Yin Y, Fan H, Zhou B, Hu Y, Fan G, Wang J, Zhou F, Nie W, Zhang C, Liu L, Zhong Z, Zhu W, Liu G, Lin Z, Liu C, Zhou J, Huang G, Li Z, Yu J, Zhang Y, Yang Y, Zhuo B, Zhang B, Chang J, Qian H, Peng Y, Chen X, Chen L, Li Z, Zhou Q, Wang W, Wei F.

Nat Commun. 2021 Nov 25;12(1):6858. doi:10.1038/s41467-021-27091-0

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer

“we identified the rapidly evolving genes (REGs) and positively selected genes (PSGs) in the M. crinifrons, M. gongshanensis, and M. muntjak vaginalis with large fused chromosomes, as well in their common ancestor node. The results showed that the PSGs and REGs in these lineages are enriched in GOs and pathways related to the maintenance of genomic stability.” “the occurrence/frequency of genomic rearrangements (>10 kb) of M. crinifrons and M. gongshanensis (3.06~3.89 events/Mb) are not significantly higher than those in M. reevesi, E. davidianus, and C. albirostris (3.11~4.56 events/Mb)”

Moreau H, Verhelst B, Couloux A, Derelle E, Rombauts S, Grimsley N, Van Bel M, Poulain J, Katinka M, Hohmann-Marriott MF, Piganeau G, Rouzé P, Da Silva C, Wincker P, Van de Peer Y, Vandepoele K.

Genome Biol. 2012 Aug 24;13(8):R74. doi:10.1186/gb-2012-13-8-r74

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage.

7,847 genes, no transposons. Two “outlier” chromosomes are found with lower GC content, like in Ostreococcus and Micromonas. Genes in the big outlier chromosomes have a high number of small AT-rich introns with no apparent conserved motifs.

Yoshida Y, Shaikhutdinov N, Kozlova O, Itoh M, Tagami M, Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Noma S, Cherkasov A, Gazizova G, Nasibullina A, Deviatiiarov R, Shagimardanova E, Ryabova A, Yamaguchi K, Bino T, Shigenobu S, Tokumoto S, Miyata Y, Cornette R, Yamada TG, Funahashi A, Tomita M, Gusev O, Kikawada T.

NAR Genom Bioinform. 2022 Apr 5;4(2):lqac029. doi:10.1093/nargab/lqac029

High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance.

Sleeping chironomid Polypedilum vanderplanki. Resists dessication. Its chr4, and the genes it encodes has a lower GC content than the others. Chr4 harbors genes and loci related to resistance to dehydratation. “One element that may have caused the diversity in Chromosome 4 is DNA damage. We have previously observed extensive DNA damage during larvae anhydrobiosis and the induction of Rad51, an activator of double strand break repair during recovery” Discusses that preference for NHEJ might have caused decrease of GC content.

Derelle E, Ferraz C, Rombauts S, Rouzé P, Worden AZ, Robbens S, Partensky F, Degroeve S, Echeynié S, Cooke R, Saeys Y, Wuyts J, Jabbari K, Bowler C, Panaud O, Piégu B, Ball SG, Ral JP, Bouget FY, Piganeau G, De Baets B, Picard A, Delseny M, Demaille J, Van de Peer Y, Moreau H.

Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11647-52. doi:10.1073/pnas.0604795103

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features.

Half of chromosome 2 and the whole of chromosome 19 differ from the rest of the genome by a lower GC content (52% instead of 59%) and a higher frequency of repeated regions (they contain 77% of the 417 repeat elements). Chr2 has also a different codon usage and smaller introns. The genes on chr19 tend to be less related the “green lineage” (photosynthetic cells that gave rise to plants).

Kabir A, Ieda R, Hosoya S, Fujikawa D, Atsumi K, Tajima S, Nozawa A, Koyama T, Hirase S, Nakamura O, Kadota M, Nishimura O, Kuraku S, Nakamura Y, Kobayashi H, Toyoda A, Tasumi S, Kikuchi K.

Proc Natl Acad Sci U S A. 2022 Jun 7;119(23):e2121469119. doi:10.1073/pnas.2121469119

Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu pufferfish.

