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Conserved Synteny

Conserved Synteny refers to the preservation of the relative order and orientation of genes across species during evolution.
It enables the identification of functionally important genomic regions and the inference of evolutionary relationships between organisms.
This concept is widely used in comparative genomics and bioinformatics to study the conservation of chromosomal organization and gene content across divergent species.
Analyzing conserved synteny can provide insights into genome evolution, assist in genome annotation, and facilitate the transfer of knowledge from well-studied model organisms to less characterized species.
Understaning the principles of conserved synteny is crucial for researchers exploring the evolutionary dynamics and functional elements within complex genomes.

Most cited protocols related to «Conserved Synteny»

1
Comparative Genomics Gene Order Analysis
In gene order comparisons, it is necessary to work with blocks of genes conserved in two or more genomes; trying to work with one gene at a time is not a robust procedure, especially with flowering plants, because most of these genomes have a whole genome duplication (WGD) in their history. The fractionation process ensuing from WGD deletes duplicate genes in a partially random pattern from one or the other duplicate (homeologous) chromosome, independently in two or more descendants of a duplicated genome [4 (link)]. This pattern, together with the possibility for some genes to transpose into different positions in the genome, makes it hard to identify unambiguously orthologous genes that are in the same gene order in two genomes. A set of five or ten genes in the same order, with few intervening genes, in two genomes can be confidently identified as a conserved syntenic block [5 (link), 6 (link)].
However, the notion of block adjacency encounters a number of operational problems; the genes in a syntenic block in one genome may differ somewhat from the same block in the other genome, the minimum number of genes to establish a block is a parameter that must be determined by some empirical experimentation, as is the number of genes allowed to intervene between two pairs of orthologs within a block in the two genomes. We will avoid these practical problems in our simulations by excluding fractionation or other gene loss, duplication and small transpositions from our model.
Zheng C, & Sankoff D. (2016). Locating rearrangement events in a phylogeny based on highly fragmented assemblies. BMC Genomics, 17(Suppl 1), 1.
Publication 2016
Chromosomes Conserved Synteny Gene Order Genes Genes, Duplicate Genome Magnoliopsida Radiotherapy Dose Fractionations Synteny
2
Sequencing and Genome Annotation of P. knowlesi
The random shotgun approach was used to obtain roughly eightfold coverage of the whole nuclear genome sequence from the erythrocyte stage of the Pk1(A+) clone of the H strain of P. knowlesi​5 (link). Sequence reads were assembled (as described in the Supplementary Information) and positional information from sequenced read pairs were used to resolve the orientation and position of the contigs. The assembled P. knowlesi contigs were iteratively ordered and oriented by alignment to P. vivax assembled sequences (described in ref. 4 ) and by manual checking. Automated predictions from the gene finding algorithms were manually reviewed by comparison to orthologues in other Plasmodium species. Artemis and Artemis Comparison Tool (ACT) were used (as described previously28 (link)) for annotation and curation and viewing the TBLASTX comparisons of regions with conserved synteny between P. knowlesi, P. vivax and P. falciparum. This also allowed us to curate gene models and identify local interruptions of synteny. Functional annotations were based on standard protocols as described previously6 (link).
Pain A., Böhme U., Berry A.E., Mungall K., Finn R.D., Jackson A.P., Mourier T., Mistry J., Pasini E.M., Aslett M.A., Balasubrammaniam S., Borgwardt K., Brooks K., Carret C., Carver T.J., Cherevach I., Chillingworth T., Clark T.G., Galinski M.R., Hall N., Harper D., Harris D., Hauser H., Ivens A., Janssen C.S., Keane T., Larke N., Lapp S., Marti M., Moule S., Meyer I.M., Ormond D., Peters N., Sanders M., Sanders S., Sargeant T.J., Simmonds M., Smith F., Squares R., Thurston S., Tivey A.R., Walker D., White B., Zuiderwijk E., Churcher C., Quail M.A., Cowman A.F., Turner C.M., Rajandream M.A., Kocken C.H., Thomas A.W., Newbold C.I., Barrell B.G, & Berriman M. (2008). The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature, 455(7214), 799-803.
Publication 2008
Clone Cells Conserved Synteny Erythrocytes Genes Genome Plasmodium Strains Synteny
3
Comparative Genomics of Secondary Metabolite Clusters
Secondary metabolite biosynthesis gene clusters are highly modular, and their genes are transferred frequently from one gene cluster to another during evolution (25 (link),26 (link)). Therefore, when trying to obtain a functional understanding of a gene cluster, it is highly beneficial to be able to compare it with (parts of) other gene clusters which show similarity to it and which may have been characterized experimentally. In order to facilitate this, we applied our annotated database of gene clusters to link up protein sequences with their parent gene clusters and create a comparison tool—based on the most recent BLAST+ implementation (27 (link))—which ranks gene clusters by similarity to a queried gene cluster. Clusters are sorted first based on an empirical similarity score S = h + H + s + S + B, in which h is the number of query genes with a significant hit, H is the number of core query genes with a significant hit, s is the number of gene pairs with conserved synteny, S is the number of gene pairs with conserved synteny involving a core gene, and B is a core gene bonus (three points given when at least one core gene has a hit in the subject cluster). If the similarity scores are equal, the hits are subsequently ranked based on the cumulative BlastP bit scores between the gene clusters. This feature enables a rapid assessment of the comparative genomics for each annotated cluster (Figure 3).

