Liu X, Liu W, Lenstra JA, Zheng Z, Wu X, Yang J, Li B, Yang Y, Qiu Q, Liu H, Li K, Liang C, Guo X, Ma X, Abbott RJ, Kang M, Yan P, Liu J.

Nat Commun. 2023 Sep 19;14(1):5617. doi:10.1038/s41467-023-41220-x

Evolutionary origin of genomic structural variations in domestic yaks.

“assemblies were constructed for 6 wild and 15 domestic yaks” “we used a uniform standard pipeline to annotate these 47 bovine genomes. We identified an average of 24,368 protein-coding genes for each assembly” “1,048,639 high-confidence SNPs were detected and used in phylogenetic analyses with the water buffalo genome as outgroup” “We further constructed a species tree on the basis of 8428 single-copy core genes through selecting one representative individual of each species” “Pangenomes were constructed for yaks and cattle and a super-pangenome for the 7 Bovini species. For the yak pangenome the total gene set approached saturation at n = 20. The percentages of core (present in all 22 genomes), near-core (present in 20–21 genomes) and variable (found in 1–19 genomes) gene families were 50.18, 10.91, 38.91%, respectively.” “ In pairwise comparisons of the assemblies constituting the pangenome, each assembly possessed 123 to 2113 genes not present in the other genome” we constructed a multi-assembly graph-based genome of the 47 genomes used in the phylogenomic and super-pangenome analyses. This comprised 3.14 gigabases (Gb) spread across 5,449,222 nodes (the number of fragments of sequences) and connected by 4,889,530 edges (the connections between nodes), with non-reference nodes spanning 387.0 Mb. The core (shared by all genomes), near-core (in 46 or 45 genomes) and variable nodes (in 44 or less samples) accounted for 60.8, 17.0, 22.2% of all nodes.” “We detected SVs ( ≥ 50 bp) in the graph-based genome using the bubble popping algorithm of gfatools25 and retained 293,712 SVs (81.7% <500 bp, 99.76% <10 kb) that could be genotyped in the BosMut3.0 yak reference genome or at least one other genome” “Next, we used the graph-genotyping software Vg (v1.36.0) on 386 bovines (233 yaks, 140 cattle, 4 bison, 8 wisent and one gaur, including the novel genome sequences for assembling the super-pangenome) for which resequencing data with >6× coverage were available. This yielded 610,921 genotyped SVs, from which 57,432 were retained after quality filtering”

Min J, Zhao J, Zagelbaum J, Lee J, Takahashi S, Cummings P, Schooley A, Dekker J, Gottesman ME, Rabadan R, Gautier J.

Mol Cell. 2023 Jul 20;83(14):2434-2448.e7. doi: 10.1016/j.molcel.2023.06.016

Mechanisms of insertions at a DNA double-strand break.

Indel-seq: double-strand breaks are induced with the AsiSI endonuclease or CRISPR, and a target locus is studied by targeted sequencing of PCR amplicons. “the median size of inserts is 120 bp [...] 39% of inserts originate from repetitive sequences, including telomeres, centromeres, Alu, and retrotransposon elements” “Inhibition [with NU7441] of DNA-PK catalytic activity [involved in NHEJ] significantly decreased insertion events. In contrast, the size and number of deletions increased.” “POLQ inhibition did not reduce [...] insertions, indicating that insertions were largely independent of microhomology-mediated end joining (MMEJ)” “Treatment with CK-666, a small-molecule inhibitor that stabilizes the Arp2/3 complex in an inactive conformation, resulted in a significant decrease in insertion events originating from AsiSI-proximal donor sequences” “siRNA-mediated downregulation of RAD51 did not affect the overall number of insertions but dramatically [increased] distal (class 3) insertions”. “8.7% of insertions originated from multiple genomic loci on different chromosomes” “more than 70% of donor sequences originated from promoters and transcribed gene body regions” “Donor sequences are spread around the AsiSI sites and span the TSS; however, insertions preferentially originate from the transcribed side [...]. In contrast, donor sequences originating from AsiSI-cleaved DSBs within a gene body or distal intergenic regions did not show any bias” ”[Insertions in] a Cas9 DSB near the TSS of the BCL6 locus in a [the OCI-Ly7 cell line] were markedly enriched in the direction of transcription.” “alpha-amanitin decreased the frequency of insertions, preferentially those originating from promoter-proximal DSBs [...]. Furthermore, donor sequences in alpha-amanitin-treated cells were no longer preferentially derived from the transcribed side.” “[Upregulating transcription of telomeric repeat-containing RNA at telomerse via] FANCM downregulation resulted in a significant increase in telomeric insertions.” “RNA-DNA hybrid disruption by RNaseH1 suppressed the bias of donor sequences that originate preferentially from the direction of transcription”

