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Synteny, genetics?

Synteny, genetics?



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Could anyone explain the concept of Synteny relating to genetics? A picture would help. I tried read the wikipedia source along with another PDF

http://gep.wustl.edu/repository/course_materials_WU/annotation/About_Synteny_Analysis.pdf

And I feel it only somewhat helped. From what I gather synteny is about the order of genes, relative to their homologous genes? Or their location in general?


Syntenic blocks contain the same genes of order between chromosomes of different species.

The figure above shows (left to right) syntenic block shared between human chromosome 17 and corresponding chromosomes in three other mammals (horse, pig and chimpanzee). And as expected, the more distinct the species (such as pig and horse) the more disarranged the order of genes are.

Ref: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758187/


What is synteny and how do we use it in genomics and genetics?

In respect to this, when comparing genomes of different species synteny is defined as?

When comparing genomes of different species, 'synteny' is defined as. the same genes in the same order along a chromosome. The term coverage, when applied to genomics, means sequencing the same base pair multiple times. You just studied 10 terms!

One may also ask, what is the purpose of synteny testing? It tests to see whether genes reside on the same chromosome. Sister chromatids separate during which phases of the cell cycle? Mitosis anaphase and Meiosis II Anaphase.

Consequently, what is a syntenic block?

A synteny block is a collection of contiguous genes located on the same chromosome. Traits provided by these genes are usually inherited together, thus violating Mendel's law of independent assortment.

How does gene duplication occur?

Gene duplication happens when an extra copy of a gene is made in an organism's genome. Sometimes, gene duplication is beneficial to the organism and may eventually lead to the development of a new species. The various types of keratin in the body are the result of duplications of a single gene.


Nomenclature of Human Genes

Symbols and Names

Once genes had been assigned to several of the chromosomes, their order along the length of the chromosome began to be established and human gene mapping had truly begun. The publication of gene orders generated the idea of a gene symbol, in addition to its name. This symbol was a shortened form of the name, memorable and recognizable, but short enough to be included in the diagrammatic representations of chromosomes called maps. These symbols usually consisted of only two or three letters in a combination that reflected the name, and perhaps with a number added if more than one gene was discovered which had a similar function. Example: ADH1, ADH2 (the genes encoding different forms of an enzyme, alcohol dehydrogenase).

Clearly, a gene symbol alone has no intrinsic meaning, it is only meaningful in relation to the longer and more descriptive name. Whilst a name may be varied considerably and still maintain the same meaning (amylase, salivary and salivary amylase clearly have the same meaning), the more limited letter and number combinations of a short symbol must be invariable to avoid ambiguity. The importance of a unique identifying symbol was recognized in the early years of gene mapping, and a Nomenclature Committee was formed to oversee the allocation of appropriate symbols for use in maps and to devise guidelines to ensure the greatest possible consistency. The guidelines were subject to many influences which included the established practice, in order to avoid confusion by too many symbol changes the need to reduce ambiguity, with uniqueness as the most important criteria other simpler recommendations such as avoiding Roman numerals and the more far-sighted aims of increasing accessibility and ‘searchability’ by recommendation of hierarchical systems of symbol construction. The guidelines were also influenced by the restrictions of early electronic storage and communication, such as the elimination of Greek letters which could not easily be represented in electronic databases, and the restrictions on use of punctuation to facilitate searching.


Deeply conserved synteny resolves early events in vertebrate evolution

Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid-late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.

Conflict of interest statement

D.S.R. is a member of the Scientific Advisory Board of Dovetail Genomics. R.E.G. is the founder of Dovetail Genomics. N.H.P. is an employee of Dovetail Genomics. D.S.R., R.E.G. and N.H.P. are all shareholders in Dovetail Genomics. The other authors declare no competing interests.

Figures

Fig. 1. Conserved syntenies between amphioxus and…

Fig. 1. Conserved syntenies between amphioxus and various species.

Fig. 2. Contributions of the 17 ancestral…

Fig. 2. Contributions of the 17 ancestral CLGs to contemporary vertebrate genomes.

Fig. 3. Organization of bony vertebrate chromosomes…

Fig. 3. Organization of bony vertebrate chromosomes after 2R.

The majority of CLGs have four…

Fig. 4. Duplications, fusions and mixing in…

Fig. 4. Duplications, fusions and mixing in bony vertebrates.

Fig. 5. Auto- then allotetraploidy scenario for…

Fig. 5. Auto- then allotetraploidy scenario for vertebrate evolution.

Schematic of the auto- then allotetraploidy…

Extended Data Fig. 1. Chromatin and genetic…

Extended Data Fig. 1. Chromatin and genetic maps of amphioxus genome.

Extended Data Fig. 2. Dot-plots showing conserved…

Extended Data Fig. 2. Dot-plots showing conserved syntenies between amphioxus and human and frog.

Extended Data Fig. 3. Dot-plots showing conserved…

Extended Data Fig. 3. Dot-plots showing conserved syntenies between lamprey and amphioxus.

Extended Data Fig. 4. Dot-plots showing conserved…

Extended Data Fig. 4. Dot-plots showing conserved syntenies between amphioxus and selected invertebrates.

Extended Data Fig. 5. Chicken-spotted gar orthologs…

Extended Data Fig. 5. Chicken-spotted gar orthologs and paralogs.

“Oxford’ dotpot between chicken (Gallus gallus,…

Extended Data Fig. 6. Oxford grid between…

Extended Data Fig. 6. Oxford grid between bony vertebrate chromosomes and chordate linkage groups (CLGs).

Extended Data Fig. 7. Oxford grid showing…

Extended Data Fig. 7. Oxford grid showing associations between 50 gene segments of bony vertebrate…

Extended Data Fig. 8. Oxford grid between…

Extended Data Fig. 8. Oxford grid between sea lamprey germline chromosomes and chordate linkage groups…


A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2-cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 5' end of the gene.

Keywords: KASP genotyping faba bean legume single nucleotide polymorphism synteny.