Example of ClusterBlast alignment of gene clusters homologous to the query gene cluster. In this case, the ten best hits to the calcium-dependent antibiotic NRPS gene cluster from Streptomyces coelicolor A3(2) are displayed. Homologous genes (BLAST e-value < 1E-05; 30% minimal sequence identity; shortest BLAST alignment covers over >25% of the sequence) are given the same colors. The ‘select gene cluster alignment’ drop-down menu provides links to one-by-one gene cluster alignments to each gene cluster hit. In the one-by-one gene cluster alignments, PubMed and/or PubChem links are provided for gene clusters associated with a known compound.

Medema M.H., Blin K., Cimermancic P., de Jager V., Zakrzewski P., Fischbach M.A., Weber T., Takano E, & Breitling R. (2011). antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, 39(Web Server issue), W339-W346.
Publication 2011
Amino Acid Sequence Anabolism Antibiotics Biological Evolution Calcium Conserved Synteny Gene Clusters Genes Parent Streptomyces coelicolor
4
Salmon Chromosome Sequences Alignment
Salmon chromosome sequences were repeat masked using a salmon repeat database and RepeatMasker v4.0.3 (ref. 72 ) and aligned against rainbow trout scaffolds13 (link) using MegaBLAST73 (link). Rainbow trout scaffolds mapping to multiple salmon chromosomes were broken when supported by information from a rainbow trout linkage map containing 31,390 SNPs constructed in a family material of 2,464 individuals using Lep-MAP74 (link). The relative positions of trout scaffolds within the salmon genome were used, together with trout linkage maps, to position, orient and concatenate 11,335 rainbow trout scaffolds into 29 single chromosome sequences (1.37 Gb). Nomenclature for rainbow trout chromosomes is based on ref. 35 . Conserved syntenic blocks between rainbow trout and Atlantic salmon were determined by aligning chromosome sequences for the two species against each other using LASTZ60 .
Lien S., Koop B.F., Sandve S.R., Miller J.R., Kent M.P., Nome T., Hvidsten T.R., Leong J.S., Minkley D.R., Zimin A., Grammes F., Grove H., Gjuvsland A., Walenz B., Hermansen R.A., von Schalburg K., Rondeau E.B., Di Genova A., Samy J.K., Olav Vik J., Vigeland M.D., Caler L., Grimholt U., Jentoft S., Inge Våge D., de Jong P., Moen T., Baranski M., Palti Y., Smith D.R., Yorke J.A., Nederbragt A.J., Tooming-Klunderud A., Jakobsen K.S., Jiang X., Fan D., Hu Y., Liberles D.A., Vidal R., Iturra P., Jones S.J., Jonassen I., Maass A., Omholt S.W, & Davidson W.S. (2016). The Atlantic salmon genome provides insights into rediploidization. Nature, 533(7602), 200-205.
Publication 2016
Asian Persons Chromosome Mapping Chromosomes Chromosomes, Human, Pair 11 Conserved Synteny Family Member Genome Oncorhynchus mykiss Salmo salar Single Nucleotide Polymorphism Trout
5
Identifying Core Genome Orthologs in E. coli/Shigella
A preliminary set of orthologs was defined by identifying unique pairwise reciprocal best hits, with at least 80% similarity (∼85% identity) in amino acid sequence and less than 20% difference in protein length. The analysis of orthology was made for every pair of E. coli/Shigella genomes. The core genome, consisting of genes ubiquitously found among all strains of the species, was defined as the intersection of pairwise lists.
For every pair of genomes this list of persistent orthologs was then supplemented, with attention to conservation of gene order. Because (i) few rearrangements are observed at these short evolutionary distances, and (ii) horizontal gene transfer is frequent, genes outside conserved blocks of synteny are likely to be xenologs or paralogs. Hence, we combined the homology analysis (protein sequence similarity ≥80%, ≤20% difference in protein length) with the classification of these genes as either syntenic or nonsyntenic, for positional orthology determination. The analysis was made for every pair of E. coli/Shigella genomes. The definitive list of orthologs of the pan-genome was then defined as the union of pairwise lists.
A syntenic block was defined as a set of consecutive pairs of genes in the core genome. Conserved order gene blocks are obtained by comparison of the localisation of best bi-directional hit pairs in the core genome, adopting a window size of one gap.
These lists were also used to perform gene accumulation curves using R, which describe the number of new genes and genes in common, with the addition of new comparative genomes (Figure 1). The procedure was repeated 1000 times by randomly modifying genome insertion order to obtain median and quartiles.
Touchon M., Hoede C., Tenaillon O., Barbe V., Baeriswyl S., Bidet P., Bingen E., Bonacorsi S., Bouchier C., Bouvet O., Calteau A., Chiapello H., Clermont O., Cruveiller S., Danchin A., Diard M., Dossat C., Karoui M.E., Frapy E., Garry L., Ghigo J.M., Gilles A.M., Johnson J., Le Bouguénec C., Lescat M., Mangenot S., Martinez-Jéhanne V., Matic I., Nassif X., Oztas S., Petit M.A., Pichon C., Rouy Z., Ruf C.S., Schneider D., Tourret J., Vacherie B., Vallenet D., Médigue C., Rocha E.P, & Denamur E. (2009). Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths. PLoS Genetics, 5(1), e1000344.
Publication 2009
Amino Acid Sequence Attention Biological Evolution Conserved Synteny Gene Order Gene Rearrangement Genes Gene Transfer, Horizontal Genome Proteins Shigella Strains Synteny