Zivanovic Y, Lopez P, Philippe H, Forterre P.

Nucleic Acids Res. 2002 May 1;30(9):1902-10. doi:10.1093/nar/30.9.1902

Pyrococcus genome comparison evidences chromosome shuffling-driven evolution.

“the extent of rearrangement that occurred after the three species diverged is much lower between P. abyssi and P. horikoshii than between these two species and P. furiosus.” “[In P. furiosus, the distribution of IS elements] is clearly non-random, since 16 of them are located near shuffled segments boundaries, five are in completely scrambled regions and only two are found within an undisturbed segment.” “the AT3 skew was less upset than the word skew (here GGTT), which was itself, as expected, less perturbed than the gene orientation skew”. Coding genes were weakly colinear with the replication direction in P. abissi and P. horikoshii, especially for highly expressed genes, but this correlation was less evident or absent for P. furiosus_.

Matteo Cossu, Violette Da Cunha, Claire Toffano-Nioche, Patrick Forterre, Jacques Oberto

Biochimie. 2015 Nov;118:313-21. doi:10.1016/j.biochi.2015.07.008

Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes

“The comparative genomics analysis presented here confirms the initial observation that Thermococcales chromosomes are highly rearranged. In these genomes, DNA sequence scrambling has reached such a high level that commonly observed prokaryotic chromosomal landmarks such as oriC and terC are no longer readily identifiable by measuring DNA composition biases.”

Hughes D.

Genome Biol. 2000;1(6):REVIEWS0006. doi: 10.1186/gb-2000-1-6-reviews0006.

Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes.

Review reporting that “almost all rearrangements conserve the axis of chromosome replication”.

Tillier ER, Collins RA

Nat Genet. 2000 Oct;26(2):195-7. doi:10.1038/79918

Genome rearrangement by replication-directed translocation.

X-shaped patterns in whole-genome comparisons dot plots. “Single-gene inversions occurred at 12 of 44 boundaries [of repositioned blocks of genes] identified in Chlamydia, compared with only 13 local inversions adjacent to any of the 643 genes not at a boundary” Proposes that origin-centered inversions caused by replication forks can generate the patterns.

D'Iorio M, Dewar K.

Life Sci Alliance. 2022 Oct 19;6(1):e202201434. doi:10.26508/lsa.202201434

Replication-associated inversions are the dominant form of bacterial chromosome structural variation.

“We assessed a total of 313 species that were represented by 10 or more complete genome sequences” “A genoform in this work refers to a group of collinear chromosomal sequences within a species with at least 80% sequence similarity and without an inversion spanning more than 50 Kb.” “In Gammaproteobacteria, the species Haemophilus influenzae, Haemophilus parainfluenzae, and Mannheimia haemolytica all contained inversions that were predominantly located away from the replication origin. We also observed species that were consistently offset from symmetry in one direction such as in B. pertussis”

Eisen JA, Heidelberg JF, White O, Salzberg SL.

Genome Biol. 2000;1(6):RESEARCH0011. doi:10.1186/gb-2000-1-6-research0011

Evidence for symmetric chromosomal inversions around the replication origin in bacteria.

X-shaped pattern observed in line plots of pairwise comparisons between E. coli and V. cholerae, or Streptococcus or Mycobacterium species. The patterns might have been generated by inversions centered on origins and termini of replication.

Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, Roote J, Ashburner M, Bergman CM.

PLoS Biol. 2007 Jun;5(6):e152. doi:10.1371/journal.pbio.0050152

Principles of genome evolution in the Drosophila melanogaster species group.

“the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences” “We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group” “The overall rate of breakage in the D. melanogaster / D. yakuba lineage is 0.0183/Mb/Myr.”

Cáceres M, Ranz JM, Barbadilla A, Long M, Ruiz A.

Science. 1999 Jul 16;285(5426):415-8. doi:10.1126/science.285.5426.415

Generation of a widespread Drosophila inversion by a transposable element.

Target Site Duplication (TSD) sites were exchanged through the recombination of two transposons inserted in opposite directions.

Brooks AN, Hughes AL, Clauder-Münster S, Mitchell LA, Boeke JD, Steinmetz LM.

Science. 2022 Mar 4;375(6584):1000-1005. doi: 10.1126/science.abg0162

Transcriptional neighborhoods regulate transcript isoform lengths and expression levels.

“a synthetic yeast genome (Sc2.0) was designed to encode a Cre-dependent system known as synthetic chromosome rearrangement and modification by LoxP-mediated evolution (SCRaMbLE), which can generate stochastic genomic rearrangements on demand directly in its genome. These rearrangements occur at 34 base pair (bp)–loxPsym sites inserted 3 bp downstream of the stop codon of all nonessential CDSs.”

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.

Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. doi:10.1073/pnas.1932072100

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.

Primary paper for chains and nets, built with the BLASTZ and AXTCHAIN programs. Chains are one-to-many alignments and allow skipping over local inversions. In human/mouse comparisons, 2.0 inversion per Mbp, median length 814. Double gaps ≥ 100 per Mbp: 398.6, median length 411. Chains are called “short” when their span is <100,000 bases (span distribution of short chains apparently bimodal). 579 “long” chains (average length 983 kb) cover 32.9% of the bases in the human genome. Collectively all chains span 96.3% of the human genome and align to 34.6% of it. The authors note that the observed distribution of gap lengths violate the usual affine model of aligners.

“A chained alignment [is] an ordered sequence of traditional pairwise nucleotide alignments (“blocks”) separated by larger gaps, some of which may be simultaneous gaps in both species. [...] intervening DNA in one species that does not align with the other because it is locally inverted or has been inserted in by lineage-specific translocation or duplication is skipped”

“The chains are then put into a list sorted with the highest-scoring chain first. [...] each iteration taking the next chain off of the list, throwing out the parts of the chain that intersect with bases already covered by previously taken chains, and then marking the bases that are left in the chain as covered. [...] If a chain covers bases that are in a gap in a previously taken chain, it is marked as a child of the previous chain. In this way, a hierarchy of chains is formed that we call a net.”

“To be considered syntenic, a chain has to either have a very high score itself or be embedded in a larger chain, on the same chromosome, and come from the same region as the larger chain. Thus, inversions and tandem duplications are considered syntenic.”

“We define the (human) span of a chain to be the distance in bases in the human genome from the first to the last human base in the chain, including gaps, and we define the size of the chain as the number of aligning bases in it, not including gaps.”

Delprat A, Negre B, Puig M, Ruiz A.

PLoS One. 2009 Nov 18;4(11):e7883. doi:10.1371/journal.pone.0007883

The transposon Galileo generates natural chromosomal inversions in Drosophila by ectopic recombination.

In D. buzzatii, the 2z(3) inversion is flanked by several transposable elements, among which two Galileo repeats (cut-and-paste mechanism, members of the P element family), that “(i) are inserted in opposite orientation; (ii) present exchanged target site duplications; and (iii) are both chimeric”, suggesting ectopic recombination.

Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE.

Nat Genet. 2012 Jul 1;44(8):872-80. doi:10.1038/ng.2335

Structural diversity and African origin of the 17q21.31 inversion polymorphism.

