Reciprocal chromosome painting illuminates the history of genome evolution of the domestic cat, dog and human

Domestic cats and dogs are important companion animals and model animals in biomedical research. The cat has a highly conserved karyotype, closely resembling the ancestral karyotype of mammals, while the dog has one of the most extensively rearranged mammalian karyotypes investigated so far. We have constructed the first detailed comparative chromosome map of the domestic dog and cat by reciprocal chromosome painting. Dog paints specific for the 38 autosomes and the X chromosomes delineated 68 conserved chromosomal segments in the cat, while reverse painting of cat probes onto red fox and dog chromosomes revealed 65 conserved segments. Most conserved segments on cat chromosomes also show a high degree of conservation in G-banding patterns compared with their canine counterparts. At least 47 chromosomal fissions (breaks), 25 fusions and one inversion are needed to convert the cat karyotype to that of the dog, confirming that extensive chromosome rearrangements differentiate the karyotypes of the cat and dog. Comparative analysis of the distribution patterns of conserved segments defined by dog paints on cat and human chromosomes has refined the human/cat comparative genome map and, most importantly, has revealed 15 cryptic inversions in seven large chromosomal regions of conserved synteny between humans and cats.

Comparative genome maps of the pangolin, hedgehog, sloth, anteater and human revealed by cross-species chromosome painting: further insight into the ancestral karyotype and genome evolution of eutherian mammals

To better understand the evolution of genome organization of eutherian mammals, comparative maps based on chromosome painting have been constructed between human and representative species of three eutherian orders: Xenarthra, Pholidota, and Eulipotyphla,

The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii : Cyprinifonnes) and an altemative pattem of mitogenomic evolution in vertebrate

The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S) 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely 9 related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny. (C) 2007 Published by Elsevier B.V.

Contrast features of CpG islands in the promoter and other regions in the dog genome

The recent release of the domestic dog genome provides us with an ideal opportunity to investigate dog-specific genomic features. In this study, we performed a systematic analysis of CpG islands (CGIs), which are often considered gene markers, in the dog

DIFFERENT RATES OF MITOCHONDRIAL-DNA SEQUENCE EVOLUTION IN KIRK DIK-DIK (MADOQUA-KIRKII) POPULATIONS

We have investigated evolutionary rates of the mitochondrial genome among individuals of Madoqua kirkii using the relative rate test. Our results demonstrate that individuals of two chromosome races, East African cytotype A and Southwest African cytotype D, evolve about 2.3 times faster than East African cytotype B. Cytogenetic changes, DNA repair efficiency, mutagens, and more likely, hitherto unrecognized factors will account for the rate difference we have observed. Our results suggest additional caution when using molecular clocks in the estimation of divergence time, even within lineages of closely related taxa. Rate heterogeneity in microevolutionary timescales represents a potentially important aspect of basic evolutionary processes and may provide additional insights into factors which affect genome evolution. (C) 1995 Academic Press, Inc.