The genome of the green puffer (Takifugu alboplumbeus or T. niphobles) was assembled. SNP analysis of multiple species showed that in three fugu species (T. niphobles, T. snyderi and T. vermicularis), the sex determination locus is not Amrh2 anymore (like it is in T. rubripes), but a new supergene containing GsdfY. This supergene appears to have moved to a new autosome more than once in the evolutionary history of these species.

Bredeson JV, Lyons JB, Oniyinde IO, Okereke NR, Kolade O, Nnabue I, Nwadili CO, Hřibová E, Parker M, Nwogha J, Shu S, Carlson J, Kariba R, Muthemba S, Knop K, Barton GJ, Sherwood AV, Lopez-Montes A, Asiedu R, Jamnadass R, Muchugi A, Goodstein D, Egesi CN, Featherston J, Asfaw A, Simpson GG, Doležel J, Hendre PS, Van Deynze A, Kumar PL, Obidiegwu JE, Bhattacharjee R, Rokhsar DS.

Nat Commun. 2022 Apr 14;13(1):2001. doi:10.1038/s41467-022-29114-w

Chromosome evolution and the genetic basis of agronomically important traits in greater yam.

Very broad peri-centromeric regions containg mostly repeats and confining the genes in the subtelomeric regions.

Mathog D, Hochstrasser M, Gruenbaum Y, Saumweber H, Sedat J.

Nature. 1984 Mar 29-Apr 4;308(5958):414-21. doi:10.1038/308414a0

Characteristic folding pattern of polytene chromosomes in Drosophila salivary gland nuclei.

Drosophila polytene chromosome arms form isolated topoplogical domains in interphase. Centromeres are clustered near the nuclear enveloppe and telomeres tend to be on the opposite side (the Rabl conformation).

Yamamoto K, Hamaji T, Kawai-Toyooka H, Matsuzaki R, Takahashi F, Nishimura Y, Kawachi M, Noguchi H, Minakuchi Y, Umen JG, Toyoda A, Nozaki H.

Proc Natl Acad Sci U S A. 2021 May 25;118(21):e2100712118. doi:10.1073/pnas.2100712118

Three genomes in the algal genus Volvox reveal the fate of a haploid sex-determining region after a transition to homothallism

Volvox has a sex-determining region (SDR) of ~1 Mb. The homothallic species Volvox africanus has a SDR-like region ressembling the female one, and a multicopy array of the male-determining gene (MID) at a different location.

Sergey Nurk, Brian P Walenz, Arang Rhie, Mitchell R Vollger, Glennis A Logsdon, Robert Grothe, Karen H Miga, Evan E Eichler, Adam M Phillippy, Sergey Koren

Genome Res. 2020 Sep;30(9):1291-1305. doi:10.1101/gr.263566.120

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

“HiCanu modifies the input reads by compressing every homopolymer to a single nucleotide.” “Outputs contigs as “pseudo-haplotypes” that preserve local allelic phasing but may switch between haplotypes”

Payen C, Fischer G, Marck C, Proux C, Sherman DJ, Coppée JY, Johnston M, Dujon B, Neuvéglise C.

Genome Res. 2009 Oct;19(10):1710-21. doi:10.1101/gr.090605.108

Unusual composition of a yeast chromosome arm is associated with its delayed replication.

“high GC content (52.9%) of the 1-Mb left arm of chromosome C (abbreviated here as ‘C-left’)” “The replication timing of C-left is delayed compared with the rest of the genome” “The global gene density, transcriptional orientations, proportion of orthologs to S. cerevisiae essential genes, and proportion of genes in families are comparable between C-left and the rest of the genome. The only differences are modest: the complete absence of any traces of LTR retrotransposons, an overrepresentation of microsatellites, and a moderate increase in CDS length.”

Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum.

Marinov GK, Trevino AE, Xiang T, Kundaje A, Grossman AR, Greenleaf WJ.

Nat Genet. 2021 May;53(5):613-617. doi: 10.1038/s41588-021-00848-5.

“each dinoTAD corresponded to a pair of divergent gene arrays” “α-amanitin treatment resulted in a dose-dependent, progressive dinoTAD decompaction”

Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum.

Nand A, Zhan Y, Salazar OR, Aranda M, Voolstra CR, Dekker J.

