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Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
- Dongying Xie,
- Pohao Ye,
- Yiming Ma,
- and Zhongying Zhao
Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
...and categorizes both large-scale SVs and small-scale sequence variations based on pairwise alignments. Genomic regions that cannot be properly aligned in a one-to-one correspondence within the existing high-quality (excluding cases in which absence of alignments arise from incomplete assembly) are classified...
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Resource: RNA-seq analysis of the C. briggsae transcriptome
- Bora Uyar,
- Jeffrey S.C. Chu,
- Ismael A. Vergara,
- Shu Yi Chua,
- Martin R. Jones,
- Tammy Wong,
- David L. Baillie,
- and Nansheng Chen
Genome Res. August 2012 22: 1567-1580; Published in Advance July 6, 2012, doi:10.1101/gr.134601.111
...subsequent analyses such as ortholog assignment, cis -regulatory element finding, and synteny detection. In this project, we have reannotated the genome of Caenorhabditis briggsae , the best studied sister species of the model organism Caenorhabditis elegans . First, we applied a homology-based gene...
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METHODS: LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
- Michael Brudno,
- Chuong B. Do,
- Gregory M. Cooper,
- Michael F. Kim,
- Eugene Davydov,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- Arend Sidow,
- and Serafim Batzoglou
Genome Res. April 1, 2003 13: 721-731; Published in Advance March 12, 2003, doi:10.1101/gr.926603
...LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA Michael Brudno 1 , Chuong B. Do 1 , Gregory M. Cooper 2 , Michael F. Kim 1 , Eugene Davydov 1 , NISC Comparative Sequencing Program 1...
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LETTER: Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
- Scott William Roy and
- David Penny
Genome Res. October 2006 16: 1270-1275; Published in Advance September 8, 2006, doi:10.1101/gr.5410606
...: a sexually-transmitted nuclear parasite. Genetics 101 : 519 – 531 . ↵ Jeffares, D.C. , Mourier, T. , Penny, D. ( 2006 ) The biology of intron gain and loss . Trends Genet. 22 : 16 – 22 . ↵ Kent, W.J. , Zahler, A.M. ( 2000 ) Conservation, regulation, synteny, and introns in a large-scale C. briggsae...
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Methods: Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
- Aaron C.E. Darling,
- Bob Mau,
- Frederick R. Blattner,
- and Nicole T. Perna
Genome Res. July 2004 14: 1394-1403; doi:10.1101/gr.2289704
...Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements Aaron C.E. Darling 1 , 2 , 6 , Bob Mau 2 , 3 , Frederick R. Blattner 4 , 5 , and Nicole T. Perna 2 , 5 1 Department of Computer Science, University...
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Research: Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints
- Manuel Irimia,
- Juan J. Tena,
- Maria S. Alexis,
- Ana Fernandez-Miñan,
- Ignacio Maeso,
- Ozren Bogdanović,
- Elisa de la Calle-Mustienes,
- Scott W. Roy,
- José L. Gómez-Skarmeta,
- and Hunter B. Fraser
Genome Res. December 2012 22: 2356-2367; Published in Advance June 21, 2012, doi:10.1101/gr.139725.112
...= 100), and ZMYM3-NONO (r = 0.83, rank = 100). Genomic regulatory blocks (GRBs) Another major cause of conserved gene linkage may be preservation of GRBs. The typical GRB comprises a trans-dev gene and one or more functionally unrelated bystander genes, whose introns harbor cis-regulatory sequences...
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Methods: Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
- Steven G. Kuntz,
- Erich M. Schwarz,
- John A. DeModena,
- Tristan De Buysscher,
- Diane Trout,
- Hiroaki Shizuya,
- Paul W. Sternberg,
- and Barbara J. Wold
Genome Res. December 2008 18: 1955-1968; Published in Advance November 3, 2008, doi:10.1101/gr.085472.108
...-way comparison of ceh-13/lin-39 sequences from C. elegans , C. briggsae , and C. brenneri with 30-bp windows identified several conserved regions ( Fig. 2A ). In C. elegans , the ceh-13/lin-39 locus includes 19 kb of intergenic sequence and 8 kb of intronic sequence, of which only ∼2% was highlighted in MUSSA...
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Resource: Adaptive seeds tame genomic sequence comparison
- Szymon M. Kiełbasa,
- Raymond Wan,
- Kengo Sato,
- Paul Horton,
- and Martin C. Frith
Genome Res. March 2011 21: 487-493; Published in Advance January 5, 2011, doi:10.1101/gr.113985.110
...: 656– 664. Kent WJ, Zahler AM. 2000. Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment.Genome Res 10: 1115–1125. Kucherov G, Noe´ L, Roytberg M. 2006. A unifying framework for seed sensitivity and its application to subset seeds. J Bioinform Comput...
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ARTICLE: A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution
- Soochin Cho,
- Suk-Won Jin,
- Adam Cohen,
- and Ronald E. Ellis
Genome Res. July 2004 14: 1207-1220; doi:10.1101/gr.2639304
.... elegans ( Fig 6E , bottom). Our alignment implies that the C. briggsae intron was inserted into this sequence along with additional nucleotides that caused a shift in the reading frame. Because fog-1 intron 10 was created after the split between C. briggsae and C. sp. CB5161 , it cannot be related to fog...
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Methods: Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics
- Yueyi Liu,
- X. Shirley Liu,
- Liping Wei,
- Russ B. Altman,
- and Serafim Batzoglou
Genome Res. March 2004 14: 451-458; doi:10.1101/gr.1327604
...-like alignment tool. Genome Res. 12 : 656 –664. ↵ Kent, W.J. and Zahler, A.M. 2000 . Conservation, regulation, synteny, and introns in a large-scale C. briggsae – C. elegans genomic alignment. Genome Res. 10 : 1115 –1125. ↵ Liu, J.S., Neuwald, A.F., and Lawrence, C.E. 1995 . Bayesian Models for multiple local...

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