Sporadic amplification of ID elements in rodents

ID sequences are members of a short interspersed element (SINE) repetitive DNA family within the rodent genome. The copy number of individual ID elements varies by up to three orders of magnitude between species. This amplification has been highly sporadic in the order Rodentia and does not follow any phylogenetic trend. Using library screening and dot-blot analysis, we estimate there are 25,000 copies of ID elements in the deer mouse, 1,500 copies in the gerbil (both cricetid rodents), and 60,000 copies of either ID or ID-like elements in a sciurid rodent (squirrel). By dot-blot analysis, we estimate there are 150,000, 4,000, 1,000, and 200 copies of ID elements in the rat, mouse, hamster, and guinea pig, respectively (which is consistent with previous reports) and 200 copies in the hystricognath rodent, nutria. Therefore, a rapid amplification took place not only after the divergence of rat and mouse but also following the deer mouse (Peromyscus) and hamster split, with no evidence of increased amplifications in hystricognath rodents. No notable variations of sequences from the BC1 genes of several myomorphic rodents were observed that would possibly explain the varied levels of ID amplification. We did observe subgenera and species-group-specific variation in the ID core sequence of the BC1 gene within the genus Peromyscus. Sequence analysis of cloned ID elements in Peromyscus show most ID elements in this genus arose prior to Peromyscus subgenus divergence. Correspondence of the consensus sequence of individual ID elements in gerbil and deer mouse further confirms BC1 as a master gene in ID amplification. Several possible mechanisms responsible for the quantitative variations are explored.The nucleotide sequences reported in this paper have been submitted to the GenBank/EMBL Data Bank with accession numbers: U33850, U33851, U33852 (BC1 sequences); and U33853, U33854, U33855, U33856, U33857, U33858, U33859, U33860, U33861, U33862, U33863, U33864, U33865, U33866, U33867 (ID sequences) Correspondence to: D.H. Kass     

Retrotransposon Mys was active during evolution of the Peromyscus leucopus-maniculatus complex

Mys is a retrovirus-like transposable element found throughout the genus Peromyscus. Several mys subfamilies identified on the basis of restriction site variation occur in more than one species. The distribution of these subfamilies is consistent with the accepted species phylogeny, suggesting that mys was present in the ancestor of Peromyscus and has been active through much of the evolution of this genus. Quantitative Southern blot analysis was used to examine the variability of subfamilies in P. leucopus and maniculatus. We found that subfamilies with phylogenetically narrow distributions were more variable in copy number both within and between species than subfamilies with a broader distribution. Taken together, our data suggest that mys has undergone multiple rounds of transposition since the peromyscine radiation, and that five subfamilies have been amplified during the evolution of the leucopus-maniculatus species complex. Correspondence to: H.A. Wichman     

Mus and Peromyscus chromosome homology established by FISH with three mouse paint probes

Fluorescence-labeled DNA probes constructed from three whole house mouse (Mus domesticus) chromosomes were hybridized to metaphase spreads from deer mouse (Peromyscus maniculatus) to identify homologies between the species. Mus Chr 7 probe hybridized strongly to the ad-centromeric two-thirds of Peromyscus Chr 1q. Most of Mus 3 probe hybridized principally to two disjunct segments of Peromyscus Chr 3. Mus Chr 9 probe hybridized entirely to the whole Peromyscus Chr 7. Three Peromyscus linkage groups were assigned to chromosomes, based on linkage homology with Mus. The data also are useful in interpretation of chromosomal evolutionary history in myomorphic rodents. Received: 1 December 1998 / Accepted: 17 February 1999     

Evidence for multiple functional copies of the male sex-determining locus, sry, in African murine rodents

