燕麦属细胞遗传学研究进展

整理燕麦属(Avena L.)细胞遗传学研究文献,总结相关研究进展。燕麦属有7组29种植物,分属5个基因组类型(A、C、AB、AC、ACD)。基于荧光原位杂交技术和种间杂交实验表明,A、C基因组染色体结构差异较大,A基因组二倍体物种具有等臂染色体,C基因组二倍体物种具有不等臂染色体。燕麦属植物D基因组和A基因组间分化程度较小,B基因组有可能是A基因组的变型——A′基因组。普遍观点认为A基因组二倍体物种可能是燕麦属六倍体物种母系亲本,砂燕麦(A.strigosa)为该属多倍体物种A基因组祖先的假说备受争议,有学者认为加那利燕麦(A.canariensis)可能是多倍体物种A或D基因组的供体。燕麦属多倍体物种基因组互换及染色体重排事件,增加燕麦属种间亲缘关系、多倍体物种基因组起源研究的困难。结合基因组学、分子细胞遗传学技术,有望为上述问题提供新证据。     

西瓜含有JmjC结构域的组蛋白去甲基化酶家族的生物信息学分析

利用生物信息学方法,对西瓜（Citrullus lanatus（Thunb.）Matsum.&Nakai）JmjC基因家族的成员进行鉴定,对该基因家族的染色体定位、基因结构、蛋白结构域、选择压力和酶活位点进行分析,并对该基因家族与其它物种的系统进化及共线性关系进行研究。结果显示：西瓜全基因组含有17个JmjC候选基因,核苷酸序列长度为1209~5541 bp;这些基因均含有JmjC结构域,分别位于9条染色体上,归属8个亚族。系统进化、选择压力以及共线性分析结果表明,西瓜与黄瓜（Cucumis sativus L.）亲缘关系较近,JmjC家族基因数量相同,其中14个成员呈现一对一的共线性关系;而西瓜与拟南芥（Arabidopsis thaliana（L.）Heynh）亲缘关系较远,但西瓜和拟南芥同一亚族中JmjC基因间K_a/K_s的比值均小于1,推测西瓜各个亚族成员的编码蛋白功能与同一亚族的拟南芥成员功能极为相似。酶活位点分析结果表明西瓜JmjC基因家族中有10个成员具有潜在的组蛋白去甲基化酶活性。     

一株海洋藻类的分子鉴定及分类

海洋藻类种类繁多,由于形态的易变性和生活史的复杂性,传统的形态分类往往十分困难.分子标记技术的发展,使DNA分子成为区分物种的有效手段,成功地解决了许多疑难藻种的分类鉴定问题.本研究测定和比较了一株海洋藻类ST3的18srDNA基因部分核苷酸序列,序列长度为1733bp,通过与GenBank中序列数据进行比较分析,对其进行了分子鉴定和分类.研究结果表明藻株ST3属于硅藻门海链藻目,与骨条藻属的亲缘关系较海链藻属为近,但与骨条藻属遗传距离远大于骨条藻属种间差异,说明ST3可能是硅藻门海链藻目新的藻属.18srDNA可用于海洋藻类分子分类与鉴定.     

同域分布的3种木蓼属植物叶绿体基因组比较

刺木蓼(Atraphaxis spinosa)、额河木蓼(A. jrtyschensis)和细枝木蓼(A. decipiens)是同域分布在我国新疆北部的3种木蓼属物种。通过二代高通量测序,对叶绿体基因组进行组装和注释,比较3个物种的叶绿体基因组差异并进行系统发育分析。结果表明,木蓼属3个物种的叶绿体全基因组大小为164 106–164 216 bp,与其它绿色植物类似,由1个大单拷贝区(LSC)、1个小单拷贝区(SSC)及介于二者之间的2个反向重复区(IRa/IRb)组成。在刺木蓼、额河木蓼和细枝木蓼中检测到48–49个串联重复序列及59–63个简单重复序列(SSR)。3个物种的核苷酸多样性平均值为0.000 96,Ka/Ks平均值为0.030 3,遗传距离平均值为0.001 0。通过对3个物种的叶绿体基因组进行比较,发现编码区比非编码区更保守。系统发育分析结果显示3个物种的亲缘关系较近。该研究基于叶绿体基因组对木蓼属物种的亲缘关系进行分析,揭示了3个同域分布的物种之间的亲缘关系以及木蓼属在蓼科中的系统位置。研究结果可为木蓼属的分类学、系统学和生物地理学研究提供参考。     