Nat Genet. 2021 May;53(5):618-629. doi: 10.1038/s41588-021-00841-y

“We find two chromosome-scale patterns of GC content fluctuations: (1) GC content increases towards the ends of the chromosomes and (2) GC content dips to form small local minima at Hi-C domain boundaries.” “most domain boundaries observed by Hi-C are located at positions where transcription of blocks of unidirectional genes converges.” “chromatin conformation is sensitive to treatment of cells with triptolide and DRB.”

Mudd AB, Bredeson JV, Baum R, Hockemeyer D, Rokhsar DS

Commun Biol. 2020 Sep 1;3(1):480. doi:10.1038/s42003-020-1096-9

Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution.

“Comparative Hi-C analysis showed that the chromosome fusions on the M. muntjak lineage altered long-range, three-dimensional chromosome organization relative to M. reevesi in interphase nuclei including A/B compartment structure. This reshaping of multi-megabase contacts occurred without notable change in local chromatin compaction, even near fusion sites.”

“During the ~4.9 million years since the divergence of M. muntjak and M. reevesi, the M. muntjak lineage experienced 26 fusions for a rate of ~5.3 changes per million years.” “M. muntjak and M. reevesi [...] genomes are locally very similar, with 98.5% identity in aligned regions and a nucleotide divergence of 0.0130 substitutions per site, based on fourfold degenerate positions.” “The pairwise alignment of the muntjac genomes contains 2.45 Gb of contig sequence [...] average sequence identity of 98.5%, excluding indels [...] In comparison, alignments of red deer, reindeer, and muntjacs to B. taurus contain 1.80–2.21 Gb of contig sequences with 92.7–93.2% average identity.” “The nucleotide and temporal divergence between the two muntjac species is comparable to the divergence between humans and chimpanzees. The observed chromosome dynamism in muntjacs, however, far exceeds the rate in the chimpanzee and human lineages” “we noted the maintenance of distinct Hi-C boundaries in several examples, such as the junction between the X and autosomal segments on MMU3_X circa 133 Mb. Other fusion sites, however, show no notable difference compared with the rest of the genome in M. muntjak. As expected, M. reevesi shows a clear distinction between intra- and inter-chromosome contacts, including across fusion sites in M. muntjak.”

Postma ED, Dashko S, van Breemen L, Taylor Parkins SK, van den Broek M, Daran JM, Daran-Lapujade P.

Nucleic Acids Res. 2021 Feb 22;49(3):1769-1783. doi:10.1093/nar/gkaa1167

A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae.

Circular neochromosome assembled in vivo by homologous recombination of fragments containing short homology regions (60 bp). Includes “a centromere and autonomously replicating sequences (ARS) spaced every 30–40 kb, and markers to facilitate [...] selection”. Used as “landing pads” for integration of ~30kb-scale fragments, using CRISPR/Cas9 to cleave the integration site. The neochromosomes can contain entire metabolic pathways, either endogenous (after knocking-out the endogenous copies) or exogenous.

Cechova M, Vegesna R, Tomaszkiewicz M, Harris RS, Chen D, Rangavittal S, Medvedev P, Makova KD.

Proc Natl Acad Sci U S A. 2020 Oct 20;117(42):26273-26280. doi:10.1073/pnas.2001749117

Dynamic evolution of great ape Y chromosomes.

“Unexpectedly, the rates of gene death were similar between ampliconic and X-degenerate genes.”

Mitter M, Gasser C, Takacs Z, Langer CCH, Tang W, Jessberger G, Beales CT, Neuner E, Ameres SL, Peters JM, Goloborodko A, Micura R, Gerlich DW.

Nature. 2020 Oct;586(7827):139-144. doi:10.1038/s41586-020-2744-4

Conformation of sister chromatids in the replicated human genome.

