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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...) and micro (lighter color) chromosomes. (Cii) Enlarged view of the inter-/intrachromosomal interactions analyzed for birds and turtles (demarcated by the dashed line in Ci). (D) Chromosome-specific contact probability P(s) as a function of genomic distance in all species analyzed.Our multispecies analysis...
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Research: Limited allele-specific gene expression in highly polyploid sugarcane
- Gabriel Rodrigues Alves Margarido,
- Fernando Henrique Correr,
- Agnelo Furtado,
- Frederik C. Botha,
- and Robert James Henry
Genome Res. February 2022 32: 297-308; Published in Advance December 23, 2021, doi:10.1101/gr.275904.121
...with the standard TruSeq RNA protocol, and the cDNA was sequenced (in pools with additional indexed libraries) on the Illumina NovaSeq 6000. Samples were split into four lanes of one S4 flowcell, with a data volume corresponding to 90 samples per lane. With this multiplexing strategy, the expected yield was of more...
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Research: Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish
- Amaury Herpin,
- Manfred Schartl,
- Alexandra Depincé,
- Yann Guiguen,
- Julien Bobe,
- Aurélie Hua-Van,
- Edward S. Hayman,
- Anna Octavera,
- Goro Yoshizaki,
- Krista M. Nichols,
- Giles W. Goetz,
- and J. Adam Luckenbach
Genome Res. August 2021 31: 1366-1380; Published in Advance June 28, 2021, doi:10.1101/gr.274266.120
...(H), ovary (O), testis (T), muscle (M), kidney (K), spleen (S), liver (L), intestine (I), and stomach (St). Transcript levels of eef1a1l1 were assessed to verify quality and loading of cDNAs. (B) Ontogenetic gene expression profiles of gsdfX and gsdfY sex-specific allelic variants during early...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...) inclusion of seven full-length stranded cDNA libraries derived from three time points (0 h, 24 h, and 48 h post infection) (Tandel et al. 2019), covering ∼90% of the protein-coding genes in C. parvum; and (2) by using synteny information to construct a consistent annotation between three different closely...
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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...) and L9 (generation F7). All PCR products were confirmed by Sanger sequencing. Genomic DNA (G) and cDNA (H) were used as templates. Amplicons from the locus encoding the elongation factor EF1ALPHA was used as a loading control.We finally investigated whether these chimeric genes were transcribed. A first...
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Resource: The genome of the vervet (Chlorocebus aethiops sabaeus)
- Wesley C. Warren,
- Anna J. Jasinska,
- Raquel García-Pérez,
- Hannes Svardal,
- Chad Tomlinson,
- Mariano Rocchi,
- Nicoletta Archidiacono,
- Oronzo Capozzi,
- Patrick Minx,
- Michael J. Montague,
- Kim Kyung,
- LaDeana W. Hillier,
- Milinn Kremitzki,
- Tina Graves,
- Colby Chiang,
- Jennifer Hughes,
- Nam Tran,
- Yu Huang,
- Vasily Ramensky,
- Oi-wa Choi,
- Yoon J. Jung,
- Christopher A. Schmitt,
- Nikoleta Juretic,
- Jessica Wasserscheid,
- Trudy R. Turner,
- Roger W. Wiseman,
- Jennifer J. Tuscher,
- Julie A. Karl,
- Jörn E. Schmitz,
- Roland Zahn,
- David H. O'Connor,
- Eugene Redmond,
- Alex Nisbett,
- Béatrice Jacquelin,
- Michaela C. Müller-Trutwin,
- Jason M. Brenchley,
- Michel Dione,
- Martin Antonio,
- Gary P. Schroth,
- Jay R. Kaplan,
- Matthew J. Jorgensen,
- Gregg W.C. Thomas,
- Matthew W. Hahn,
- Brian J. Raney,
- Bronwen Aken,
- Rishi Nag,
- Juergen Schmitz,
- Gennady Churakov,
- Angela Noll,
- Roscoe Stanyon,
- David Webb,
- Francoise Thibaud-Nissen,
- Magnus Nordborg,
- Tomas Marques-Bonet,
- Ken Dewar,
- George M. Weinstock,
- Richard K. Wilson,
- and Nelson B. Freimer
Genome Res. December 2015 25: 1921-1933; Published in Advance September 16, 2015, doi:10.1101/gr.192922.115
...cDNA libraries derived from a diverse set of tissue types, as well as human RefSeq and GenBank transcripts and primate proteins. The currently identified set of protein coding genes (21,128) and noncoding genes (8520) is comparable in number to that observed for other primate s (http...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...-seq libraries were generated with Illumina's TruSeq Ribo-Zero strand-specific kit and then sequenced on the Illumina HiSeq 2000 platform with 100-bp paired-end reads. The annotation of the Abp gene clusters was refined with a combination of BLAST (Altschul et al. 1990), hmmsearch (Finn et al. 2011...