© 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.


Scientists create program that finds synteny blocks in different animals

Credit: Dmitry Lisovsky, ITMO.NEWS

Modern genetics implies working with immense amounts of data which cannot be processed without the help of complex mathematical algorithms. For this reason, the task of developing special processing programs is no less important for bioinformatics specialists than that of genomic sequencing of specific animals. An international team of scientists that included researchers from ITMO University developed a software tool that makes it possible to quickly and efficiently find similar parts in the genomes of different animals, which is essential for understanding how closely related two species are, and how far they have evolved from their common ancestor. The research was published in GigaScience.

There are millions of biological species on planet Earth, and this diversity is laid down on the genetic level. Animals' anatomy, size, color patterns and habits are defined by their genes. Then again, the diversity of genes themselves is not that great: by today, scientists have only identified about over 20,000. Therefore, species are different in not only the sets of genes they have but also in how their genes are arranged. In the language of comparative genomics, this is called synteny, i.e. the arrangement of genes and regulatory elements.

"Let's take a gorilla and a chimpanzee as an example," says Ksenia Krasheninnikova, a researcher and engineer at ITMO University. "These two species have the same set of genes, but their regulatory elements and genome mutations create slightly different orders which results in differences between these primates."

Therefore, for the purposes of understanding how close two species are from the evolutionary standpoint, scientists need to know not just their genes but also how they are arranged in a chromosome, and how many common genome fragments, or synteny blocks, as geneticists call them, there are. Then again, looking for them manually is impossible: the amount of data is just too big. Genomes of mammals consist of millions and billions of base pairs, which makes processing without big data technologies next to impossible. For this reason, scientists create programs of their own that make it possible to solve this new category of tasks which has emerged in the course of the development of this science. And this is what the research team that included scientists from ITMO's Laboratory of Genomic Diversity did.

The new software tool was named halSynteny. According to its authors, it can search for synteny blocks better and faster than other programs developed for this purpose. What's more, halSynteny works with data in two standard and well-documented formats.

"Our goal was to create an algorithm that could be easily applied to accessible data," says Ksenia, who is the first author of this research. "Some of the approaches to the identification of synteny sequences are based on annotating genes in advance our method is different. We don't use any additional annotation. We use the alignment method, when different parts of one genome are aligned by their degree of similarity with parts of another genome. This way, we can identify homogeneous parts, parts that are of the same origin."

The program makes it possible to speed up the computations by over two times in comparison with SatsumaSynteny2, another popular tool. Such high efficiency was attained by implementing a mathematically effective algorithm using C++.

The proposed method and software tool were tested by comparing cat and dog genomes.

Ksenia says, "We showed that large fragments of cat chromosomes and some fragments of dog chromosomes unite in synteny blocks, which means that they've evolved from similar chromosomes of a common ancestor. And this can be used as a basis for making conclusions about their evolutionary process. Previous research in the field of 'wet' biology demonstrated that cats' genome changed less from the genome of their common ancestor in comparison with that of dogs. This can be seen in comparison with other species that are not part of the carnivora order. The results that we got confirm these conclusions and make them more accurate. This means that in some specific part, the genome of a cat and the species taken for comparison is similar, and in dogs, it is rearranged."

In future, this algorithm will be used in other research in the field of comparative genomics that takes place at ITMO University.


RESULTS

Time of divergence:

To estimate the time of divergence of lepidopteran lineages, we calculated a molecular clock using a tree based on well-established taxonomic assignments and the DNA sequences of two highly conserved proteins ( Figure 1). The estimated time of divergence between the B. mori and H. melpomene lineages was 103 ± 8.6 MY, based on an estimated age of 190 MY for the Lepidoptera–Diptera divergence.

Phylogeny used to estimate time of divergence between B. mori and H. melpomene. The dashed line indicates the approximate age of divergence between these lineages (∼103 MY). Arrows indicate constrained nodes (see materials and methods ). Numbers in circles indicate the haploid number of chromosomes for B. mori, H. melpomene, and basal taxa.

Phylogeny used to estimate time of divergence between B. mori and H. melpomene. The dashed line indicates the approximate age of divergence between these lineages (∼103 MY). Arrows indicate constrained nodes (see materials and methods ). Numbers in circles indicate the haploid number of chromosomes for B. mori, H. melpomene, and basal taxa.

Linkage analysis:

In total, 64 cDNA-derived markers were assigned to H. melpomene linkage groups in this study. Of these markers, 8 were assigned to LGs on the basis of visible length polymorphisms from indels, and the other 56 markers were assigned to LGs on the basis of genotype scoring from restriction digestion at SNPs ( Table 1 and supplemental Table 1 at http://www.genetics.org/supplemental/). High sequence similarity of amplified products to EST consensus sequences and B. mori coding sequences supported our hypothesis of orthology.