动物远缘杂交研究进展

远缘杂交是指亲缘关系在种间及种间以上的生物之间的杂交,它可以使基因组从一个物种转移到另一个物种中,从而导致杂交后代的表现型和基因型都发生改变.如果远缘杂交后代两性可育,则可以通过自交繁衍形成遗传变异的品系,它们在生物进化、遗传和育种方面具有重要作用.本文在分析和归纳大量国内外有关动物远缘杂交文献的基础上,结合本实验室长期从事鱼类远缘杂交的研究结果,对动物远缘杂交研究的最近概况及其相关问题进行了较全面综述,其中介绍了动物门间、纲间、目间、科间、亚科间、属间和种间的杂交状况,阐述了鱼类远缘杂交品系的形成规律和遗传变异特性及它们在生产上的应用等.本文在生物进化和动物遗传育种方面具有意义.     

基因组原位杂交技术及其在园艺植物基因组研究中的应用

基因组原位杂交(GISH)技术可以鉴定植物多倍体物种起源、杂种亲本染色体来源和组成,分析栽培种与其近缘野生种的亲缘关系,研究减数分裂染色体行为等。基因组原位杂交包括多色基因组原位杂交、比较基因组原位杂交和自身基因组原位杂交等。基因组原位杂交技术的关键步骤是染色体制片、探针制备及长度优化、探针与封阻的浓度比例和杂交后洗脱强度。该文对近年来国内外有关基因组原位杂交技术的发展及其在园艺植物基因组研究中的应用现状进行了综述,并指出随着多种园艺植物全基因组的测定,未来应从基因组信息中寻找更多的染色体特异性标记,结合荧光显带及荧光原位杂交技术,为深入研究园艺植物的起源以及遗传关系鉴定等提供技术支持。     

丝兰属6种植物叶绿体基因组特征分析

为了理清丝兰属（Yucca）叶绿体基因组特征和序列变异情况,进行丝兰属植物叶绿体比较基因组学分析,并构建基于叶绿体基因组的系统发育树。利用高通量测序技术获得无刺龙舌兰（Y. treculeana）叶绿体基因组序列,结合丝兰属现已发表的叶绿体基因组,使用生物信息学方法对6种丝兰属植物叶绿体全基因组进行基本结构、重复序列、边界收缩与扩张以及序列变异分析等在内的比较基因组学研究,并进行系统发育分析。结果表明：6种丝兰属植物叶绿体基因组大小、基因的类型及数目相近,种间基因组结构比较保守;从丝兰属植物叶绿体基因组中检测到多条重复序列,其中SSR位点多是由单核苷酸、双核苷酸和四核苷酸组成,且偏好使用A、T碱基;根据核酸多态性指数π≥0.008,在6种丝兰属植物叶绿体基因组中筛选出了psbK-psbl-trnS-GCU、rpl20-rps12和ccsA-ndhD 3个高变异区域;基于叶绿体全基因组和LSC+SSC区序列构建的系统发育关系基本一致,确定了6种丝兰属植物间的系统发育关系,其中无刺龙舌兰与克雷塔罗丝兰（Y. queretaroensis）的亲缘关系最近。本研究测序获得了无刺龙舌兰叶绿体基因组,揭示了6种丝兰属植物叶绿体基因组特征和序列变异情况,明确了各物种间的亲缘关系,研究结果可为后续丝兰属植物分子标记开发及系统发育研究提供参考。     