Southern hybridization data suggest that the male sex-determining locus, Sry, is often duplicated in rodents. Here we explore DNA sequence evolution of orthologous and paralogous copies of Sry isolated from six species of African murines. PCR amplification followed by direct sequencing revealed from two to four copies of Sry per species. All copies include a long open reading frame, with a stop codon that coincides closely with the stop codon of the house mouse, Mus musculus, a species known to have a single copy of Sry. A phylogenetic analysis suggests that there are at least seven paralogous copies of Sry in this group of rodents. Putative orthologues are identical; sequence divergence among putative paralogues ranges from 1 to 8% (excluding the CAG repeat), with much lower levels of divergence in the high-mobility group (HMG-box) region than in the C-terminal region. A high proportion of nucleotide substitutions in both regions result in amino-acid replacement. The long open reading frame, conserved HMG-box, and pattern of evolution of the putative paralogues suggest that they are functional. Received: 4 October 1996 / Accepted: 17 January 1997     

Evolution of a B2 tagged sequence from a long-range repeat family in the genus Mus

A long-range repeat family of more than 50 kb repeat size is clustered in Chromosomes (Chr) 1 of Mus musculus and M. spretus. In M. musculus this long-range repeat family shows considerable variation of copy-number frequency and contains coding regions for at least two genes. In an intron of a gene, which is part of the repeat, a B2 small interspersed repetitive element (SINE) is inserted at identical positions. The B2 element is present in all copies of the long-range repeat family; it was presumably a component of the ancestral single-copy precursor sequence that gave rise by amplification to the repeat family. Copies of the long-range repeat family vary with respect to the number of TAAA tandem repeats in the A-rich 3 end region of the B2 element. As inferred from polymerase chain reaction (PCR) data, presence and frequency of repeat number variants in the (TAAA)_n block are strain and species specific. The B2 element and its flanking regions were sequenced from two copies of the long-range repeat family. Sequence divergence between the two copies (only non-CG base substitutions and deletions/insertions) was determined to be 2.6%. Based on the drift rate in human Alu elements and a correction for the higher drift rates in rodents, and estimate for the divergence time of 1.7 million years was calculated. Since the long-range repeat family is present in M. musculus and M. spretus, it must have evolved by amplification before the separation of the two species about 1–4 million years ago.     

Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae)

We investigated the evolutionary dynamics of duplicated copies of the granule-bound starch synthase I gene (GBSSI or Waxy) within polyploid Spartina species. Molecular cloning, sequencing, and phylogenetic analyses revealed incongruences between the expected species phylogeny and the inferred gene trees. Some genes within species were more divergent than expected from ploidy level alone, suggesting the existence of paralogous sets of Waxy loci in Spartina. Phylogenetic analyses indicate that this paralogy originated from a duplication that occurred prior to the divergence of Spartina from other Chloridoideae. Gene tree topologies revealed three divergent homoeologous sequences in the hexaploid S. alterniflora that are consistent with the proposal of an allopolyploid origin of the hexaploid clade. Waxy sequences differ in insertion–deletion events in introns, which may be used to diagnose gene copies. Both paralogous and homoeologous coding regions appear to evolving under selective constraints.     

The occurrence of the transposable elementpogo inDrosophila melanogaster

We examined the genomic occurrence of the transposable elementpogo in over 120 strains ofDrosophila melanogaster, from around the world and from different eras. All had multiple copies of a 2.1 kilobase (kb)pogo element, and multiple copies of several size classes between 1.0 and 1.8 kb. There were differences between strains in intensities or presences of deletion-derivative size classes, suggesting current or recent mobility in the species. We were unable to find anypogo-hybridization in eight other species in the genus, in three subgenera, or in the relatedScaptomyza pallida. Thepogo element may be a ‘middle-aged’ element in the genome ofD. melanogaster, having entered the species since its divergence from its sibling species, but long before theP andhobo elements.     