Conserved loci mapped in H. melpomene and orthologs in B. mori

Marker name . Abbreviation . H. melpomene linkage group . GenBank accession no. . B. mori linkage group a . GenBank accession no. .
Alanyl-tRNA synthetase Aats-ala1 EF207962 4 M55993
Dopa decarboxylase bDDC1 AY437802 4 AF372836
Ribosomal protein L3 bRpL31 EE743523 4 AB024901
Wingless cWg1 AY745485 4 D14169
Ribosomal protein L6 RpL62 EF207960 16 AY769273
Ribosomal protein P2 RpP22 EF207959 16 AY769269
Glutathione S-transferase GST3 EF207961 6 AJ006502
Ribosomal protein L15 dRpL153 DN172764 6 AY769285
Mannose–phosphate isomerase cMPI3 AY332460
Ribosomal protein S6 RpS64 EF207950 21 AY769320
Ribosomal protein S15 RpS154 EF207951 21 AY706957
Ribosomal protein S17 RpS174 EF207952 21 AY769333
Ribosomal protein L11 bRpL115 CO729501 3 AY769280
Ribosomal protein L13A RpL13A5 EF207949 3 AY769283
Ecdysteroid-inducible angiotensin-converting enzyme-related gene product Ance6 EF207953 9 AB026110
Ribosomal protein S14 dRpS146 CX700812 9 AY706956
Engrailed eng7 AY745328 2 M64335
Invected cInv7 DQ445457 2 M64336
Ribosomal protein S21 RpS217 DN172654, CX700448 2 AY578154
Ribosomal protein S28 RpS287 EF452418 2 AY583363
Ribosomal protein L14 RpL147 EF207954 11 AY769284
Ribosomal protein L18 RpL187 EF207955, EF211970 11 AY769287
Ribosomal Sop2 Sop27 DT663968, EF211973 11 AY763110
Distal less cDll7 DQ445415
Mitotic checkpoint control protein (bub3) gene Bub37 CX700513
Polycomb protein Su(z)12 Su(z)127 DT662097
Ribosomal protein S25 RpS258 EF207956 25 AY769340
chiB (chitinase precursor) Cht9 CX700556, EF211966 7 AF052914
Ribonuclease L inhibitor homolog RLI9 EF207958 7 AB164193
Ribosomal protein S27 RpS279 EF207957 7 AY769342
Cyclin-dependent kinases regulatory subunit Cks9 CX700558
Elongation factor 1α bEf1a10 AY747994 5 D13338
Elongation factor 1δ Ef1d10 CX700886 5 AB046366
Patched bPtc10 AY745373 5 AADK01000387
Ribosomal protein L13 dRpL1310 CO729603 5 AY769282
Ribosomal protein L19 bRpL1910 CX700796 5 AY769289
Ribosomal protein S11 dRpS1110 CX700450 P AY706955
Opsin1 bOPS111 AF126751 15 AB047924
Ribosomal protein L5 bRpL511 CO729889 15 AY769272
Ribosomal protein L7A RpL7A11 EF207963 15 AY769275
Ribosomal protein L10A bRpL10A11 CO729740 15 AY769279
Ribosomal protein P0 bRpP011 CO729821 15 AJ457827
Ribosomal protein S5 bRpS511 CO729660 15 AY769319
Ribosomal protein S8 bRpS811 CX700851 15 AY769322
Ribosomal protein L8 RpL811 EF207977, EF211969
Ribosomal protein L30 dRpL3011 CO729949
Glycine-rich protein GRP12 EF207964, EF211967 8 AB197877
Beta-tubulin Btub12 EF207965, EF211964 20 AB003287
Ribosomal protein S7 RpS712 EF207966 20 AY769321
Ribosomal protein S20 RpS2012 CX700684 20 AY769336
Enolase Eno12 EF207979
Ribosomal protein L7 dRpL712 CX700625
Ribosomal protein L27 RpL2712 EF207978
Ribosomal protein S12 dRpS1212 CX700631
Ribosomal protein S16 RpS1613 EF207967 14 AY769332
Calreticulin Crc13 EF207968 22 AB090887
Cuticle protein (EDG84A homolog) EDG84A13 CO729743 22 AB017550
PCNA PCNA13 CV526328 22 AB002264, AB002265
Ribosomal protein L37 RpL3713 DN172717 22 AY769308
Ribosomal protein S4 RpS413 CO729938
Vermillion bv13 AY691422
Ribosomal protein L12 RpL1214 EF207969 19 AY769281
Eukaryotic translation elongation factor 2 eEF214 CX700527
Ribosomal protein S9 cRpS914 CX700565
Ribosomal protein L22 cRpL2215 CX700470 17 AY769291
Ribosomal protein P40 cRpP4015 CX700776 17 AB062685
Ribosomal protein S24 RpS2415 EF207970, EF211972 17 AY578155
Eukaryotic initiation factor 3B eiF3B15 EF207980
Forkhead box J1 cFox15 CR974474
Rab geranygeranyl transferase cGerTra15 CR974474
Elongation factor 1γ Ef1g16 EF207971 18 AB046361
Heat shock protein hsp21.4 Hsp21.417 EF207972 13 AB195972
Lim protein Mlp17 DT663321 13 AY461436
Ribosomal protein L21 RpL2117 CO729978 13 AY769290
Ribosomal protein L31 cRpL3117 CX700740 13 AY769301
ADP/ATP translocase ANT17 EF207974, EF211962 24 AY227000
Ribosomal protein L32 RpL3217 EF207973 24 AB048205
Sui1 Sui117 CO729706, EF211974 24 AY426343
Ribosomal protein L27a RpL27a17 EF207981
Ribosomal protein S10 RpS1017 EF207982
Scalloped cSd17 DQ674429
Bm44 Bm4418 DT664299 23 AB158647
Inhibitor of Apoptosis protein IAP18 CV526245, EF211968 23 AF281073
Ribosomal protein S30 RpS3018 CX700724 23 AY769346
Cubitus interruptus bci18 AY429297 U AF529422
90-kDa heat-shock protein 90hsp18 CO729719, EF211960 U AB060275
α-Tubulin atub18 EF207983, EF211963
O-Glycosyltransferase dOgt18 CV526007
Decapentaplegic bDpp19 AY747899 12 BAAB01102755
J-domain-containing protein JDP19 DT662955 12 AF176014
Ribosomal protein L9 RpL919 EF207975 12 AY769277
Muscular protein 20 Mp2019 CO729543
Prophenol oxidase-activating enzyme precursor PPAE19 CO729777
Ribosomal protein L44 cRpL4419 CX700847
Caspase-1 caspase20 EF207976, EF211965 10 AF448494
Cytosolic juvenile hormone binding protein Jhbp20 DT661817 10 AF098303
Actin 1 Act20 EF207985, EF211961
Calcium ATPase Ca-P20 CO729824
Ribosomal protein L23A RpL23A20 EF207984, EF211971
Apterous bapt21 (Z) AY747887 1(Z) AB024903