高山松的二倍体杂种起源-来自三个基因组的证据

利用松科植物特殊的遗传体系（叶绿体基因组一父系遗传、线粒体基因组—母系遗传、核基因组一双亲遗传），我们对高山松及其两个亲本种进行了广泛的群体取样，通过线粒体基因nadl、叶绿体基因rbcL和trnL-F基因间区以及低拷贝核基因4CL的序列分析或PCR-RFLP分析，为高山松同倍体杂种起源假说提供了翔实的遗传学证据，同时在个体水平上探讨了高山松不同群体的遗传组成、群体遗传结构、基因交流方向、群体建立过程以及杂种基因组的进化。具体结果如下： 1．细胞质基因组分析 1)线粒体基因nudl分析 本研究对油松、高山松和云南松的19个群体、295个个体的线粒体基因nadl的一个内含子进行了序列分析或PCR-RFLP分析，共检测到3种线粒体DNA单倍型-A、B和C。油松所有的取样群体仅含单倍型A;除BX群体外，所有的云南松群体仅含单倍型B; 10个高山松群体中，5个群体固定单倍型A，4个群体固定单倍型B，1个群体(ZD)分布有A和B两种单倍型。2)叶绿体rbcL基因分析 对同一组群体的rbcL基因进行序列分析或PCR-RFLP分析，共检测到两个变异位点和三种叶绿体单倍型（TT、TC和GC）。TT和GC分别是油松和云南松种特异性叶绿体单倍型，而在高山松群体里则三种单倍型均有分布，而且TC单倍型广泛地分布在7个杂种群体中，该单倍型很可能来源于点突变或第三个已灭绝的亲本。rbcL基因检测到的高山松群体分化系数很高(Gst=0.533)。 3)叶绿体trn L-F区序列分析 叶绿体trnL-F分子标记检测到的不同单倍型的差异主要是由引物“e”下游120碱基处一个多聚T结构的长度变异所致（叶绿体SSR位点）。10个高山松群体中共检测到5种叶绿体单倍型，其中两种主要的单倍型(9T和11T)分别为油松和云南松的种特异性单倍型，其他单倍型均为非典型单倍型。群体遗传结构分析表明：杂种群体表现最高的遗传多样性，而且trnL-F分析得到的高山松群体的分化系数也很高( Gst=0.443)。 总之，对高山松、油松和云南松的同一组群体取样进行的细胞质基因组分析表明：高山松群体分布有油松和云南松种特异性的线粒体和叶绿体单倍型，该细胞质DNA单倍型的地理分布为假说“高山松为油松和云南松的的二倍体杂种”提供了翔实的遗传学证据。油松和云南松在不同的杂种群体中分别做父本和母本，即两亲本在杂交过程中发生了双向基因交流。群体遗传结构分析发现高山松群体表现最高的遗传多样性，而且群体间的分化系数很高。不同的杂种群体在遗传组成上的差异表明他们经历过不同的建立和进化历史。从线粒体和叶绿体单倍型的地理分布可以看出杂种群体的建立曾经历强烈的奠基者效应和回交。青藏高原的隆升对高山松的起源、杂种群体的适应辐射以及保持产生了重要的影响。川西南和滇西北作为青藏高原的东边边界，很可能是当初云南松和油松分布的重叠区及杂交地带，即高山松的起源地。 2．核基因4CL分析 对高山松、油松和云南松的19个群体、32个个体的低拷贝核基因4CL进行了克隆及序列分析，获得的78条序列可分为两种类型（类型A和类型B）。这两种类型明显的差别是类型A相对于类型B在内含子区有- 20bp的缺失。以华山松的3条序列为外类群，对得到的78条序列进行基因谱系分析，发现所有的序列分成明显的两支，分别对应于类型A和类型B，而且每一支均包含三个种的部分序列，表明4CL基因在这三个种分化之前就已发生重复。另一个明显的特点是某个种的一条序列与另一个种的序列比其与同种的其他序列关系更近，可能因基因交流（杂交和渐渗）、非共祖、致同进化和重组等进化事件所致。三种松树中共检测到4CL基因序列的两种类型和六个亚类型，高山松群体中没有发现杂种独特的类型或亚类型。高山松和云南松共享三种序列亚类型以及最多的序列多态性，表明这两个种之间曾存在广泛的基因交流。

基因组的演化与人类起源

人类起源是生命演化的奇迹,也是长期以来生命科学领域最受关注的重大课题之一.作为目前已知的唯一高级智慧生物,人类对自身的起源问题一直十分关心.了解自身是人类最基本的愿望.在远古时代,人们就开始思考我们究竟是什么?我们从哪里来?历史上有很多关于人类起源的传说,比如女娲造人、亚当夏娃的故事、海猿说、杂交说、外星人说等.随着科学的发展,特别是自达尔文发表划时代的进化论以来,"人类跟其他动物一样,是自然进化的产物,从一个远古的似猿祖先进化而来"的思想已经被大家普遍接受.