Most recents protocols related to «Conserved Synteny»

1
Ancestral Genome Reconstruction and Rearrangement Analysis
Ancestral genomes reconstructed by AGORA from Ensembl v.102 were filtered to retain the most contiguous reconstructions, resulting in 73 ancestral genomes with G50 > 230 and L70 < 40. Conserved syntenic blocks between successive ancestral genomes in internal branches, and between ancestral genomes and their extant descendant in terminal branches, were computed with PhylDiag72 (link). Ends of blocks corresponding to likely evolutionary breakpoints were identified using ad hoc scripts. Orthologous genes between successive genomes were also compared in terms of their assignation to scaffolds or chromosomes larger than 200 genes using AGORA’s src/misc.compareGenomes.py script in ‘printOrthologousChrom’ mode. Groups of at least 20 genes relocating to more than 1 chromosome in a descendant genome, and inversely groups of at least 20 genes from 2 or more ancestral chromosomes relocating on the same descendant chromosome, were considered interchromosomal rearrangements. Breakpoint and rearrangement rates per million years were computed using branch length estimates from TimeTree73 (link). A full description of the parameters and selection thresholds are provided in the Supplementary Information (‘Vertebrate genome evolutionary dynamics’).
Muffato M., Louis A., Nguyen N.T., Lucas J., Berthelot C, & Roest Crollius H. (2023). Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom. Nature Ecology & Evolution, 7(3), 355-366.
Publication 2023
Biological Evolution Chromosomes Chromosomes, Human, Pair 1 Conserved Synteny Gene Rearrangement Genes Genome Reconstructive Surgical Procedures Vertebrates
2
Optimizing Genome Assembly Using PacBio Reads
PacBio CLR raw reads were subsampled at different depths of coverage and size distributions (i.e., removing reads shorter or longer than a specified range of length). This subsampling of reads served as an assembly optimization process (Rayamajhi et al. 2022 ). See supplements for more details on the subsampling optimization. For C. esox, the highest quality assembly was derived from a subsample of reads 10–50 kb in length that provided 70× coverage, based on an initial genome size estimation of 1.1 Gb, yielding 3.8 million reads with a 20.4 kb mean length and 23 kb read N50. For C. gunnari, the most optimal subsample contained reads over 15 kb and 80× coverage, yielding a 29.5 kb mean length and a 32 kb N50. Contig-level assemblies were made using two different assemblers, Flye (Kolmogorov et al. 2019 (link)) and wtdbg2 (Ruan and Li 2020 (link)). Each assembly was assessed for contiguity using QUAST v4.4 (Gurevich et al. 2013 (link)) and gene completeness using BUSCO v3.0.1 (Simão et al. 2015 (link)), using the actinopterygii_odb9 lineage data set. For both species, Flye v2.5 generated superior contig-level assemblies based on quality and completeness scores (supplementary methods) and was selected as the primary assembly for downstream analyses. The wtdbg2 v2.5 assembly is referred to as the secondary assembly and was used for comparison purposes (supplementary table S13, Supplementary Material online).
The Hi-C data were then integrated into both the primary and secondary assemblies to generate chromosome-level super-scaffolds using Juicer v1.6.2 (Durand et al. 2016 (link)) to identify the Hi-C junctions, and then with Juicer's 3d-dna program to complete the integration of scaffolds. In addition, conserved synteny analysis (described below) between primary and secondary assemblies was used to perform manual curation of the scaffolding process. For example, we employed manual insertions, inversions, or translocations of whole contigs when discrepancies were found between the primary and secondary assemblies, and evidence, such as contig or scaffold boundaries, that supported one assembly to be correct. We used a custom Python program to propagate these changes through the constituent assembly files, such as the structure (AGP), annotation (GFF), and sequence files (FASTA). Following scaffolding and manual curation, a re-assessment of the contiguity of the final assembly was done using QUAST v4.4 and an assessment of gene completeness was performed with both BUSCO v3.0.1 and BUSCO v5.1.3 (Manni et al. 2021 (link)), using the actinopterygii_odb9 and actinopterygii_odb10 gene data sets, respectively.
Rivera-Colón A.G., Rayamajhi N., Minhas B.F., Madrigal G., Bilyk K.T., Yoon V., Hüne M., Gregory S., Cheng C.H, & Catchen J.M. (2023). Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish. Molecular Biology and Evolution, 40(3), msad029.
Publication 2023
Chromosomes Conserved Synteny Dietary Supplements Esox Genes Insertion Mutation Inversion, Chromosome Python Translocation, Chromosomal
3
Comparative Genomic Synteny Analysis of Notothenioid Fishes