Diversity and endemism of Murinae rodents in Thai limestone karsts

This study aims to investigate the species diversity of rodents living in karst ecosystems of Thailand. A survey has been conducted throughout Thailand, 122 karsts sampled and 477 Murinae rodents live-trapped. Phylogenetic reconstructions were carried out using two mitochondrial markers (cytb, COI). A sequence-based species delimitation method completed by the analysis of the level of genetic divergence was then applied to define species boundaries within our dataset. The phylogenetic position of Niviventer hinpoon was also investigated and sequences obtained from the holotype specimen of this species were used to reliably identify samples of N. hinpoon. A total of 12 described Murinae species, corresponding to 17 deeply divergent genetic lineages, were encountered in limestone karsts of Thailand. Our study revealed an important genetic diversity within the traditionally recognized species Maxomys surifer (four highly divergent genetic lineages), Leopoldamys neilli (two highly divergent genetic lineages) and Berylmys bowersi (two highly divergent genetic lineages). These species could be considered as species complex and require further taxonomic work. This study also provides valuable information on the distribution of the two rodent species endemic to limestone karsts of Thailand, L. neilli and N. hinpoon. Leopoldamys neilli was the most abundant species encountered in Thai karsts during our survey. However, L. neilli specimens from western Thailand are genetically highly divergent from the remaining populations of L. neilli and could represent a separate species. Niviventer hinpoon, phylogenetically closely related to N. fulvescens, is much rarer and its distribution limited to central Thailand. Most of the other captured species are typically associated with forest ecosystems. This study suggests that limestone karsts play a key role in the preservation of the rodent species endemic to such habitat, but they would also provide refuges for the forest-dwelling Murinae rodents in deforested regions.     

利用叶绿体基因组数据解析锦葵科梧桐亚科的系统位置和属间关系

分子系统学研究将传统梧桐科与锦葵科、木棉科和椴树科合并为广义锦葵科,并进一步分为9个亚科.然而,9个亚科之间的关系尚未完全明确,且梧桐亚科内的属间关系也未得到解决.为了明确梧桐亚科在锦葵科中的系统发育位置,厘清梧桐亚科内部属间系统发育关系,该研究对锦葵科8个亚科进行取样,共选取55个样本,基于叶绿体基因组数据,采用最大...     

Chloroplast DNA variation in diploid and polyploid species of Bromus (Poaceae) subgenera Festucaria and Ceratochloa

Summary Chloroplast DNA (cpDNA) restriction endonuclease patterns are used to examine phylogenetic relationships between Bromus subgenera Festucaria and Ceratochloa. Festucaria is considered monophyletic based on the L genome, while Ceratochloa encompasses two species complexes: the B. catharticus complex, which evolved by combining three different genomes, and the B. carinatus complex, which is thought to have originated from hybridization between polyploid species of B. catharticus and diploid members of Festucaria. All species of subgenus Ceratochloa (hexaploids and octoploids) were identical in chloroplast DNA sequences. Similarly, polyploid species of subgenus Festucaria, except for B. auleticus, were identical in cpDNA sequences. In contrast, diploid species of subgenus Festucaria showed various degrees of nucleotide sequence divergence. Species of subgenus Ceratochloa appeared monophyletic and phylogenetically closely related to the diploid B. anomalus and B. auleticus of subgenus Festucaria. The remaining diploid and polyploid species of subgenus Festucaria appeared in a distinct grouping. The study suggests that the B. catharticus complex must have been the maternal parent in the proposed hybrid origin of B. carinatus complex. Although there is no direct evidence for the paternal parent of the latter complex, the cpDNA study shows the complex to be phylogenetically very related to the diploid B. anomalus of subgenus Festucaria.     

Altered expression of gap junction connexin proteins may partly underlie heart rhythm disturbances in the streptozotocin-induced diabetic rat heart

The present work involves the assessment of level of genetic relatedness or divergence amongst the six North-Indian species of Lepidoptera belonging to family Pieridae and sub family Pierinae on the basis of sequence variation of 16S ribosomal RNA. The PCR amplified products of these species were directly sequenced using ABI Prism BigDye Terminator Sequencing Kits (Applied Biosystems). The multiple nucleotide sequence alignment analysis has revealed several differences across these species. Significantly high percentage of A + T base composition content ranging between 73.13% (Ixias pyrene ) and 79.20 % (Pieris brassica) was observed in studied species. The percentage divergence in the investigated species of Pieridae family varied from 5.5% to 21.7%. The two species of Catopsilia revealed minimum sequence divergence of only 5.5%, whereas the other two groups of Ixias and Pieris revealed 15.5% and 8.6% sequence divergence, respectively. Pieris canidia and Ixias pyrene are genetically most divergent (21.7%) amongst the studied lepidopteran species. Phylogenetic analysis based on 16S rRNA nucleotide sequence revealed grouping of six species of Lepidoptera in the form of two different clusters, each cluster being represented by two species from the same genera. The separate taxonomic grouping of these Indian species has been observed when compared with several species of Piernae and Coliadinae subfamilies from other country isolates.     