Triose–phosphate isomerase bTPI21 (Z) AY548151 1(Z) AY734490
Marker name . Abbreviation . H. melpomene linkage group . GenBank accession no. . B. mori linkage group a . GenBank accession no. .
Alanyl-tRNA synthetase Aats-ala1 EF207962 4 M55993
Dopa decarboxylase bDDC1 AY437802 4 AF372836
Ribosomal protein L3 bRpL31 EE743523 4 AB024901
Wingless cWg1 AY745485 4 D14169
Ribosomal protein L6 RpL62 EF207960 16 AY769273
Ribosomal protein P2 RpP22 EF207959 16 AY769269
Glutathione S-transferase GST3 EF207961 6 AJ006502
Ribosomal protein L15 dRpL153 DN172764 6 AY769285
Mannose–phosphate isomerase cMPI3 AY332460
Ribosomal protein S6 RpS64 EF207950 21 AY769320
Ribosomal protein S15 RpS154 EF207951 21 AY706957
Ribosomal protein S17 RpS174 EF207952 21 AY769333
Ribosomal protein L11 bRpL115 CO729501 3 AY769280
Ribosomal protein L13A RpL13A5 EF207949 3 AY769283
Ecdysteroid-inducible angiotensin-converting enzyme-related gene product Ance6 EF207953 9 AB026110
Ribosomal protein S14 dRpS146 CX700812 9 AY706956
Engrailed eng7 AY745328 2 M64335
Invected cInv7 DQ445457 2 M64336
Ribosomal protein S21 RpS217 DN172654, CX700448 2 AY578154
Ribosomal protein S28 RpS287 EF452418 2 AY583363
Ribosomal protein L14 RpL147 EF207954 11 AY769284
Ribosomal protein L18 RpL187 EF207955, EF211970 11 AY769287
Ribosomal Sop2 Sop27 DT663968, EF211973 11 AY763110
Distal less cDll7 DQ445415
Mitotic checkpoint control protein (bub3) gene Bub37 CX700513
Polycomb protein Su(z)12 Su(z)127 DT662097
Ribosomal protein S25 RpS258 EF207956 25 AY769340
chiB (chitinase precursor) Cht9 CX700556, EF211966 7 AF052914
Ribonuclease L inhibitor homolog RLI9 EF207958 7 AB164193
Ribosomal protein S27 RpS279 EF207957 7 AY769342
Cyclin-dependent kinases regulatory subunit Cks9 CX700558
Elongation factor 1α bEf1a10 AY747994 5 D13338
Elongation factor 1δ Ef1d10 CX700886 5 AB046366
Patched bPtc10 AY745373 5 AADK01000387
Ribosomal protein L13 dRpL1310 CO729603 5 AY769282
Ribosomal protein L19 bRpL1910 CX700796 5 AY769289
Ribosomal protein S11 dRpS1110 CX700450 P AY706955
Opsin1 bOPS111 AF126751 15 AB047924
Ribosomal protein L5 bRpL511 CO729889 15 AY769272
Ribosomal protein L7A RpL7A11 EF207963 15 AY769275
Ribosomal protein L10A bRpL10A11 CO729740 15 AY769279
Ribosomal protein P0 bRpP011 CO729821 15 AJ457827
Ribosomal protein S5 bRpS511 CO729660 15 AY769319
Ribosomal protein S8 bRpS811 CX700851 15 AY769322
Ribosomal protein L8 RpL811 EF207977, EF211969
Ribosomal protein L30 dRpL3011 CO729949
Glycine-rich protein GRP12 EF207964, EF211967 8 AB197877
Beta-tubulin Btub12 EF207965, EF211964 20 AB003287
Ribosomal protein S7 RpS712 EF207966 20 AY769321
Ribosomal protein S20 RpS2012 CX700684 20 AY769336
Enolase Eno12 EF207979
Ribosomal protein L7 dRpL712 CX700625
Ribosomal protein L27 RpL2712 EF207978
Ribosomal protein S12 dRpS1212 CX700631
Ribosomal protein S16 RpS1613 EF207967 14 AY769332
Calreticulin Crc13 EF207968 22 AB090887
Cuticle protein (EDG84A homolog) EDG84A13 CO729743 22 AB017550
PCNA PCNA13 CV526328 22 AB002264, AB002265
Ribosomal protein L37 RpL3713 DN172717 22 AY769308
Ribosomal protein S4 RpS413 CO729938
Vermillion bv13 AY691422
Ribosomal protein L12 RpL1214 EF207969 19 AY769281
Eukaryotic translation elongation factor 2 eEF214 CX700527
Ribosomal protein S9 cRpS914 CX700565
Ribosomal protein L22 cRpL2215 CX700470 17 AY769291
Ribosomal protein P40 cRpP4015 CX700776 17 AB062685
Ribosomal protein S24 RpS2415 EF207970, EF211972 17 AY578155
Eukaryotic initiation factor 3B eiF3B15 EF207980
Forkhead box J1 cFox15 CR974474
Rab geranygeranyl transferase cGerTra15 CR974474
Elongation factor 1γ Ef1g16 EF207971 18 AB046361
Heat shock protein hsp21.4 Hsp21.417 EF207972 13 AB195972
Lim protein Mlp17 DT663321 13 AY461436
Ribosomal protein L21 RpL2117 CO729978 13 AY769290
Ribosomal protein L31 cRpL3117 CX700740 13 AY769301
ADP/ATP translocase ANT17 EF207974, EF211962 24 AY227000
Ribosomal protein L32 RpL3217 EF207973 24 AB048205
Sui1 Sui117 CO729706, EF211974 24 AY426343
Ribosomal protein L27a RpL27a17 EF207981
Ribosomal protein S10 RpS1017 EF207982
Scalloped cSd17 DQ674429
Bm44 Bm4418 DT664299 23 AB158647
Inhibitor of Apoptosis protein IAP18 CV526245, EF211968 23 AF281073
Ribosomal protein S30 RpS3018 CX700724 23 AY769346
Cubitus interruptus bci18 AY429297 U AF529422
90-kDa heat-shock protein 90hsp18 CO729719, EF211960 U AB060275
α-Tubulin atub18 EF207983, EF211963
O-Glycosyltransferase dOgt18 CV526007
Decapentaplegic bDpp19 AY747899 12 BAAB01102755
J-domain-containing protein JDP19 DT662955 12 AF176014
Ribosomal protein L9 RpL919 EF207975 12 AY769277
Muscular protein 20 Mp2019 CO729543
Prophenol oxidase-activating enzyme precursor PPAE19 CO729777
Ribosomal protein L44 cRpL4419 CX700847
Caspase-1 caspase20 EF207976, EF211965 10 AF448494
Cytosolic juvenile hormone binding protein Jhbp20 DT661817 10 AF098303
Actin 1 Act20 EF207985, EF211961
Calcium ATPase Ca-P20 CO729824
Ribosomal protein L23A RpL23A20 EF207984, EF211971
Apterous bapt21 (Z) AY747887 1(Z) AB024903
Triose–phosphate isomerase bTPI21 (Z) AY548151 1(Z) AY734490

