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Method: Chromosome assembly of large and complex genomes using multiple references
- Mikhail Kolmogorov,
- Joel Armstrong,
- Brian J. Raney,
- Ian Streeter,
- Matthew Dunn,
- Fengtang Yang,
- Duncan Odom,
- Paul Flicek,
- Thomas M. Keane,
- David Thybert,
- Benedict Paten,
- and Son Pham
Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
...of multiple outgroup s in addition to a single reference. The investigators showed that consistent adjacency information across multiple outgroups is a more powerful predictor of adjacencies in the target assembly than single s alone. Similar to other rearrangement approaches, RACA relies on the decomposition...
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Resource: A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection
- Mats E. Pettersson,
- Christina M. Rochus,
- Fan Han,
- Junfeng Chen,
- Jason Hill,
- Ola Wallerman,
- Guangyi Fan,
- Xiaoning Hong,
- Qiwu Xu,
- He Zhang,
- Shanshan Liu,
- Xin Liu,
- Leanne Haggerty,
- Toby Hunt,
- Fergal J. Martin,
- Paul Flicek,
- Ignas Bunikis,
- Arild Folkvord,
- and Leif Andersson
Genome Res. November 2019 29: 1919-1928; Published in Advance October 24, 2019, doi:10.1101/gr.253435.119
...et al. 2016). The markers formed 26 linkage groups in perfect agreement with the assembly, and the linkage map confirmed the linear order of genomic segments along the chromosomes. The total length of the sex-average linkage map was 1660 cM, and the average recombination rate was 2.54 cM/Mb (Table 2...
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Method: Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data
- Wen-Biao Jiao,
- Gonzalo Garcia Accinelli,
- Benjamin Hartwig,
- Christiane Kiefer,
- David Baker,
- Edouard Severing,
- Eva-Maria Willing,
- Mathieu Piednoel,
- Stefan Woetzel,
- Eva Madrid-Herrero,
- Bruno Huettel,
- Ulrike Hümann,
- Richard Reinhard,
- Marcus A. Koch,
- Daniel Swan,
- Bernardo Clavijo,
- George Coupland,
- and Korbinian Schneeberger
Genome Res. May 2017 27: 778-786; Published in Advance February 3, 2017, doi:10.1101/gr.213652.116
...represent the ancestral karyotype of the Brassicaceae family (Schranz et al. 2006) and usually share at least some conserved centromereswith other Brassicaceae species. Thirdly, we analyzed the repeat and gene densities across each scaffold, as a typical Brassicaceae chromosome has low repeat and high gene...
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Research: Hominoid fission of chromosome 14/15 and the role of segmental duplications
- Giuliana Giannuzzi,
- Michele Pazienza,
- John Huddleston,
- Francesca Antonacci,
- Maika Malig,
- Laura Vives,
- Evan E. Eichler,
- and Mario Ventura
Genome Res. November 2013 23: 1763-1773; Published in Advance September 27, 2013, doi:10.1101/gr.156240.113
.../15 association and shows perfect marker order conservation with respect to the two human-derivative chromosomes (Ventura et al. 2003). To gain insights into the genomic organization of the hominoid fission region, we constructed a 1.6-Mb contig of 61 macaque BAC clones on MMU7 spanning the 14/15 Figure 1...
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Method: Efficient identification of Y chromosome sequences in the human and Drosophila genomes
- Antonio Bernardo Carvalho and
- Andrew G. Clark
Genome Res. November 2013 23: 1894-1907; Published in Advance August 6, 2013, doi:10.1101/gr.156034.113
...). This procedure assumes homogeneous gain and loss rates across the lineages. Efficient identification of Y chromosome sequences Genome Research 1901 www..org silkworm and rat) (Rat Genome Sequencing Project Consortium 2004; Xia et al. 2004). In these cases, the study of the Y (or W) chromosomes would require...
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LETTER: Evolutionarily Conserved Sequences on Human Chromosome 21
- Kelly A. Frazer,
- John B. Sheehan,
- Renee P. Stokowski,
- Xiyin Chen,
- Roya Hosseini,
- Jan-Fang Cheng,
- Stephen P.A. Fodor,
- David R. Cox,
- and Nila Patil
Genome Res. October 1, 2001 11: 1651-1659; doi:10.1101/gr.198201
.... ↵ Wiltshire T. , Pletcher M. , Cole S.E. , Villanueva M. , Birren B. , Lehoczky J. , Dewar K. , Reeves R.H. ( 1999 ) Perfect conserved linkage across the entire mouse chromosome 10 region homologous to human chromosome 21. Genome Res. 9 : 1214 – 1222 . ↵ Wynn S.L. , Fisher R.A. , Pagel C. , Price M. , Liu Q...
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Methods: Two-parameter characterization of chromosome-scale recombination rate
- Wentian Li and
- Jan Freudenberg
Genome Res. December 2009 19: 2300-2307; Published in Advance September 14, 2009, doi:10.1101/gr.092676.109
...are not perfect and, in particular for telomeres, missing some data. This can be seen for the chicken s, where the two chromosomes fall below the minimum genetic length of 50 cM in the older map and climb to ;50 cM in the newer map (Supplemental Fig. S4). Data selectively missing crossovers at the telomeres might...
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LETTER: Hemizygous subtelomeres of an African trypanosome chromosome may account for over 75% of chromosome length
- Sergio Callejas,
- Vanessa Leech,
- Christopher Reitter,
- and Sara Melville
Genome Res. September 2006 16: 1109-1118; Published in Advance August 9, 2006, doi:10.1101/gr.5147406
...-M. These microarray analyses suggested that copy number variation of perfect tandem repeats and of subtelomeric gene families are important sources of chromosome size polymorphism, but their contribution to the final length of much larger chr I homologs appeared relatively small. In Figure 6A we compare the maximum...
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REPORT: Chromosome Evolution: The Junction of Mammalian Chromosomes in the Formation of Mouse Chromosome 10
- Mathew T. Pletcher,
- Bruce A. Roe,
- Fang Chen,
- Trang Do,
- Ahn Do,
- Eda Malaj,
- and Roger H. Reeves
Genome Res. October 1, 2000 10: 1463-1467; doi:10.1101/gr.146600
.... , Birren B. , Lehoczky J. , Dewar K. , Reeves R.H. ( 1999 ) Perfect conserved linkage across the entire mouse chromosome 10 region homologous to human chromosome 21. Genome Res. 9 : 1214 – 1222 . ↵ Xu Y. , Mural R. , Shah M. , Uberbacher E. ( 1994 ) Recognizing exons in genomic sequence using GRAIL II...
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LETTER: Genome structure and emerging evidence of an incipient sex chromosome in Populus
- Tongming Yin,
- Stephen P. DiFazio,
- Lee E. Gunter,
- Xinye Zhang,
- Michell M. Sewell,
- Scott A. Woolbright,
- Gery J. Allan,
- Collin T. Kelleher,
- Carl J. Douglas,
- Mingxiu Wang,
- and Gerald A. Tuskan
Genome Res. March 2008 18: 422-430; Published in Advance February 6, 2008, doi:10.1101/gr.7076308
...in the peritelomeric region of chromosome XIX that suggest this region of the Populus is in the process of developing characteristics of a sex chromosome. We have identified a gender-associated locus that consistently maps to this region. Furthermore, comparison of genetic maps across multiple Populus families reveals...

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