“In conclusion, we propose that the ancestral H2′ haplotype arose in eastern or central Africa and spread to southern Africa before the emergence of anatomically modern humans (Fig. 6). Approximately 2.3 million years ago, the inversion rearranged to what we now refer as the direct orientation haplotype (H1′).”

Donnelly MP, Paschou P, Grigorenko E, Gurwitz D, Mehdi SQ, Kajuna SL, Barta C, Kungulilo S, Karoma NJ, Lu RB, Zhukova OV, Kim JJ, Comas D, Siniscalco M, New M, Li P, Li H, Manolopoulos VG, Speed WC, Rajeevan H, Pakstis AJ, Kidd JR, Kidd KK.

Am J Hum Genet. 2010 Feb 12;86(2):161-71. doi:10.1016/j.ajhg.2010.01.007

The distribution and most recent common ancestor of the 17q21 inversion in humans.

“Short tandem repeat polymorphism data indicate a very recent date for the most recent common ancestor, with dates ranging from 13,600 to 108,400 years, depending on assumptions and estimation methods”

Stefansson H, Helgason A, Thorleifsson G, Steinthorsdottir V, Masson G, Barnard J, Baker A, Jonasdottir A, Ingason A, Gudnadottir VG, Desnica N, Hicks A, Gylfason A, Gudbjartsson DF, Jonsdottir GM, Sainz J, Agnarsson K, Birgisdottir B, Ghosh S, Olafsdottir A, Cazier JB, Kristjansson K, Frigge ML, Thorgeirsson TE, Gulcher JR, Kong A, Stefansson K.

Nat Genet. 2005 Feb;37(2):129-37. doi:10.1038/ng1508

A common inversion under selection in Europeans.

A 900-kb inversion polymorphism on 17q21.31 that has diverged ~3 million years ago. One allele is rare exept in Europe, where it is positively selected. Low-copy repeat sequences were found in the vicinity of the inversion.

Machado CA, Haselkorn TS, Noor MA.

Genetics. 2007 Mar;175(3):1289-306. doi:10.1534/genetics.106.064758

Evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific gene flow in Drosophila pseudoobscura and D. persimilis.

“suppression of crossovers in inversion heterozygotes also extends to loci located outside the inversion but close to it (within 1–2 Mb)”

Dobzhansky T, Sturtevant AH

Genetics. 1938 Jan;23(1):28-64. doi:10.1093/genetics/23.1.28

Inversions in the Chromosomes of Drosophila Pseudoobscura.

Observation of polytene chromosomes in salivary glands of hybrid D. pseudoobscura crossed form different populations showed lage-scale inversions in the 3rd chromosome. The collection of haplotypes can be represented as a graph linking single inversion events. Multiple haplotypes may coexist in the same geographical region.

Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14433-7. doi:10.1073/pnas.240462997

Seoighe C, Federspiel N, Jones T, Hansen N, Bivolarovic V, Surzycki R, Tamse R, Komp C, Huizar L, Davis RW, Scherer S, Tait E, Shaw DJ, Harris D, Murphy L, Oliver K, Taylor K, Rajandream MA, Barrell BG, Wolfe KH.

Prevalence of small inversions in yeast gene order evolution

Classifies pairs of gene orientations as ”parallel”, “convergent”, “divergent” and “alternative parallel” and studies combinations of these orientations in 298 adjacent gene paris from the S. cerevisiae and the C. albicans genomes, and the number of inversions they imply. “We estimate that about 1,100 single-gene inversions have occurred since the divergence between these species” (divergence happened ~200 million years ago) “Our results suggest that successive random small inversions frequently cause a gene's chromosomal position and orientation to drift during its evolution. This process would alter gene order and orientation without moving any genes very far from their starting points.”

Hämälä T, Wafula EK, Guiltinan MJ, Ralph PE, dePamphilis CW, Tiffin P.

Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):e2102914118. doi:10.1073/pnas.2102914118

Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree.

31 × 2 haplotype assemblies using Illumina and 10x Genomics linked reads. dN/dS (interspecies) and πN/πS (intraspecies) values in SVs are higher than expectation and vary according the type of SV and the proximity to the SV's breakpoints. Genes with allele-specific expression were over-represented at heterozygous inversions. Genetic load is higher at inversions, as expected if they suppress recombination.