Comparison of Pax1/9 locus reveals 500-Myr-old syntenic block and evolutionary conserved noncoding regions

Identification of conserved genomic regions within and between different genomes is crucial when studying genome evolution. Here, we described regions of strong synteny conservation between vertebrate deuterostomes (tetrapods and teleosts) and invertebrat

Stepwise loss of motilin and its specific receptor genes in rodents

Specific interactions among biomolecules drive virtually all cellular functions and underlie phenotypic complexity and diversity. Biomolecules are not isolated particles, but are elements of integrated interaction networks, and play their roles through specific interactions. Simultaneous emergence or loss of multiple interacting partners is unlikely. If one of the interacting partners is lost, then what are the evolutionary consequences for the retained partner? Taking advantages of the availability of the large number of mammalian genome sequences and knowledge of phylogenetic relationships of the species, we examined the evolutionary fate of the motilin (MLN) hormone gene, after the pseudogenization of its specific receptor, MLN receptor (MLNR), on the rodent lineage. We speculate that the MLNR gene became a pseudogene before the divergence of the squirrel and other rodents about 75 mya. The evolutionary consequences for the MLN gene were diverse. While an intact open reading frame for the MLN gene, which appears functional, was preserved in the kangaroo rat, the MLN gene became inactivated independently on the lineages leading to the guinea pig and the common ancestor of the mouse and rat. Gain and loss of specific interactions among biomolecules through the birth and death of genes for biomolecules point to a general evolutionary dynamic: gene birth and death are widespread phenomena in genome evolution, at the genetic level; thus, once mutations arise, a stepwise process of elaboration and optimization ensues, which gradually integrates and orders mutations into a coherent pattern.

The origin of new genes: Glimpses from the young and old

Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.

PCR survey of Hox genes in the goldfish Carassius auratus auratus

A tetraploidization event took place in the cyprinid lineage leading to goldfishes about 15 million years ago. A PCR survey for Hox genes in the goldfish Carassius auratus auratus (Actinopterygii: Cyprinidae) was performed to assess the consequences of this genome duplication. Not surprisingly, the genomic organization of the Hox gene clusters of goldfish is similar to that of the closely related zebrafish (Danio rerio). However, the goldfish exhibits a much larger number of recent pseudogenes, which are characterized by indels. These findings are consistent with the hypothesis that dosage effects cause selection pressure to rapidly silence crucial developmental regulators after a tetraploidization event.

C-values of seven marine mammal species determined by flow cytometry

C-values, which estimate genome size, have puzzled geneticists for years because they bear no relationship to organismal complexity. Though C-values have been estimated for thousands of species, considerably more data are required in order to better understanding genome evolution. This is particularly true for mammals, in which C-values are known for less than 8% of the total number of mammalian species. Among marine mammals, a C-value has been estimated only for the bottlenose dolphin (Tursiops truncatus). Thus examination of additional species of marine mammals is necessary for comparative purposes. It will enable a better understanding of marine mammal genome evolution, and it is also relevant to conservation, because larger genome size has been linked to increased likelihood of extinction in some plant and animal groups. Our study presents C-values of seven marine mammal species, including five cetacean species that are endangered to varying degrees. Similarly to the results for other groups, our results suggest that larger genome size in cetaceans is related to an increased likelihood of extinction.

Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting

With complete sets of chromosome-specific painting probes derived from flow-sorted chromosomes of human and grey squirrel (Sciurus carolinensis), the whole genome homologies between human and representatives of tree squirrels (Sciurus carolinensis, Callosciurus erythraeus), flying squirrels (Petaurista albiventer) and chipmunks (Tamias sibiricus) have been defined by cross-species chromosome painting. The results show that, unlike the highly rearranged karyotypes of mouse and rat, the karyotypes of squirrels are highly conserved. Two methods have been used to reconstruct the genome phylogeny of squirrels with the laboratory rabbit (Oryctolagus cuniculus) as the out-group: ( 1) phylogenetic analysis by parsimony using chromosomal characters identified by comparative cytogenetic approaches; ( 2) mapping the genome rearrangements onto recently published sequence-based molecular trees. Our chromosome painting results, in combination with molecular data, show that flying squirrels are phylogenetically close to New World tree squirrels. Chromosome painting and G-banding comparisons place chipmunks ( Tamias sibiricus), with a derived karyotype, outside the clade comprising tree and flying squirrels. The superorder Glires (order Rodentia + order Lagomorpha) is firmly supported by two conserved syntenic associations between human chromosomes 1 and 10p homologues, and between 9 and 11 homologues.