Sister-chromatid-sensitive Hi-C (scsHi-C) “4-thio-thymidine (4sT) converted into 5mC by OsO4/NH4Cl” “A read was assigned to the Watson strand if it contained two or more A-to-G mutations and no T-to-C mutations. Similarly, if a read contained two or more T-to-C mutations, but no A-to-G mutations it was assigned to the Crick strand. Then, contacts were classified as cis sister contacts if (after correcting for the opposite read-strandedness of Illumina sequencing of the two mates) both mates mapped to the same strand. Conversely, contacts were classified as trans sister contacts if the two mates mapped to opposing strands.”“Highly paired TADs were markedly enriched in trimethylation of lysine 27 of histone 3 (H3K27me3).” “Trans sister contacts were particularly enriched at many TAD boundaries.“ The cohesin loading factor NIPBL was homozygously tagged with auxin-inducible degrons to deplete loop-forming cohesin. “Loop-forming cohesin is necessary to separate sister chromatids within TADs, resulting in locally enriched sister-chromatid contacts at TAD boundaries.” Sororin was homozygously tagged with AID to deplete the pool of cohesin that mediates sister-chromatid cohesion. “The sororin-stabilized pool of cohesin is [...] not required to form intra-chromatid loops or TADs in G2, but it is required to prevent the separation of sister chromatids and to maintain their global alignment during the G2 phase.”

Rafati N, Chen J, Herpin A, Pettersson ME, Han F, Feng C, Wallerman O, Rubin CJ, Péron S, Cocco A, Larsson M, Trötschel C, Poetsch A, Korsching K, Bönigk W, Körschen HG, Berg F, Folkvord A, Kaupp UB, Schartl M, Andersson L.

Proc Natl Acad Sci U S A. 2020 Sep 16:202009925. doi:10.1073/pnas.2009925117

Reconstruction of the birth of a male sex chromosome present in Atlantic herring.

A ~500-kbp region on Chr8 is sex-associated, and within it, two ~100 kbp windows are only found in males in a single copy. Thus the Chr8 is an X/Y pair. The Y chromosome does not lack genes present on the X chromosome. It is estimated that it evolved prior the divergence of the Atlantic and Pacific species 2 My ago.

Ranz JM, Casals F, Ruiz A.

Genome Res. 2001 Feb;11(2):230-9. doi:10.1101/gr.162901

How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila.

186 DNA probes on Muller element E (density: 1 / 175 kbp in D. mel and 1 / 219 in D. rep) for comparing gene order in D. repleta and D. melanogaster. Random distribution of breakpoints. “177.07 (±28.88) breakpoints or 89 (±14) paracentric inversions fixed in this chromosomal element between D. melanogaster and D. repleta.” “Application of [a] ML method [...] yielded an estimate of 228 (±28) fixed breakpoints, that is, 114 ± 14 fixed inversions.” “We estimate an evolution rate of 0.9–1.4 chromosomal inversions fixed per million years.” “A significant correlation of gene order was found.” “If large inversions have a low probability of fixation because of their fertility effects (Navarro et al. 1997), which seems to be the case (Cáceres et al. 1997), then the randomization of gene order would proceed at a slower rate than is implied in Figure 2.”

Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS.

Nat Ecol Evol. 2020 Jun;4(6):820-830. doi:10.1038/s41559-020-1156-z

Deeply conserved synteny resolves early events in vertebrate evolution.

Most of the 19 amphioxus (lancelet) chromosomes directly correspond to one of the 17 ancestral chordate linkage groups. Pattern of paralogue elimination show that autotetraploidy was followed by allotetraploidy in bony vertebrates. Vertebrate and amphioxus mini-chromosomes descend from the ancestral linkage groups too.

Peichel CL, McCann SR, Ross JA, Naftaly AFS, Urton JR, Cech JN, Grimwood J, Schmutz J, Myers RM, Kingsley DM, White MA.

Genome Biol. 2020 Jul 19;21(1):177. doi:10.1186/s13059-020-02097-x

Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution.

“debris” fragments wrongly identified by 3D-DNA were added back to the assembly. Centromere of chrY different from the one of chrX.

Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Lindsay TAG, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM.

Nature. 2020 Jul 14. doi: 10.1038/s41586-020-2547-7.

Telomere-to-telomere assembly of a complete human X chromosome.

The Hi-C contact map of the human X chromosome shows that its long arm is divided in two large areas that have reduced interactions with each other.

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.”

Bracewell R, Tran A, Chatla K, Bachtrog D.

G3 (Bethesda). 2020 Mar 5;10(3):891-897. doi:10.1534/g3.119.400922

Chromosome-Level Assembly of Drosophila bifasciata Reveals Important Karyotypic Transition of the X Chromosome.

Chromosome arms do not interact much with each other. Large and highly repetitive pericentric regions in which it is hard to map the Hi-C reads.

Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS.