Chromosomal and molecular divergence in the Indian pygmy field mice Mus booduga-terricolor lineage of the subgenus Mus

Mus booduga and Mus terricolor both have 2n=40. Unlike M. booduga, with all acrocentric chromosomes, M. terricolor invariably has large submetacentric X and acrocentric Y due to an increase of heterochromatin. In contrast to the conservative karyotype of the co-existing sibling species booduga, three chromosome types of terricolor are found in different populations and their divergent karyotypes have autosomal heterochromatin variations established in the homozygous condition. The average genetic distance determined from electrophoretic study of 20 protein loci ranges from lowest (D=0.106) between chromosome types I & II to highest (D=0.185) between types II & III. In terricolor, booduga and M. m. tytleri high mean values of variations per locus (range A=1.604 to 1.928) and heterozygosity per individual per locus (range H=0.180 to 0.336) have been observed. Sequence divergence of 0.39 to 1.2%, calculated from restriction profiles of mtDNA, shows that the terricolor chromosome types have diverged recently. Hybridizations between type I females and type III males gave a preponderance of males in the F1 with varying degrees of sterility. The terricolor complex is an interesting system for critical probing for the role of heterochromatin in the process of speciation. MtDNA, protein loci and AT-rich musculus-related major and minor satellite DNA data indicate that progenitors of the booduga-terricolor lineage might have evolved simultaneously with the caroli-cookii-cervicolor lineage in the evolution of the subgenus Mus.     

Molecular phylogeny of the genus Ceanothus (Rhamnaceae) using rbc L and ndh F sequences

 Intrageneric phylogeny among ten representative Ceanothus species was investigated using DNA sequences of the chloroplast encoded ndhF and rbcL genes. Parsimony analysis of the ndhF sequences identified two main clades corresponding to two subgenera Ceanothus and Cerastes. The phylogenetic results suggest that three monophyletic clades within the subgenus Ceanothus can be delimited on the basis of (1) evergreen or (2) deciduous leaves and (3) thorn presence within the evergreen clade. The estimated divergence time based on rbcL sequences suggests that the two subgenera diverged 18–39 million years ago whereas species within each subgenus diverged more recently. Taken together, the results support the division of Ceanothus into two monophyletic subgenera and are consistent with the postulated recent divergence of many species within each subgenus. Received: 25 September 1996/Accepted: 8 November 1996     

Determination of copy number and linkage relationships among five actin gene subfamilies in Petunia hybrida

The actin gene superfamily of Petunia hybrida cv. Mitchell contains greater than 100 gene members which have been divided into several highly divergent subfamilies [1]. Five subfamily-specific probes have been used to compare the actin genes among the Mitchell, Violet 23 (V23) and Red 51 (R51) cultivars of P. hybrida. The sum total of actin genes in these five subfamilies was estimated to be between 10 and 34 members in both V23 and R51. Restriction fragment length polymorphisms (RFLPs) between V23 and R51 were examined with these five probes and eleven different restriction endonucleases. Among the 55 comparisons, 87% exhibited RFLPs. These data indicate extreme divergence between V23 and R51 in DNA sequence and/or the presence of small insertions and deletions surrounding these actin gene subfamilies. This divergence suggests that V23 and R51, which have contrasting phenotypic marker loci on every chromosome, may be useful for the development of a complete RFLP linkage map of the Petunia genome. The segregation of Hind III RFLPs among the progeny of two backcrosses demonstrated that representatives of the five subfamilies of Petunia actin genes exist at four distinct genetic locations and suggested that two of these loci are tightly linked. Apparently, amplification of the numerous members of the Petunia actin gene superfamily occurred via gene dispersal of the original subfamily progenitors and not primarily as a result of amplification of a single chromosomal region.     

