐coding sequences. The high‐quality chromosome‐level reference genome of E. akaara was assembled for the first time and will be a valuable resource for molecular breeding and functional genomics studies of red‐spotted grouper in the future.     

张家口土壤蜘蛛群落结构及多样性研究

1996年8月中旬,在张家口地区4种生境中共捕获土壤蜘蛛461头,隶属于12科54种(属)。研究表明:4种生境中的土壤蜘蛛群落相似性很小,群落结构组成不同,丰富度、多样性指数、均匀度、优势度也不同。植被类型、疏密程度是影响群落结构的主要生态因子,农事活动是另一个重要影响因素。     

Comparison of gene flow among species that occur within the same geographic locations versus gene flow among populations within species reveals introgression among several Elymus species

One of the challenges in evolutionary biology is to understand the evolution of speciation with incomplete reproductive isolation as many taxa have continued gene flow both during and after speciation. Comparison of population structure between sympatric and allopatric populations can reveal specific introgression and determine if introgression occurs in a unidirectional or bidirectional manner. Simple sequence repeat markers were used to characterize sympatric and allopatric population structure of plant species, Elymus alaskanus (Scribn. and Merr.) Löve, E. caninus L., E. fibrosus (Schrenk) Tzvel., and E. mutabilis (Drobov) Tzvelev. Our results showed that genetic diversity (H_E) at species level is E. caninus (0.5355) > E. alaskanus (0.4511) > E. fibrosus (0.3924) > E. mutabilis (0.3764), suggesting that E. caninus and E. alaskanus are more variable than E. fibrosus and E. mutabilis. Gene flow between species that occurs within the same geographic locations versus gene flow between populations within species was compared to provide evidence of introgression. Our results indicated that gene flow between species that occur within the same geographic location is higher than that between populations within species, suggesting that gene flow resulting from introgressive hybridization might have occurred among the sympatric populations of these species, and may play an important role in partitioning of genetic diversity among and within populations. The migration rate from E. fibrosus to E. mutabilis is highest (0.2631) among the four species studied. Asymmetrical rates of gene flow among four species were also observed. The findings highlight the complex evolution of these four Elymus species.     

Twelve novel polymorphic microsatellite loci for the Yellow grouper (Epinephelus awoara) and cross-species amplifications

Yellow grouper (Epinephelus awoara) is a commercially important marine fish species. A dinucleotide-enriched genomic library of E. awoara was constructed using the method of FIASCO. Twelve loci were polymorphic in a test population with alleles per locus ranging from two to eight, and observed and expected heterozygosities per locus from 0.13 to 1.00 and from 0.20 to 0.86, respectively. Five loci significantly deviated from Hardy–Weinberg equilibrium and no significant linkage disequilibrium was found between pairs of loci. Cross-species amplification of these polymorphic microsatellite loci was performed in additional two related species. These polymorphic microsatellite loci would be useful for investigating genetic diversity of E. awoara and related species. L. Zhao and C. Shao have contributed equally to this work.     

Six new and one previously described species of Pseudorhabdosynochus (Monogenoidea, Diplectanidae) infecting the gills of groupers (Perciformes, Serranidae) from the Pacific coasts of Mexico and Panama

Six new and 1 previously described species of Pseudorhabdosynochus (Diplectanidae) are described and/or reported from the gill lamellae of 5 serranid (Perciformes) fish species from the Pacific waters in Guerrero State of Mexico and Panama City, Panama. These species are Pseudorhabdosynochus guerreroensis n. sp. from the Pacific mutton hamlet Alphestes inmaculatus Breder (type host), rivulated mutton hamlet Alphestes multiguttatus (Günther), and spotted grouper Epinephelus analogus Gill from Mexico; Pseudorhabdosynochus urceolus n. sp. from the Pacific graysby Cephalopholis panamensis (Steindachner) from Taboga Island in Panama; Pseudorhabdosynochus spirani n. sp. from the starry grouper Epinephelus labriformis (Jenyns) from Mexico and the Perlas Archipelago and Taboga Island in Panama; Pseudorhabdosynochus fulgidus n. sp. from E. labriformis from Mexico and the Perlas Archipelago and Taboga Island (type locality) in Panama; Pseudorhabdosynochus tabogaensis n. sp. from E. labriformis from Mexico and the Perlas Archipelago and Taboga Island (type locality) in Panama; Pseudorhabdosynochus anulus n. sp. from E. labriformis from Mexico and Taboga Island (type locality) in Panama; and Pseudorhabdosynochus amplidiscatum (Bravo-Hollis, 1954) Kritsky and Beverley-Burton, 1986 from E. analogus and E. labriformis from Mexico and the Perlas Archipelago and Taboga Island in Panama. All new species are mainly distinguished from other species of the genus by the shape and size of the sclerotized vagina and haptoral structures. The present specimens of Alphestes, Cephalopholis, and Epinephelus spp. represent new host records and Panama represents a new geographic record for species of Pseudorhabdosynochus. The apparent common feature supporting a close similarity of these diplectanids is a single, secondary ejaculatory bulb with thickened wall.