Nature. 2008 Jun 19;453(7198):1064-71. doi:10.1038/nature06967

The amphioxus genome and the evolution of the chordate karyotype.

17 ancestral chordate chromosomes.

“We estimate that the haploid amphioxus genome contains 21,900 protein-coding loci. [...] The observed heterozygosity shows correlations at short distances that decay on scales greater than ∼1 kb, indicating extensive recombination in the population. [...] Wwe reconstructed the gene complements of 17 linkage groups (that is, proto-chromosomes) of the last common chordate ancestor. [...] This analysis shows that most of the human genome (112 segments spanning 2.68 Gb, or 95% of the euchromatic genome) was affected by large-scale duplication events on the vertebrate stem before the bony vertebrate radiation (that is, the teleost/tetrapod split), and that nearly all of the ancient chordate chromosomes were quadruplicated. [...] Allowing for a range of nearly parsimonious reconstructions of 2R, we estimate that the bony vertebrate ancestor had between 37 and 49 chromosomes.”

Berthelot C, Muffato M, Abecassis J, Roest Crollius H.

Cell Rep. 2015 Mar 24;10(11):1913-24. doi: 10.1016/j.celrep.2015.02.046

The 3D organization of chromatin explains evolutionary fragile genomic regions.

Explains the power law distribution of breakpoints in mammals and yeast with chromosome contacts (Hi-C) and open chromatin (ENCODE).

“We [...] reconstruct the ancestral gene order in the 95-million-year-old ancestral genome of Boreoeutheria, the last common ancestor of primates, rodents, and laurasiatherians. [...] This reconstructed genome was further annotated with respect to its intergenic regions [...] their lengths, GC content and their proportion of conserved non-coding sequence as defined by GERP. [...] We then identified evolutionary rearrangement breakpoints that have occurred in the human, mouse, dog, cow, and horse lineages. [...] We identified a total of 751 breakpoints, 20 of which correspond to independent breakpoint reuse. [...] The identified breakpoints show the typical characteristics of rearrangement breakpoints; i.e., they occur in GC-rich, gene-dense regions possessing lower proportions of conserved non-coding sequence. [...] Breakpoint events per intergene increase as a power law of intergene length rather than a proportionality law. [...] Ancestral intergenes with high CNE content have been disrupted by significantly fewer breakpoints than intergenes of similar length with lower CNE content. [...] Rpeated elements and recombination frequencies are distributed radically differently from breakpoints, eliminating them as potential candidates to explain the breakpoint pattern. [...] The density of open chromatin is similar to the pattern of breakpoints with the proportion of DNA in an open state decreasing as intergene size increases. [...] Simulating inversions in the human genome according to contact probability [...] rearrangements were allowed to occur only between open chromatin regions, using chromatin state profiles for different cell types published by the ENCODE consortium. Under this model, the simulated average number of breakpoints per intergene closely reproduces the relationship with intergene length observed in real data.”

Sacerdot C, Louis A, Bon C, Berthelot C, Roest Crollius H.

Genome Biol. 2018 Oct 17;19(1):166. doi:10.1186/s13059-018-1559-1

Chromosome evolution at the origin of the ancestral vertebrate genome.

“The pre-1R karyotype comprised 17 chromosomes, duplicated into 34 chromosomes after the first WGD and followed by seven fusions. The resulting 27 chromosomes were duplicated in the second WGD leading to 54 Vertebrata chromosomes, at the origin of the approximately 60,000 extant species of vertebrates.” “The 54 chromosomes in the post-2R Vertebrata led to a Euteleostomi karyotype of 50 chromosomes (4 fusions) and to an Amniota karyotype of 49 chromosomes.” “The structure of the 17 pre-1R chromosomes is still strikingly apparent in the human genome, with some chromosomes almost entirely composed of genes from a single pre-1R chromosome (e.g., chromosomes 14 and 15).“ “We note that although all chromosome tetrads corresponding to pre-1R chromosomes are complete (i.e., are composed of 4 CARs), the 49 reconstructed Amniota chromosomes display large differences in gene numbers: the largest contains 862 genes (chromosome 37) and the smallest only 16 genes (chromosome 49). This could reflect either a more intense process of gene inactivation and loss on chromosomes with fewer genes, or a more intense rate of rearrangement on those chromosomes, leading to greater difficulties in reconstructing them.“

Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL.