Distribution of the Transposable Element Minos in the Genus Drosophila

We analyzed 28 species of the genus Drosophilafor the presence of the Tc1-like transposable element Minosusing Southern blot hybridization under high stringency conditions. The Minostransposon was found in members of both the Drosophilaand the Sophophorasubgenus showing a distribution that is wider if compared to other well-studied Drosophilatransposons such as the Pelement, hoboand mariner. The presence of Minos-hybridizing sequences was discontinuous in the Sophophorasubgenus, especially in the melanogasterspecies group. Using the Polymerase Chain Reaction we amplified a portion corresponding to the putative Minostransposase from different Drosophilaspecies. Cloning and sequence analysis of randomly selected Minoscopies from D. mojavensisis, D. saltansand D. willistonisupports the idea that event(s) of horizontal transfer may have contributed to the spreading of this transposon in the Drosophilagenus. This revised version was published online in July 2006 with corrections to the Cover Date.     

DNA inversion mediated by the r-determinant of plasmid NR1: evidence for the intramolecular replicative transposition of a 23 kb IS1-flanked transposon?

Summary The r-determinant (r-det) of the R plasmid NR1-Basel is a 23 kb, IS1-flanked transposon, called Tn2671, which has been shown to transpose to the genome of bacteriophage P7. Among the derivatives of phage P7::r-det we found one which carried two copies of the r-det as inverted repeats and which also contained the P7 genome segment between them in inverted orientation. Its generation is best explained by assuming that the entire 23 kb Tn2671 transposon has undergone intramolecular replicative transposition.     

Three highly divergent subfamilies of the impala transposable element coexist in the genome of the fungus Fusarium oxysporum

The transposable element impala is a member of the widespread superfamily of Tc1-mariner transposons, identified in the genome of the plant pathogenic fungus Fusarium oxysporum. This element is present in a low copy number and is actively transposed in the F.␣oxysporum strain F24 that is pathogenic for melons. The structure of the impala family was investigated by cloning and sequencing all the genomic copies. The analysis revealed that this family is composed of full-length and truncated copies. Four copies contained a long open reading frame that could potentially encode a transposase of 340 amino acids. The presence of conserved functional domains (a nuclear localisation signal, a catalytic DDE domain and a DNA-binding domain) suggests that these four copies may be autonomous elements. Sequence comparisons and phylogenetic analysis of the impala copies defined three subfamilies, which differ by a high level of nucleotide polymorphism (around 20%). The coexistence of these divergent subfamilies in the same genome may indicate that the impala family is of ancient origin and/or that it arose by successive horizontal transmission events. Received: 2 December 1997 / Accepted: 28 April 1998     

Evolutionary conservation of linkage groups: Additional evidence from murid and cricetid rodents

In Mus musculus, family Muridae, the glucosephosphate isomerase (Gpi-1), pink-eyed dilution (p), albinism (c), and -type globin (Hbb) loci are known to be linked in the order Gpi-1-p-c-Hbb. In Rattus norvegicus, another murid rodent, the p, c, and Hbb loci are known to be linked in the same order and with similar recombination frequencies. In Peromyscus maniculatus, family Cricetidae, it was previously known that p and c are linked and by analogy to Mus musculus that linkage group should be bounded by Gpi-1 near p and by a -globin locus near c. Linkage has now been established between Gpi-1 and the Hbe globin locus in Peromyscus. However, the observed recombination frequency in Peromyscus (16.3%) is significantly lower than in Mus, suggesting that perhaps a chromosomal inversion has occurred during the evolutionary divergence of the two rodent families. Linkage relationships were also tested between the Hbc ¹, Hbd ¹, and Hbe ¹ globin variants. Hbc ¹ (presumably an -type globin) segregated independently from Hbd ¹ and Hbe ¹ (presumably -type globins). No recombination was observed between Hbd ¹ and Hbe ¹. Those two globin genes may be alleles at a single locus, although circumstantial evidence suggests that they represent tightly linked duplicate loci.This work was supported by NSF DEB7716104 and by the Committee on Research, UCR.