Conserved loci mapped in H. melpomene and orthologs in B. mori

Marker name . Abbreviation . H. melpomene linkage group . GenBank accession no. . B. mori linkage group a . GenBank accession no. .
Alanyl-tRNA synthetase Aats-ala1 EF207962 4 M55993
Dopa decarboxylase bDDC1 AY437802 4 AF372836
Ribosomal protein L3 bRpL31 EE743523 4 AB024901
Wingless cWg1 AY745485 4 D14169
Ribosomal protein L6 RpL62 EF207960 16 AY769273
Ribosomal protein P2 RpP22 EF207959 16 AY769269
Glutathione S-transferase GST3 EF207961 6 AJ006502
Ribosomal protein L15 dRpL153 DN172764 6 AY769285
Mannose–phosphate isomerase cMPI3 AY332460
Ribosomal protein S6 RpS64 EF207950 21 AY769320
Ribosomal protein S15 RpS154 EF207951 21 AY706957
Ribosomal protein S17 RpS174 EF207952 21 AY769333
Ribosomal protein L11 bRpL115 CO729501 3 AY769280
Ribosomal protein L13A RpL13A5 EF207949 3 AY769283
Ecdysteroid-inducible angiotensin-converting enzyme-related gene product Ance6 EF207953 9 AB026110
Ribosomal protein S14 dRpS146 CX700812 9 AY706956
Engrailed eng7 AY745328 2 M64335
Invected cInv7 DQ445457 2 M64336
Ribosomal protein S21 RpS217 DN172654, CX700448 2 AY578154
Ribosomal protein S28 RpS287 EF452418 2 AY583363
Ribosomal protein L14 RpL147 EF207954 11 AY769284
Ribosomal protein L18 RpL187 EF207955, EF211970 11 AY769287
Ribosomal Sop2 Sop27 DT663968, EF211973 11 AY763110
Distal less cDll7 DQ445415
Mitotic checkpoint control protein (bub3) gene Bub37 CX700513
Polycomb protein Su(z)12 Su(z)127 DT662097
Ribosomal protein S25 RpS258 EF207956 25 AY769340
chiB (chitinase precursor) Cht9 CX700556, EF211966 7 AF052914
Ribonuclease L inhibitor homolog RLI9 EF207958 7 AB164193
Ribosomal protein S27 RpS279 EF207957 7 AY769342
Cyclin-dependent kinases regulatory subunit Cks9 CX700558
Elongation factor 1α bEf1a10 AY747994 5 D13338
Elongation factor 1δ Ef1d10 CX700886 5 AB046366
Patched bPtc10 AY745373 5 AADK01000387
Ribosomal protein L13 dRpL1310 CO729603 5 AY769282
Ribosomal protein L19 bRpL1910 CX700796 5 AY769289
Ribosomal protein S11 dRpS1110 CX700450 P AY706955
Opsin1 bOPS111 AF126751 15 AB047924
Ribosomal protein L5 bRpL511 CO729889 15 AY769272
Ribosomal protein L7A RpL7A11 EF207963 15 AY769275
Ribosomal protein L10A bRpL10A11 CO729740 15 AY769279
Ribosomal protein P0 bRpP011 CO729821 15 AJ457827
Ribosomal protein S5 bRpS511 CO729660 15 AY769319
Ribosomal protein S8 bRpS811 CX700851 15 AY769322
Ribosomal protein L8 RpL811 EF207977, EF211969
Ribosomal protein L30 dRpL3011 CO729949
Glycine-rich protein GRP12 EF207964, EF211967 8 AB197877
Beta-tubulin Btub12 EF207965, EF211964 20 AB003287
Ribosomal protein S7 RpS712 EF207966 20 AY769321
Ribosomal protein S20 RpS2012 CX700684 20 AY769336
Enolase Eno12 EF207979
Ribosomal protein L7 dRpL712 CX700625
Ribosomal protein L27 RpL2712 EF207978
Ribosomal protein S12 dRpS1212 CX700631
Ribosomal protein S16 RpS1613 EF207967 14 AY769332
Calreticulin Crc13 EF207968 22 AB090887
Cuticle protein (EDG84A homolog) EDG84A13 CO729743 22 AB017550
PCNA PCNA13 CV526328 22 AB002264, AB002265
Ribosomal protein L37 RpL3713 DN172717 22 AY769308
Ribosomal protein S4 RpS413 CO729938
Vermillion bv13 AY691422
Ribosomal protein L12 RpL1214 EF207969 19 AY769281
Eukaryotic translation elongation factor 2 eEF214 CX700527
Ribosomal protein S9 cRpS914 CX700565
Ribosomal protein L22 cRpL2215 CX700470 17 AY769291
Ribosomal protein P40 cRpP4015 CX700776 17 AB062685
Ribosomal protein S24 RpS2415 EF207970, EF211972 17 AY578155
Eukaryotic initiation factor 3B eiF3B15 EF207980
Forkhead box J1 cFox15 CR974474
Rab geranygeranyl transferase cGerTra15 CR974474
Elongation factor 1γ Ef1g16 EF207971 18 AB046361
Heat shock protein hsp21.4 Hsp21.417 EF207972 13 AB195972
Lim protein Mlp17 DT663321 13 AY461436
Ribosomal protein L21 RpL2117 CO729978 13 AY769290
Ribosomal protein L31 cRpL3117 CX700740 13 AY769301
ADP/ATP translocase ANT17 EF207974, EF211962 24 AY227000
Ribosomal protein L32 RpL3217 EF207973 24 AB048205
Sui1 Sui117 CO729706, EF211974 24 AY426343
Ribosomal protein L27a RpL27a17 EF207981
Ribosomal protein S10 RpS1017 EF207982
Scalloped cSd17 DQ674429
Bm44 Bm4418 DT664299 23 AB158647
Inhibitor of Apoptosis protein IAP18 CV526245, EF211968 23 AF281073
Ribosomal protein S30 RpS3018 CX700724 23 AY769346
Cubitus interruptus bci18 AY429297 U AF529422
90-kDa heat-shock protein 90hsp18 CO729719, EF211960 U AB060275
α-Tubulin atub18 EF207983, EF211963
O-Glycosyltransferase dOgt18 CV526007
Decapentaplegic bDpp19 AY747899 12 BAAB01102755
J-domain-containing protein JDP19 DT662955 12 AF176014
Ribosomal protein L9 RpL919 EF207975 12 AY769277
Muscular protein 20 Mp2019 CO729543
Prophenol oxidase-activating enzyme precursor PPAE19 CO729777
Ribosomal protein L44 cRpL4419 CX700847
Caspase-1 caspase20 EF207976, EF211965 10 AF448494
Cytosolic juvenile hormone binding protein Jhbp20 DT661817 10 AF098303
Actin 1 Act20 EF207985, EF211961
Calcium ATPase Ca-P20 CO729824
Ribosomal protein L23A RpL23A20 EF207984, EF211971
Apterous bapt21 (Z) AY747887 1(Z) AB024903