Mérot C, Berdan E, Cayuela H, Djambazian H, Ferchaud AL, Laporte M, Normandeau E, Ragoussis J, Wellenreuther M, Bernatchez L.

Mol Biol Evol. 2021 May 7:msab143. doi:10.1093/molbev/msab143

Locally adaptive inversions modulate genetic variation at different geographic scales in a seaweed fly.

Chromosomal assembly of Coelopa frigida. SNP analysis and PCA revealed known and candidate genomic inversions.

“We sampled the seaweed fly Coelopa frigida along a bioclimatic gradient stretching across 10° of latitude, a salinity gradient and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyse 1,446 low-coverage whole genomes collected along those gradients.“ “Analyses of more than 1,400 whole genomes of C. frigida flies revealed four large chromosomal inversions affecting a large fraction of the genome (36.1Mb, 15%), and three low recombining genomic regions.” “Among the 124,701 candidate SNPs identified by the GWAS, more than 99.8% were located in Cf-Inv(1)” “At a finer geographic scale, outlier SNPs associated with wrackbed abiotic characteristics (depth, temperature and salinity) were strongly enriched in the inverted region Cf-Inv(1) with an odds ratio of 5, including outliers with very strong support”

Satou Y, Sato A, Yasuo H, Mihirogi Y, Bishop J, Fujie M, Kawamitsu M, Hisata K, Satoh N.

Genome Biol Evol. 2021 Jun 8;13(6):evab068. doi:10.1093/gbe/evab068

Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages.

Chromosoma assembly of Ciona intestinalis finds ~20 inversions compared to C. robusta. Some inversions are heterozygous.

“Chromosomal-level assemblies for the two type-B individuals, sampled at Roscoff (France; specimen R) and Plymouth (England; specimen P)” “For each specimen, we built contigs from long Nanopore reads with the NECAT assembler and polished obtained contigs with Illumina reads using the Nextpolish software [and removed overlaping contigs] using the purge_dups software [...]. Both of these contig sets were 140 Mb in length (table 1).” “Although the heterozygosity rate of type-A animals has been estimated to be 1.1–1.2% (Dehal et al. 2002; Satou et al. 2012), those of specimens R and P were 3.0% and 3.6%, respectively.”

“Exons are highly conserved between type-A and type-B animals, whereas intergenic regions are highly varied between the two types.” [Supplemental material shows 97% similarity in aligned regions between R and P and 94% similarity between R/P and A]

“To identify translocations, we searched the genomic sequences for blocks containing three or more genes that were not found in the positions expected from the type-A genome. We found two small interchromosomal translocations between the genomes of specimen P and type A, [but] we did not find such translocations between the genomes of specimen R and type A.”

“Similarly, to identify inversions, we searched the genomic sequences for blocks containing three or more genes that were mapped in the reverse direction to the order in the type-A genome. We found 21 and 20 inversions in the genomes of specimens R and P, respectively (supplementary fig. S7, Supplementary Material online). Among them, 15 sites were common, and the remaining 11 sites were specific to specimen R or P (supplementary fig. S10 and tables S3 and S4, Supplementary Material online). Thus, our data indicate that there are structural variations not only between type-A and type-B animals but also between specimens R and P.”

“We found R-derived haplotype contigs that were structurally different from the chromosome of specimen R, but the same as both the specimen-P and the type-A chromosomes. [In “an inversion in chromosome 7 [that] contained the largest number of genes over an ∼900-kb region”] genomic PCR using four primers flanking the junctional sites demonstrated that specimen R was indeed heterozygous” “We also confirmed experimentally an inversion on chromosome 3 [...]. A PCR analysis demonstrated that specimen P was indeed heterozygous in this region.” “we manually inspected genomic alignments of the two type-B specimens against the type-A genome, and found nine additional inversions.” “To understand how prevalent the inversions we found were in type-B populations, we collected eight wild specimens at Roscoff and Plymouth, RO1–RO4 and PL1–PL4, respectively, and performed genomic PCR [that demonstrated that] type-B animals indeed have inversion polymorphisms.” “The inversions we found in the present study are relatively small (3 kb ∼ 873 kb)” “our data highlight the likely importance of inversions in speciation of Ciona, an invertebrate with mating governed by interactions of aquatic gametes”.