An analysis of conserved synteny was performed at different stages of the assembly using the Synolog software (Catchen et al. 2009 (link); Small et al. 2016 (link)). Annotated coding sequences from C. esox and C. gunnari primary and secondary assemblies, and other species of interest, were first reciprocally matched using the blastp algorithm from BLAST + v2.4.0. The BLAST results and genome annotation coordinates were fed to Synolog, which (1) establishes reciprocal best BLAST hits to identify orthologous genes, (2) uses the genome coordinates of each best hit to define clusters of conserved synteny between the genomes, (3) refines ortholog assignments using the defined clusters, and (4) defines orthology between chromosomes/scaffolds based on the conserved synteny patterns. In addition to the C. esox and C. gunnari genomes described here, for comparative purposes, we included other high-quality notothenioid assemblies including C. aceratus (Kim et al. 2019 (link)), P. georgianus (Bista et al. 2022 ), Gymnodraco acuticeps (Bista et al. 2022 ), and Trematomus bernacchii (Bista et al. 2022 ; supplementary table S2, Supplementary Material online).
This conserved synteny analysis was initially used to manually curate the assemblies, by identifying discrepancies between primary and secondary assemblies, and/or to identify structural variants located within scaffold boundaries indicating a misassembly. Once the curated chromosome-level sequences were generated, conserved synteny was determined between the genomes of C. esox and C. gunnari against the genome of E. maclovinus, the closest sister species to the Antarctic clade, in order to identify and name orthologous chromosomes. The E. maclovinus assembly (Cheng et al., in preparation) was first compared against the Xiphophorus maculatus reference assembly, which contains the ancestral teleost karyotype number of 24 chromosomes (Amores et al. 2014 (link)). Chromosomes were named accordingly to these patterns of conserved synteny.
Rivera-Colón A.G., Rayamajhi N., Minhas B.F., Madrigal G., Bilyk K.T., Yoon V., Hüne M., Gregory S., Cheng C.H, & Catchen J.M. (2023). Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish. Molecular Biology and Evolution, 40(3), msad029.
Publication 2023
Chromosomes Conserved Synteny Esox Exons Genes Genome Karyotype Xiphophorus
4
Switchgrass Cell Wall QTLs Colocalization
A total of 56 QTLs related to cell wall traits in switchgrass were retrieved from the results of Ali, Serba, Walker, Jenkins, Schmutz, Bhamidimarri, and Saha [21 (link)] (Supplementary Table S5). Colocalization between these QTLs and the switchgrass SQTLs was analyzed with an analogous procedure to miscanthus. Specifically, 100 sets of 56 random QTL regions from the switchgrass genome mirroring the size distribution of the 56 QTLs from Ali, Serba, Walker, Jenkins, Schmutz, Bhamidimarri, and Saha [21 (link)] were computed. The proportion of QTLs colocalizing for >50% of their bp length with SQTLs was then calculated for every set, and binomial tests were performed to assess presence and significance of a decrement in such proportion (custom R script).
As performed in miscanthus, the cell wall genes in colocalizing regions were identified by using the set of angiosperm cell wall genes developed in our previous SQTL study [1 (link)]. Moreover, angiosperm-wide syntenic conservation of those genes was analyzed by retrieving their syntenic homologs from the synteny network developed by Pancaldi, van Loo, Schranz, and Trindade [75 (link)] and Pancaldi, Vlegels, Rijken, van Loo, and Trindade [1 (link)].
Pancaldi F., van Loo E.N., Senio S., Al Hassan M., van der Cruijsen K., Paulo M.J., Dolstra O., Schranz M.E, & Trindade L.M. (2023). Syntenic Cell Wall QTLs as Versatile Breeding Tools: Intraspecific Allelic Variability and Predictability of Biomass Quality Loci in Target Plant Species. Plants, 12(4), 779.
Publication 2023
Cell Wall Conserved Synteny Genes Genome Magnoliopsida Panicum virgatum Quantitative Trait Loci Synteny Vorinostat Walkers
5
Miscanthus QTL-SQTL Colocalization Analysis
Colocalization between SQTLs and the 91 QTLs found by the miscanthus GWAS was performed by developing 100 sets of 91 random QTL regions from the miscanthus genome mirroring the size distribution of the QTLs from GWAS results (custom R script). The proportion of QTLs colocalizing for >50% of their bp length with SQTLs was then calculated for every set, and binomial tests were performed to assess if random QTLs co-localized with SQTLs significantly less than the QTLs from the GWAS (custom R script).
In addition to calculating the statistical significance of the colocalization between miscanthus SQTLs and QTLs, the cell wall genes in colocalizing regions were identified by using the set of angiosperm cell wall genes developed in our previous SQTL study [1 (link)]. Moreover, angiosperm-wide syntenic conservation of those genes was analyzed by retrieving their syntenic homologs from the synteny network developed by Pancaldi, et al. [75 (link)] and Pancaldi, Vlegels, Rijken, van Loo, and Trindade [1 (link)].
Pancaldi F., van Loo E.N., Senio S., Al Hassan M., van der Cruijsen K., Paulo M.J., Dolstra O., Schranz M.E, & Trindade L.M. (2023). Syntenic Cell Wall QTLs as Versatile Breeding Tools: Intraspecific Allelic Variability and Predictability of Biomass Quality Loci in Target Plant Species. Plants, 12(4), 779.
Publication 2023
Cell Wall Conserved Synteny Genes Genome Genome-Wide Association Study Magnoliopsida Quantitative Trait Loci Synteny