Triose–phosphate isomerase bTPI21 (Z) AY548151 1(Z) AY734490
Marker name . Abbreviation . H. melpomene linkage group . GenBank accession no. . B. mori linkage group a . GenBank accession no. .
Alanyl-tRNA synthetase Aats-ala1 EF207962 4 M55993
Dopa decarboxylase bDDC1 AY437802 4 AF372836
Ribosomal protein L3 bRpL31 EE743523 4 AB024901
Wingless cWg1 AY745485 4 D14169
Ribosomal protein L6 RpL62 EF207960 16 AY769273
Ribosomal protein P2 RpP22 EF207959 16 AY769269
Glutathione S-transferase GST3 EF207961 6 AJ006502
Ribosomal protein L15 dRpL153 DN172764 6 AY769285
Mannose–phosphate isomerase cMPI3 AY332460
Ribosomal protein S6 RpS64 EF207950 21 AY769320
Ribosomal protein S15 RpS154 EF207951 21 AY706957
Ribosomal protein S17 RpS174 EF207952 21 AY769333
Ribosomal protein L11 bRpL115 CO729501 3 AY769280
Ribosomal protein L13A RpL13A5 EF207949 3 AY769283
Ecdysteroid-inducible angiotensin-converting enzyme-related gene product Ance6 EF207953 9 AB026110
Ribosomal protein S14 dRpS146 CX700812 9 AY706956
Engrailed eng7 AY745328 2 M64335
Invected cInv7 DQ445457 2 M64336
Ribosomal protein S21 RpS217 DN172654, CX700448 2 AY578154
Ribosomal protein S28 RpS287 EF452418 2 AY583363
Ribosomal protein L14 RpL147 EF207954 11 AY769284
Ribosomal protein L18 RpL187 EF207955, EF211970 11 AY769287
Ribosomal Sop2 Sop27 DT663968, EF211973 11 AY763110
Distal less cDll7 DQ445415
Mitotic checkpoint control protein (bub3) gene Bub37 CX700513
Polycomb protein Su(z)12 Su(z)127 DT662097
Ribosomal protein S25 RpS258 EF207956 25 AY769340
chiB (chitinase precursor) Cht9 CX700556, EF211966 7 AF052914
Ribonuclease L inhibitor homolog RLI9 EF207958 7 AB164193
Ribosomal protein S27 RpS279 EF207957 7 AY769342
Cyclin-dependent kinases regulatory subunit Cks9 CX700558
Elongation factor 1α bEf1a10 AY747994 5 D13338
Elongation factor 1δ Ef1d10 CX700886 5 AB046366
Patched bPtc10 AY745373 5 AADK01000387
Ribosomal protein L13 dRpL1310 CO729603 5 AY769282
Ribosomal protein L19 bRpL1910 CX700796 5 AY769289
Ribosomal protein S11 dRpS1110 CX700450 P AY706955
Opsin1 bOPS111 AF126751 15 AB047924
Ribosomal protein L5 bRpL511 CO729889 15 AY769272
Ribosomal protein L7A RpL7A11 EF207963 15 AY769275
Ribosomal protein L10A bRpL10A11 CO729740 15 AY769279
Ribosomal protein P0 bRpP011 CO729821 15 AJ457827
Ribosomal protein S5 bRpS511 CO729660 15 AY769319
Ribosomal protein S8 bRpS811 CX700851 15 AY769322
Ribosomal protein L8 RpL811 EF207977, EF211969
Ribosomal protein L30 dRpL3011 CO729949
Glycine-rich protein GRP12 EF207964, EF211967 8 AB197877
Beta-tubulin Btub12 EF207965, EF211964 20 AB003287
Ribosomal protein S7 RpS712 EF207966 20 AY769321
Ribosomal protein S20 RpS2012 CX700684 20 AY769336
Enolase Eno12 EF207979
Ribosomal protein L7 dRpL712 CX700625
Ribosomal protein L27 RpL2712 EF207978
Ribosomal protein S12 dRpS1212 CX700631
Ribosomal protein S16 RpS1613 EF207967 14 AY769332
Calreticulin Crc13 EF207968 22 AB090887
Cuticle protein (EDG84A homolog) EDG84A13 CO729743 22 AB017550
PCNA PCNA13 CV526328 22 AB002264, AB002265
Ribosomal protein L37 RpL3713 DN172717 22 AY769308
Ribosomal protein S4 RpS413 CO729938
Vermillion bv13 AY691422
Ribosomal protein L12 RpL1214 EF207969 19 AY769281
Eukaryotic translation elongation factor 2 eEF214 CX700527
Ribosomal protein S9 cRpS914 CX700565
Ribosomal protein L22 cRpL2215 CX700470 17 AY769291
Ribosomal protein P40 cRpP4015 CX700776 17 AB062685
Ribosomal protein S24 RpS2415 EF207970, EF211972 17 AY578155
Eukaryotic initiation factor 3B eiF3B15 EF207980
Forkhead box J1 cFox15 CR974474
Rab geranygeranyl transferase cGerTra15 CR974474
Elongation factor 1γ Ef1g16 EF207971 18 AB046361
Heat shock protein hsp21.4 Hsp21.417 EF207972 13 AB195972
Lim protein Mlp17 DT663321 13 AY461436
Ribosomal protein L21 RpL2117 CO729978 13 AY769290
Ribosomal protein L31 cRpL3117 CX700740 13 AY769301
ADP/ATP translocase ANT17 EF207974, EF211962 24 AY227000
Ribosomal protein L32 RpL3217 EF207973 24 AB048205
Sui1 Sui117 CO729706, EF211974 24 AY426343
Ribosomal protein L27a RpL27a17 EF207981
Ribosomal protein S10 RpS1017 EF207982
Scalloped cSd17 DQ674429
Bm44 Bm4418 DT664299 23 AB158647
Inhibitor of Apoptosis protein IAP18 CV526245, EF211968 23 AF281073
Ribosomal protein S30 RpS3018 CX700724 23 AY769346
Cubitus interruptus bci18 AY429297 U AF529422
90-kDa heat-shock protein 90hsp18 CO729719, EF211960 U AB060275
α-Tubulin atub18 EF207983, EF211963
O-Glycosyltransferase dOgt18 CV526007
Decapentaplegic bDpp19 AY747899 12 BAAB01102755
J-domain-containing protein JDP19 DT662955 12 AF176014
Ribosomal protein L9 RpL919 EF207975 12 AY769277
Muscular protein 20 Mp2019 CO729543
Prophenol oxidase-activating enzyme precursor PPAE19 CO729777
Ribosomal protein L44 cRpL4419 CX700847
Caspase-1 caspase20 EF207976, EF211965 10 AF448494
Cytosolic juvenile hormone binding protein Jhbp20 DT661817 10 AF098303
Actin 1 Act20 EF207985, EF211961
Calcium ATPase Ca-P20 CO729824
Ribosomal protein L23A RpL23A20 EF207984, EF211971
Apterous bapt21 (Z) AY747887 1(Z) AB024903
Triose–phosphate isomerase bTPI21 (Z) AY548151 1(Z) AY734490