Science. 2017 Apr 7;356(6333):92-95. doi:10.1126/science.aal3327

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.

Hi-C contacts between telomeres and between centromeres. Few contacts between arms of the same chromosome.

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 ?

Meisel RP, Delclos PJ, Wexler JR.

BMC Biol. 2019 Dec 5;17(1):100. doi:10.1186/s12915-019-0721-x

The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence.

“We provide two lines of evidence that the X chromosome of the German cockroach, B. germanica, is homologous to Muller element F, which is X-linked in most flies. First, there is a reduced sequencing coverage of nearly half of the Muller element F homologs in male cockroach, consistent with a haploid dose of the X chromosome in males (Fig. 2). Second, there is a decreased heterozygosity of element F homologs in male cockroach, including those with reduced male sequencing coverage (Fig. 3). We therefore hypothesize that element F is an ancient X chromosome that was present in the most recent common ancestor (MRCA) of flies and cockroaches, and it has been conserved as an X chromosome in the German cockroach and many fly species.”

Sankaranarayanan SR, Ianiri G, Coelho MA, Reza MH, Thimmappa BC, Ganguly P, Vadnala RN, Sun S, Siddharthan R, Tellgren-Roth C, Dawson TL Jnr, Heitman J, Sanyal K.

Elife. 2020 Jan 20;9. pii: e53944. doi: 10.7554/eLife.53944 doi:10.7554/eLife.53944

Loss of centromere function drives karyotype evolution in closely related Malassezia species.

Hypothetises that AT-richness at centromeres can trigger breaks, and structural changes. Centromeres detected by ChIP-seq on GFP-Mtw1 in M. sympodialis. ”PhyloGibbs-MP predicted a 12 bp long AT-rich 239 motif common to all of the centromere sequences.” “In each chromosome, the centromere region shows between 7 and 13 motif matches, while no other 500 bp window shows more than 3 matches.” “In the absence of any centromere exclusive DNA sequence, the unique and distinguishing features of centromere regions in M. sympodialis are an AT-rich core region of <1 kb [...] enriched with the 12 bp motif in a kinetochore protein-bound region of 3 to 5 kb [containing] a reduced level of histone H3.” “Syntenic regions of all 8 M. sympodialis centromeres are present in the genomes of M. globosa and M. slooffiae [(each carries 9 chromosomes)].” “In the case of M. restricta, 7 putative centromeres are completely syntenic with M. sympodialis centromeres and one centromere retained partial gene synteny.” “No gene synteny conservation was observed at the centromeres of Chr2 in M. globosa, Chr5 in M. slooffiae, or Chr8 in M. restricta, indicative of loss of a centromere during the transition from the 9-chromosome state to the 8-302 chromosome state.”

Zoolog Sci. 2005 May;22(5):511-6 doi:10.2108/zsj.22.511

Shoguchi E, Kawashima T, Nishida-Umehara C, Matsuda Y, Satoh N.

Molecular cytogenetic characterization of Ciona intestinalis chromosomes.

Ciona intestinalis has 10 metacentric pairs and 8 submetacentric or subtelomeric pairs of chromosomes.

Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM; NISC Comparative Sequencing Program, Mullikin JC, Burgess SM.

Sci Adv. 2019 Jun 26;5(6):eaav0547. doi:10.1126/sciadv.aav0547

De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.

Genomes and transcriptomes from the goldfish. Because of whole-genome duplication (WGD), “fifty-eight percent of the BUSCO genes could be found in two complete copies”. Speciation time ~11 Ma ago and WGD time ~14.4 Ma ago. Subgenomes were well conserved: “No large interchromosomal translocations were found between the 25 zebrafish chromosomes and the 50 goldfish LGs”. However, some large intrachromosomal variations were found. Cross-study with the common carp (which last common ancestor with goldfish was after the WGD, and the grass carp (pre-WGD) showed that gene “expression distance increased as the sequence identity decreased” and that “the loss of CNEs reduced the expression variance among different tissues (dynamic range) rather than affected the expression divergence between ohnolog gene pairs, i.e., CNE loss reduced tissue-specific expression variation”.

Nature. 2012 Apr 11;485(7398):376-80. doi:10.1038/nature11082

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B.