利用SSR技术研究花生属种间亲缘关系

用44对SSR特异引物对花生属不同区组的21份种质进行了分析,获得能稳定揭示花生属种间差异的SSR引物34对。34对引物在21份种质中共检测到190个等位基因变异,每个位点上检测的等位变异数为3~11个,平均为5.59个。21份材料间存在很大的遗传变异,平均遗传距离为0.63,变异范围为0.08~0.95。聚类分析表明,区组间的遗传分化大于区组内的遗传分化,匍匐区组的遗传分化大于其他区组的遗传分化,同一物种不同种质间也存在很大的差异。栽培种花生与花生区组材料的亲缘关系相对较近,与花生属的植物学分类一致,其中A基因组的A.duranensis和A.villosa及B基因组的A.bati-zocoi与栽培种花生的亲缘关系更近一些。     

基于全基因组的微生物亲缘关系与分类系统研究工具——CVTree

组分矢量构树(CVTree)方法是基于全基因组的、不用序列联配的物种亲缘关系研究方法。CVTree3是我们最新开发的CVTree网络服务器,它基于并行化的核心程序,以适应当前基因组数据的海量增加;它自动对比物种亲缘关系与分类系统,并在网页上以交互作用形式显示,从而使研究更加直观。使用CVTree3网络服务器,用户可以快速的对未知的全基因组序列进行亲缘关系分析,并对其分类地位进行初步鉴定。由于合理利用全基因组信息,CVTree方法能对种以下的亲缘关系与分类具有高分辨力。随着CVTree方法的深入与完善,希望其能成为阐明原核生物亲缘关系与分类系统的定义性的工具。     

芸薹属A，B和C基因组之间关系研究进展

芸薹属A,B和C基因组之间的亲缘关系近年来取得了很大进展,大量细胞遗传学和分子生物学的研究结果表明A和C基因组之间的亲缘关系较A和B基因组以及B和C基因组之间更为接近。A,B和C基因组之间的比较基因组结果表明,这3个基因组是由更加原始物种进化而来的。在芸薹属基因组演化过程中发生了大量的染色体变异,如重复、缺失、重排等,从而造成了现在不同基因组之间的差别。最后,文章对芸薹属不同基因组和拟南芥基因组之间的亲缘关系进行了综述。     

A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F(8) population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ～800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits.     

Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH

Arachis hypogaea is a natural, well-established allotetraploid (AABB) with 2n = 40. However, researchers disagree on the diploid genome donor species and on whether peanut originated by a single or multiple events of polyploidization. Here we provide evidence on the genetic origin of peanut and on the involved wild relatives using double GISH (genomic in situ hybridization). Seven wild diploid species (2n = 20), harboring either the A or B genome, were tested. Of all genomic DNA probe combinations assayed, A. duranensis (A genome) and A. ipaensis (B genome) appeared to be the best candidates for the genome donors because they yielded the most intense and uniform hybridization pattern when tested against the corresponding chromosome subsets of A. hypogaea. A similar GISH pattern was observed for all varieties of the cultigen and also for A. monticola. These results suggest that all presently known subspecies and varieties of A. hypogaea have arisen from a unique allotetraploid plant population, or alternatively, from different allotetraploid populations that originated from the same two diploid species. Furthermore, the bulk of the data demonstrated a close genomic relationship between both tetraploids and strongly supports the hypothesis that A. monticola is the immediate wild antecessor of A. hypogaea.     

利用栽培稻C0t-1DNA和基因组DNA比较分析斑点野生稻和短药野生稻基因组

通过荧光原位杂交(FISH)利用来源于A基因组栽培稻的中高度重复序列C0t-1DNA和基因组DNA作为探针,对栽培稻、斑点野生稻和短药野生稻进行了比较基因组分析。结果发现C0t-1DNA杂交信号主要分布在这3种染色体的着丝粒、近着丝粒和端粒区域,在斑点野生稻染色体上的信号多于短药野生稻,与gDNA作为探针FISH的结果相一致,说明A和B基因组间的亲缘关系明显近于A和F基因组。确定了含有中高度重复序列的C0t-1DNA用于属内种间关系研究的可行性,并根据C0t-1DNA的FISH结果进行了染色体核型分析。     

Genomic in situ hybridization in Avena sativa.