Synteny analysis:

Of the newly mapped cDNA-derived markers, 47 were orthologous to those mapped in B. mori, which, along with 25 orthologous markers mapped previously ( Jiggins et al. 2005 Papanicolaou et al. 2005 Joron et al. 2006b), resulted in 72 orthologous markers mapped in both species. These markers span all 21 chromosomes of H. melpomene and 27 of the 28 chromosomes of B. mori ( Tables 1 and 2). These markers showed completely conserved syntenic relationships between the two species and allowed identification of homologous chromosomes defined by conserved groups of anchor loci. Thirty-eight markers fell into 15 H. melpomene LGs, each of which corresponded to a single homologous chromosome in B. mori each of these LGs contained between one and seven orthologous markers ( Table 2).

Homologous linkage group summary and color-pattern markers

H. melpomene linkage group . B. mori linkage group . No. of genes common to both species . H. melpomene color pattern marker a .
1 4 4 K
2 16 2
3 6 2
4 21 3
5 3 2
6 9 2
7 2, 11 7
8 25 1
9 7 3
10 5, P 6 Ac
11 15 7
12 8, 20 4
13 14, 22 5
14 19 1
15 17 3 Yb/Sb/N
16 18 1
17 13, 24 7
18 23, U 5 B/D
19 12 3
20 10 2
21 1 2
NA 26 0
Total: 21 chromosomes Total: 28 chromosomes Total: 72
H. melpomene linkage group . B. mori linkage group . No. of genes common to both species . H. melpomene color pattern marker a .
1 4 4 K
2 16 2
3 6 2
4 21 3
5 3 2
6 9 2
7 2, 11 7
8 25 1
9 7 3
10 5, P 6 Ac
11 15 7
12 8, 20 4
13 14, 22 5
14 19 1
15 17 3 Yb/Sb/N
16 18 1
17 13, 24 7
18 23, U 5 B/D
19 12 3
20 10 2
21 1 2
NA 26 0
Total: 21 chromosomes Total: 28 chromosomes Total: 72