Topological domains in mammalian genomes identified by analysis of chromatin interactions.

A directionality index (DI), to detect topolgically associated domains, is described in the supplemental material. Bin size: 40 kbp, max distance: 2 Mbp.

Kuang YY, Zheng XH, Li CY, Li XM, Cao DC, Tong GX, Lv WH, Xu W, Zhou Y, Zhang XF, Sun ZP, Mahboob S, Al-Ghanim KA, Li JT, Sun XW.

Sci Rep. 2016 Oct 6;6:34849. doi:10.1038/srep34849

The genetic map of goldfish (Carassius auratus) provided insights to the divergent genome evolutions in the Cyprinidae family.

Linkage groups infered from RNA-seq data of 2 parents and > 70 offsprings.

Fradin H, Kiontke K, Zegar C, Gutwein M, Lucas J, Kovtun M, Corcoran DL, Baugh LR, Fitch DHA, Piano F, Gunsalus KC.

Curr Biol. 2017 Oct 9;27(19):2928-2939.e6. doi:10.1016/j.cub.2017.08.038

Genome Architecture and Evolution of a Unichromosomal Asexual Nematode.

“By comparing divergence rates with those of Caenorhabditis, we estimate that the asexual clade originated ca. 18 mya”. “We obtained a genome assembly of 158 Mb with an N50 of 124 kb”. “the haploid size [...] is ~88 Mb”. “~4% average difference between [heterozygous] alleles.” “Genomic regions in D. pachys have generally maintained the same chro- mosomal identity since diverging from Caenorhabditis”. “ we used macro- synteny with C. elegans to infer an ancestral chromosome iden- tity (ACD) for each D. pachys scaffold.” “We identified specific patterns of rearrangements consistent with an order of ACD fusions.” “The data [of reciprocal reaggangements between ACDs] thus allow us to propose that four ancestral chromosomes became fused in the order I-X-III-II” “Telomeres are either absent from the D. pachys genome or are highly divergent from the ancestral telomeric sequence.” “The combined absence of telomere sequences and mainte- nance proteins suggests a connection between chromosome fusion and loss of telomeres”. “84% of homozygous regions localize to ACDs I and X, which are neighbors in the inferred chromosomal fusion”. ”The reductional division during meiosis I is skipped; the two chromosomes condense but do not pair or synapse.” “The phenotype of C. elegans rec-8 mutants is reminiscent of the modified meiosis in D. pachys. [...] rec-8 is one of the conserved meiosis genes that was not detected in the D. pachys and D. coronatus genomes”

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

Nat Genet. 2014 Jul;46(7):693-700. doi:10.1038/ng.3010

Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, Holroyd N, Cotton JA, Stanley EJ, Zarowiecki M, Liu JZ, Huckvale T, Cooper PJ, Grencis RK, Berriman M.

Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.

Clustering scaffolds on the number of shared orthologs they have with scaffolds of a related species' genome identifies three chromosomes.

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.

Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G.

Cell. 2012 Feb 3;148(3):458-72. doi:10.1016/j.cell.2012.01.010

Three-dimensional folding and functional organization principles of the Drosophila genome.

Co-clustering of the centromeres.

Stadler MR, Haines JE, Eisen MB.

Elife. 2017 Nov 17;6. pii: e29550. doi:10.7554/eLife.29550

Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo.

High-resolution Hi-C analysis of Drosophila chromosomes in Rabl conformation during embryogenesis. “We propose a model in which insulators achieve domain separation by lowering the compaction ratio of bound chromatin, thereby converting the short lengths of insulator DNA (measured in base pairs) into large relative physical distances.”

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.

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Nature. 2014 Sep 11;513(7517):195-201. doi:10.1038/nature13679

Gibbon genome and the fast karyotype evolution of small apes.

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Renschler G, Richard G, Valsecchi CIK, Toscano S, Arrigoni L, Ramírez F, Akhtar A.

Genes Dev. 2019 Oct 10. doi: 10.1101/gad.328971.119

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling.

Found 20 synteny breakpoints (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B compartment” “Overlaps of TAD boundaries and SB breakpoints in all comparisons are highly significant”

“Hi-C data of D. melanogaster, D. virilis, and D. busckii embryos”

“D. virilis and D. busckii [...] cover ∼40 million years of evolution and multiple subgenera (Russo et al. 2013).”