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More about "Conserved Synteny"

Conserved Synteny: Unlocking Evolutionary Insights and Genomic Discoveries Conserved synteny, a fundamental concept in comparative genomics and bioinformatics, refers to the preservation of the relative order and orientation of genes across different species during the evolutionary process.
This powerful tool enables researchers to identify functionally important genomic regions, infer evolutionary relationships between organisms, and gain invaluable insights into genome evolution.
By analyzing conserved synteny, scientists can uncover the conservation of chromosomal organization and gene content across divergent species.
This knowledge is crucial for understanding the functional elements within complex genomes and tracing the evolutionary dynamics that have shaped them.
Leveraging a wide range of genomic technologies, such as the GeneRacer kit, HiSeq 2500 sequencer, and Sequencher 5.1 software, researchers can explore conserved synteny with unprecedented depth and accuracy.
From DNA extraction using the Wizard Genomic DNA Purification Kit to transcriptome analysis with the TruSeq RNA Sample Preparation Kit, these advanced tools empower scientists to investigate the preservation of genetic architecture across diverse organisms.
Furthermore, the integration of advanced imaging techniques, like the DFC340 FX camera and Image-Pro Plus 4.5 software, enables detailed visualizations of conserved syntenic regions, facilitating the intuitive interpretation of complex genomic data.
The 454 platform, a pioneering next-generation sequencing technology, has also played a pivotal role in the exploration of conserved synteny, contributing to the advancement of comparative genomics.
By understanding the principles of conserved synteny, researchers can not only unravel the evolutionary history of species but also leverage this knowledge to assist in genome annotation, facilitate the transfer of insights from well-studied model organisms to less characterized species, and ultimately drive groundbreaking discoveries in the field of biology.
Conserved synteny: the keystone of comparative genomics, unlocking the secrets of genome evolution and function.