Beyter D, Ingimundardottir H, Oddsson A, Eggertsson HP, Bjornsson E, Jonsson H, Atlason BA, Kristmundsdottir S, Mehringer S, Hardarson MT, Gudjonsson SA, Magnusdottir DN, Jonasdottir A, Jonasdottir A, Kristjansson RP, Sverrisson ST, Holley G, Palsson G, Stefansson OA, Eyjolfsson G, Olafsson I, Sigurdardottir O, Torfason B, Masson G, Helgason A, Thorsteinsdottir U, Holm H, Gudbjartsson DF, Sulem P, Magnusson OT, Halldorsson BV, Stefansson K.

Nat Genet. 2021 Jun;53(6):779-786. doi:10.1038/s41588-021-00865-4

Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits.

”We generated [long read sequencing] data from 3,622 Icelanders and identified a median of 22,636 SVs per individual (a median of 13,353 insertions and 9,474 deletions).” “We did not attempt to discover translocations and inversions.“ “We found more SVs, particularly TR SVs, near telomeres, a reflection of the sequence content of telomeres and the high mutation rate of TRs” “The ZnF domain of PRDM9 is the DNA-binding domain, and the SV alleles thus introduce alterations in the DNA-binding motif of PRDM9 and consequently change the locations of meiotic recombination57,58. All the different ZnF-motif lengths showed a strong association with the location of crossovers as measured by the fraction of crossovers that occur in recombination hotspots.”

Wang J, Wurm Y, Nipitwattanaphon M, Riba-Grognuz O, Huang YC, Shoemaker D, Keller L.

Nature. 2013 Jan 31;493(7434):664-8. doi:10.1038/nature11832

A Y-like social chromosome causes alternative colony organization in fire ants.

“The lack of recombination over more than half of the two heteromorphic social chromosomes can be explained by at least one large inversion of around 9 megabases, and this absence of recombination has led to the accumulation of deleterious mutations, including repetitive elements in the non-recombining region of Sb compared with the homologous region of SB.”

Sun J, Chen C, Miyamoto N, Li R, Sigwart JD, Xu T, Sun Y, Wong WC, Ip JCH, Zhang W, Lan Y, Bissessur D, Watsuji TO, Watanabe HK, Takaki Y, Ikeo K, Fujii N, Yoshitake K, Qiu JW, Takai K, Qian PY.

Nat Commun. 2020 Apr 8;11(1):1657. doi: 10.1038/s41467-020-15522-3.

The Scaly-foot Snail genome and implications for the origins of biomineralised armour.

Synteny dotplot in Figure S3, based on orthologue pairs, between Chrysomallon squamiferum and P. canaliculata (>400 MY distance) show genes staying on their chromosome, but moving within. Are the chromosomes acrocentric ?

Schaeffer SW

Genetics. 2018 Sep;210(1):3-13. doi:10.1534/genetics.118.301084

Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics.

Review

Proc Natl Acad Sci U S A. 1917 Sep;3(9):555-8 doi:10.1073/pnas.3.9.555

Sturtevant AH

Genetic Factors Affecting the Strength of Linkage in Drosophila.

Chromosomal inversions (not recognised as such at the time) strongly reduce crossing overs in their vicinity.

Catacchio CR, Maggiolini FAM, D'Addabbo P, Bitonto M, Capozzi O, Lepore Signorile M, Miroballo M, Archidiacono N, Eichler EE, Ventura M, Antonacci F.

Genome Res. 2018 Jun;28(6):910-920. doi:10.1101/gr.234831.118

Inversion variants in human and primate genomes.

105 validation inversions between human and either chimpanzee, gorilla, orangutan, or macaque genomes, that range in size from 103 kb to 91 Mb.

Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, Flicek P, Bunikis I, Folkvord A, Andersson L.

Genome Res. 2019 Nov;29(11):1919-1928. doi:10.1101/gr.253435.119

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.

Linkage analysis of 45,000 markers from 2 crosses with ~50 offsprings each confirmed that there are 26 linkage groups, and suggests ~1 recombination per chromosome pair at meiosis. Recombination rate is lower towards centromeres. This is in line with the known fact that 3 chromosomes are metacentric and the other are acrocentric. When comparing with other fish species, genes tend to stay on the same chromosomes, but move within (like birds and invertebrates, but unlike mammals). A 7.8-Mb region on chr12 with strange linkage desequilibrium pattern was shown to be an inversion between southern and northern individuals. It may act as a supergene. Genetic exchanges between both haplotypes is reduced by the inversion.

Puddu F, Herzog M, Selivanova A, Wang S, Zhu J, Klein-Lavi S, Gordon M, Meirman R, Millan-Zambrano G, Ayestaran I, Salguero I, Sharan R, Li R, Kupiec M, Jackson SP.

Nature. 2019 Sep;573(7774):416-420. doi:10.1038/s41586-019-1549-9

Genome architecture and stability in the Saccharomyces cerevisiae knockout collection.

Loss of short chromosomes and gains of long chromosomes, changes in rDNA and telomere repeats, ...

Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ.

Nature. 2005 Sep 1;437(7055):94-100 doi:10.1038/nature04029

Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication.

New segments are exchanged between chromosomes via the NHEJ pathway. Segments exchange internal sequences via homologous recombinations. The rate of gene creation is higher in subtelomers (and centromeres...) than in chromosomal cores.

Yue JX, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC, Fischer G, Durbin R, Liti G.

Nat Genet. 2017 Jun;49(6):913-924. doi:10.1038/ng.3847

Contrasting evolutionary genome dynamics between domesticated and wild yeasts.

Yeast subtelomeres accumulate structural variants.

“For each subtelomere, we located its proximal boundary on the basis of the sudden loss of synteny conservation and demarcated its distal boundary by the telomere-associated core X and Y′ elements”

“All previously defined essential genes in S. cerevisiae S288C28 fell into the chromosomal cores, whereas all previously described subtelomeric duplication blocks in S288C were fully enclosed in our defined S288C subtelomeres. Furthermore, the genes from our defined subtelomeres showed 36.6-fold higher CNV accumulation than those from the cores”

“subtelomeric one-to-one orthologs also showed significantly higher nonsynonymous-to-synonymous substitution rate ratio (dN/dS) than those from the cores in the S. cerevisiae–S. cerevisiae and S. cerevisiae–S. paradoxus comparisons”

“rapid evolution of subtelomeres can substantially alter the gene repertoire and generate novel recombinants with adaptive potential”

Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM.

Nat Genet. 2019 Aug;51(8):1272-1282. doi:10.1038/s41588-019-0462-3

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression.

Sequencing of balancer chromosomes. Allele-specific RNA-seq, Hi-C and Capture-C. “Genes with changes in their expression have a small but significant enrichment for differential promoter contacts”, but the converse is not true. “Loss of long-range chromatin loops has little impact on gene expression.”

Long E, Evans C, Chaston J, Udall JA.

G3 (Bethesda). 2018 Oct 3;8(10):3247-3253. doi:10.1534/g3.118.200631

Genomic Structural Variations Within Five Continental Populations of Drosophila melanogaster.

Compares breakpoint position with a +-3 bp tolerance. Uses Assemblytics.

Cretu Stancu M, van Roosmalen MJ, Renkens I, Nieboer MM, Middelkamp S, de Ligt J, Pregno G, Giachino D, Mandrile G, Espejo Valle-Inclan J, Korzelius J, de Bruijn E, Cuppen E, Talkowski ME, Marschall T, de Ridder J, Kloosterman WP.

Nat Commun. 2017 Nov 6;8(1):1326. doi:10.1038/s41467-017-01343-4

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

Primary paper for NanoSV. Fed with last-split alignments.