“conserved sequences mostly reside on the same chromosomal arms”

“we defined synteny blocks (SBs), which are chains of conserved collinear regions that are used to identify and compare homologous regions between different species. On average, we find 20 synteny breakpoints per megabase (3726 and 3252 breakpoints in the D. melanogaster vs. D. virilis comparison, respectively, and 3340 and 2776 breakpoints in the D. melanogaster vs. D. busckii comparison, respectively), corresponding to about one breakpoint every six genes.”

“Approximately 75% of SBs stay within the A or B compartment and 25% switch between compartments. In general, about double the number of SBs lie within the A compartment than the B compartment.”

“many SB breakpoints overlap with TAD boundaries”

“To identify synteny blocks (SBs) we use LASTZ (Harris 2007) with the following parameters: “–gfextend –nochain –gapped,” which identifies local alignment blocks. We then chained blocks that are within 10-kb distance, have the same orientation, and contain at least four LASTZ-defined blocks. Chained results that were <4 kb or completely overlapped a bigger synteny block were removed.”

Science. 2017 Mar 10;355(6329). pii: eaaf4791. doi:10.1126/science.aaf4791

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.

Repaired structural variants by engeneering duplications and forcing their resolution by I-SceI cleavage.

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.”

Zoolog Sci. 2004 Feb;21(2):153-7 doi:10.2108/zsj.21.153

Shoguchi E1, Ikuta T, Yoshizaki F, Satou Y, Satoh N, Asano K, Saiga H, Nishikata T.

Fluorescent in situ hybridization to ascidian chromosomes.

“Embryos at three different developmental stages (32-cell embryos, 64-cell embryos and gastrulae) were used to produce metaphase spreads, although treatment of 32-cell embryos and 64-cell embryos with 0.05% colchicine (Sigma) in seawater caused aggregated and disorganized chromosomes. After treatment with colchicine for 20–30 min, embryos were transferred to a 1.5-ml microfuge tube, to which cold methanol:glacial acetic acid (3:1) fixative was added (chilled on ice). The fixative was changed twice over a period of 1 hr and once after overnight (embryos kept at 4°C). The specimens were then stored in fixative at 4°C.”

Genome Res. 2006 Feb;16(2):297-303 doi:10.1101/gr.4156606

Shoguchi E, Kawashima T, Satou Y, Hamaguchi M, Sin-I T, Kohara Y, Putnam N, Rokhsar DS, Satoh N.

Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis.

The short arm of chromosome 4, 5 and 6 contains rDNA clusters.

Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM.

Nature. 2008 Jul 24;454(7203):479-85. doi:10.1038/nature07135

High-resolution mapping of meiotic crossovers and non-crossovers in yeast.

Spore tetrads genotypes on tiling arrays designed on their parental strains. 84% of hotspots overlap a promoter.

Bioinformatics. 2014 Jun 15;30(12):i302-9. doi:10.1093/bioinformatics/btu280

Kolmogorov M, Raney B, Paten B, Pham S.

Ragout-a reference-assisted assembly tool for bacterial genomes.

Can accept multiple reference genomes. Decomposes refernces and target in synteny blocks and assemble them in a graph.

Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S.

Genome Res. 2018 Nov;28(11):1720-1732. doi:10.1101/gr.236273.118

Chromosome assembly of large and complex genomes using multiple references.

Ragout 2 can take multiple reference genomes as input and automatically infers phylogenetic relationship between them. Polymorphisms unique to the target genome can be recovered, but chromosome fusions are typically hard to detect.

Science. 1970 Jun 12;168(3937):1364-6 doi:10.1126/science.168.3937.1364

Wurster DH, Benirschke K

Indian muntjac, Muntiacus muntjak: a deer with a low diploid chromosome number.

Males have 7 chromosomes and females have 6. The X chromosome is linked to an autosome by a thin neck, while the Y chromosome is free.

Genome Res. 2016 Mar;26(3):342-50. doi:10.1101/gr.193474.115

Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M, Calef R, Troll CJ, Fields A, Hartley PD, Sugnet CW, Haussler D, Rokhsar DS, Green RE.

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.

“Chicago”: in vitro assembly of artificial chromosomes, followed by Hi-C. Sold as a kit by Dovetail genomics.