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ARTICLE: 2006 expressed-sequence tags derived from human chromosome 7-enriched cDNA libraries.
- J W Touchman,
- G G Bouffard,
- L A Weintraub,
- J R Idol,
- L Wang,
- C M Robbins,
- J C Nussbaum,
- M Lovett,
- and E D Green
Genome Res. March 1997 7: 281-292; doi:10.1101/gr.7.3.281
....D. Gallardo, T.D. Clines, G.A. Ashley, J.A. Hilliard, C.J. Wasmuth, J.J. McPherson, J.D. and Lovett. M. 1995 . Human chromosome-specific cDNA libraries: new tools for gene identification and annotation. Genome Res. 5 : 185 – 194 . Dib, C., , Faure, S. , Fizames, C. , Samson, D. , Drouot, N. , Vignal, A...
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Chicken Special/Resources: Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
- Simon J. Hubbard,
- Darren V. Grafham,
- Kevin J. Beattie,
- Ian M. Overton,
- Stuart R. McLaren,
- Michael D.R. Croning,
- Paul E. Boardman,
- James K. Bonfield,
- Joan Burnside,
- Robert M. Davies,
- Elizabeth R. Farrell,
- Matthew D. Francis,
- Sam Griffiths-Jones,
- Sean J. Humphray,
- Christopher Hyland,
- Carol E. Scott,
- Haizhou Tang,
- Ruth G. Taylor,
- Cheryll Tickle,
- William R.A. Brown,
- Ewan Birney,
- Jane Rogers,
- and Stuart A. Wilson
Genome Res. January 2005 15: 174-183; Published in Advance December 8, 2004, doi:10.1101/gr.3011405
.... 2003 ). Full-length cDNA clones are both essential for gene identification and annotation of complex s and provide a valuable resource for experimentalists interested in gene function. Consequently, there has been a large effort to produce annotated EST and full-length cDNA collections for mammals...
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RESOURCE: A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates
- Annelie Everts-van der Wind,
- Srinivas R. Kata,
- Mark R. Band,
- Mark Rebeiz,
- Denis M. Larkin,
- Robin E. Everts,
- Cheryl A. Green,
- Lei Liu,
- Shreedhar Natarajan,
- Tom Goldammer,
- Jun Heon Lee,
- Stephanie McKay,
- James E. Womack,
- and Harris A. Lewin
Genome Res. July 2004 14: 1424-1437; doi:10.1101/gr.2554404
....L., and Lewin, H.A. 1998 . Comparative analysis of 82 expressed sequence tags from a cattle ovary cDNA library. Mamm. Genome 9 : 545 –549. ↵ Menotti-Raymond, M., David, V.A., Chen, Z.Q., Menotti, K.A., Sun, S., Schäffer, A.A., Agarwala, R., Tomlin, J.F., O'Brien, S.J., and Murphy, W.J. 2003 . Second...

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