Genomic fluorescent in situ hybridization was employed in the study of the genome organization and evolution of hexaploid oat (Avena sativa L. cv. Sun II, AACCDD, 2n = 6x = 42). Genomic DNAs from two diploid oat species, Avena strigosa (genomic constitution AsAs, 2n = 14) and Avena pilosa (genomic constitution CpCp, 2n = 14), were used as probes in the study. The DNA from A. strigosa labelled 28 of the 42 (2/3) chromosomes of the hexaploid oat, while 14 of the 42 (1/3) chromosomes were labelled with A. pilosa DNA, indicating a close relationship between the A and D genomes. Results also suggested that at least 18 chromosomes (9 pairs) were involved in intergenomic interchanges between the A and C genomes.     

Molecular phylogeny of Cucumis species as revealed by consensus chloroplast SSR marker length and sequence variation.

To investigate phylogenetic relationships in the genus Cucumis, 9 consensus chloroplast simple sequence repeat (ccSSR) primer pairs (ccSSR3, 9, 11, 13, 14, 17, 20, 21, and 23) were employed for DNA fragment length variation and 5 amplified fragments, ccSSR4, 12, 13, 19, and 20, were sequenced using total DNA from 13 accessions representing 7 African Cucumis species (x = 12), 3 Cucumis melo L. (x = 12) accessions, 2 Cucumis sativus L. (x = 7) accessions, and 1 Cucumis hystrix Chakr. (x = 12) accession. A Citrullus lanatus (Thunb.) Matsum. & Nakai (x = 11) accession was used as an outgroup. While fragment length analysis revealed the existence of 3 major species clusters (i.e., a group of African Cucumis species, a group composed of C. melo accessions, and a group containing C. sativus and C. hystrix species), sequence variation analysis identified 2 major species clusters (i.e., a group of African Cucumis species and a group composed of C. melo, C. sativus, and C. hystrix species). Comparative analysis using nuclear DNA (previous studies) and cpDNA sequence substitution data resulted in the placement of C. melo and C. sativus in different cluster groupings. Thus, both nuclear and cytoplasmic DNA should be employed and compared when a putative progenitor or specimens of an ancestral Cucumis species lineage is investigated. In addition, C. ficifolius (2x) and C. aculeatus (4x) of the African Cucumis species clustered together in this study. This result does not agree with reported isozyme analyses, but does agree with previously characterized chromosome homologies between these 2 species. Although African Cucumis species and C. hystrix do not share a close relationship, genetic affinities between C. sativus and C. hystrix are considerable. Combined evidence from previously published studies and data presented herein lend support to the hypothesis that C. hystrix is either a progenitor species of C. sativus or that they at least share a common ancestral lineage.     

Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa.

DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.     

A study of 28 Elymus species using repetitive DNA sequences.

Four repetitive DNA sequences cloned from the barley (Hordeum vulgare) genome and common for different Triticeae species were used for a molecular study of phylogenetic relationships among 28 Elymus species. Two wild Hordeum species (H genome), two Pseudoroegneria species (S genome), Agropyron cristatum (P genome), and Australopyrum velutinum (W genome) were included as genomic representatives for the genomes that supposedly were involved in the evolution of the genus Elymus. Our results are essentially congruent with the genomic classification system. This study demonstrates that Elymus is not a monophyletic genus. Based on an analysis of Southern blot hybridization we could discriminate between SY and SH species owing to the strong specific hybridization pattern of the H genome. Hexaploid SYH species gave a hybridization pattern similar to SH species for the same reason. The results support the genomic composition of Elymus batalinii as SYP and also indicated the presence of at least one H genome in Elymus enysii with a hitherto unknown genomic constitution. Elymus erianthus had a hybridization pattern distinctly different from all other species in the investigation. Key words : Elymus, RFLP, phylogeny, repetitive DNA.