Homologous linkage group summary and color-pattern markers

H. melpomene linkage group . B. mori linkage group . No. of genes common to both species . H. melpomene color pattern marker a .
1 4 4 K
2 16 2
3 6 2
4 21 3
5 3 2
6 9 2
7 2, 11 7
8 25 1
9 7 3
10 5, P 6 Ac
11 15 7
12 8, 20 4
13 14, 22 5
14 19 1
15 17 3 Yb/Sb/N
16 18 1
17 13, 24 7
18 23, U 5 B/D
19 12 3
20 10 2
21 1 2
NA 26 0
Total: 21 chromosomes Total: 28 chromosomes Total: 72
H. melpomene linkage group . B. mori linkage group . No. of genes common to both species . H. melpomene color pattern marker a .
1 4 4 K
2 16 2
3 6 2
4 21 3
5 3 2
6 9 2
7 2, 11 7
8 25 1
9 7 3
10 5, P 6 Ac
11 15 7
12 8, 20 4
13 14, 22 5
14 19 1
15 17 3 Yb/Sb/N
16 18 1
17 13, 24 7
18 23, U 5 B/D
19 12 3
20 10 2
21 1 2
NA 26 0
Total: 21 chromosomes Total: 28 chromosomes Total: 72

Chromosomal fusions:

Consistent with the difference in chromosome number between B. mori (28) and H. melpomene (21), we found evidence for 6 of the 10 predicted chromosomal fusions in the derived Heliconiini ( Figure 2). Each case suggested that two chromosomes from basal taxa, as still represented by two chromosomes in B. mori, had fused to form one H. melpomene chromosome. The additional predicted fusions could have gone undetected if they had involved either a pair of chromosomes that had also fused in the B. mori lineage or the homolog of B. mori chromosome 26, the only B. mori chromosome for which we had no shared markers in H. melpomene ( Table 2), fusing either to a chromosome already identified as fused (i.e., a three-way fusion) or to another chromosome that currently appears to be in 1:1 homology with a B. mori chromosome.

Linkage maps of putatively fused chromosomes in H. melpomene with comparison to maps of conserved markers in B. mori (A–F, corresponding to the six different putatively fused chromosomes in H. melpomene). Note the difference in scale between the maps. The lack of position bars for RpL13, ptc, and Ef1α in B. mori LG5 indicates that these markers were mapped using BAC–FISH instead of recombination linkage mapping (see Yasukochi et al. 2006). The lack of position bars for RpS16 in B. mori LG14 and H. melpomene LG13 indicates the lack of recombination mapping in B. mori and recombination mapping in a different brood (brood 44 as opposed to brood 33 see materials and methods ) in H. melpomene.

Linkage maps of putatively fused chromosomes in H. melpomene with comparison to maps of conserved markers in B. mori (A–F, corresponding to the six different putatively fused chromosomes in H. melpomene). Note the difference in scale between the maps. The lack of position bars for RpL13, ptc, and Ef1α in B. mori LG5 indicates that these markers were mapped using BAC–FISH instead of recombination linkage mapping (see Yasukochi et al. 2006). The lack of position bars for RpS16 in B. mori LG14 and H. melpomene LG13 indicates the lack of recombination mapping in B. mori and recombination mapping in a different brood (brood 44 as opposed to brood 33 see materials and methods ) in H. melpomene.

Conservation of gene order:

The six putatively fused chromosomes for which we positionally mapped new markers ( Figure 2) had a combined map length of 627 cM, in comparison with an estimated 424 cM for these same six chromosomes using the markers available previously ( Jiggins et al. 2005). This is largely due to the error detection function in MapMaker, leading to an artificially reduced estimate of recombination distance in the previous map (see materials and methods ). Thus, for example, LG7 had a map length of 51.5 cM in the previous study, which increases to 61.4 cM with the current data set using error detection. Without error detection, however, the length of the same chromosome increases to 98 cM ( Figure 2A). It therefore seems likely that the overall recombination length of the H. melpomene genome is significantly larger than that previously reported. Mapping also revealed the probable orientation of most of the chromosomal fusions ( Figure 2), assuming conservation of gene order on chromosomes with only two markers positionally mapped. Conservation of gene order was evident in the comparisons of H. melpomene chromosome 7 to B. mori chromosome 2 and of H. melpomene chromosome 10 to B. mori chromosome 5 ( Figure 2, A and B). The latter conclusion relies on comparison with markers mapped by BAC–FISH in B. mori ( Yasukochi et al. 2006 Figure 2B). An apparent reversal in gene order has occurred between Patched (ptc) and Ef1α ( Figure 2B), suggesting a chromosomal inversion in one lineage or the other. Although these loci are tightly linked, reversing their order causes a significant reduction in overall likelihood (log likelihood = 2.38, P < 0.004, of the reversed order compared to that shown in Figure 2B) mapping additional markers to this region would provide a test of this conclusion.


References

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Renwick, J.H. in Human Genetics. Proceedings of the Fourth International Congress of Human Genetics, 6-11 September 1971 (eds de Grouchy, J., Ebling, F.J.G. & Henderson, I.W.) 443–444 (Excerpta Medica, Amsterdam, 1972).

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SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes

Background: It has been repeatedly observed that gene order is rapidly lost in prokaryotic genomes. However, persistent synteny blocks are found when comparing more or less distant species. These genes that remain consistently adjacent are appealing candidates for the study of genome evolution and a more accurate definition of their functional role. Such studies require visualizing conserved synteny blocks in a large number of genomes at all taxonomic distances.

Results: After comparing nearly 600 completely sequenced genomes encompassing the whole prokaryotic tree of life, the computed synteny data were assembled in a relational database, SynteBase. SynteView was designed to visualize conserved synteny blocks in a large number of genomes after choosing one of them as a reference. SynteView functions with data stored either in SynteBase or in a home-made relational database of personal data. In addition, this software can compute on-the-fly and display the distribution of synteny blocks which are conserved in pairs of genomes. This tool has been designed to provide a wealth of information on each positional orthologous gene, to be user-friendly and customizable. It is also possible to download sequences of genes belonging to these synteny blocks for further studies. SynteView is accessible through Java Webstart at http://www.synteview.u-psud.fr.

Conclusion: SynteBase answers queries about gene order conservation and SynteView visualizes the obtained results in a flexible and powerful way which provides a comparative overview of the conserved synteny in a large number of genomes, whatever their taxonomic distances.


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