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Research: Historical RNA expression profiles from the extinct Tasmanian tiger
- Emilio Mármol-Sánchez,
- Bastian Fromm,
- Nikolay Oskolkov,
- Zoé Pochon,
- Panagiotis Kalogeropoulos,
- Eli Eriksson,
- Inna Biryukova,
- Vaishnovi Sekar,
- Erik Ersmark,
- Björn Andersson,
- Love Dalén,
- and Marc R. Friedländer
Genome Res. August 2023 33: 1299-1316; Published in Advance July 18, 2023, doi:10.1101/gr.277663.123
...but substantial amounts of total RNA (Supplemental Table 1). Subsequently, the extracted and purified RNA fragments were prepared for high-throughput sequencing using a cDNA library protocol tailored for short RNA transcripts. The library size distribution indicated a successful extraction and library preparation...
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Method: Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens
- Victor C. Mason,
- Gang Li,
- Kristofer M. Helgen,
- and William J. Murphy
Genome Res. October 2011 21: 1695-1704; Published in Advance August 31, 2011, doi:10.1101/gr.120196.111
..., two reference colugo mtDNA s and six published partial mitochondrial rRNA sequences from individuals from Peninsular Malaysia (GVA 1–3) andWest Java (GVA 4–6) ( Janečka et al. 2008). Enforcing different read depth thresholds for inclusion of a site in the alignment (e.g., read depth 53–253) had...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...Mature miRNA 650 Population genomics of rhesus macaques Genome Research 1655 www..org but more similar between species than the counts of synonymous variants (7810.1 in rhesus versus 6551.7 in humans; t-test P = 7.66 × 10−47) (see also Yuan et al. 2012). Consequently, the ratio of nonsynonymous...
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Method: A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
- Marta Tomaszkiewicz,
- Samarth Rangavittal,
- Monika Cechova,
- Rebeca Campos Sanchez,
- Howard W. Fescemyer,
- Robert Harris,
- Danling Ye,
- Patricia C.M. O'Brien,
- Rayan Chikhi,
- Oliver A. Ryder,
- Malcolm A. Ferguson-Smith,
- Paul Medvedev,
- and Kateryna D. Makova
Genome Res. April 2016 26: 530-540; Published in Advance March 2, 2016, doi:10.1101/gr.199448.115
...lost, on the chimpanzee Y (Fig. 3; Hughes et al. 2010). We assembled the RNA-seq data from gorilla testis (Supplemental Table S9) and used various filtering strategies and additional gorilla and human data to reconstruct the gorilla Y-Chromosome genes (Methods; Supplemental File S1). This was performed...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
.... Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe...
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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
...is the only other primate curated to this degree of detail for chromosomal accuracy. To annotate the vervet for gene content, we utilized the collective methods deployed at NCBI (http://www.ncbi.nlm. nih.gov//annotation_euk/process/), taking as input RNA sequencing (RNA-seq) data from total RNA and small RNA...
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Perspective: Reading TE leaves: New approaches to the identification of transposable element insertions
- David A. Ray and
- Mark A. Batzer
Genome Res. June 2011 21: 813-820; doi:10.1101/gr.110528.110
...et al. 2000). If the transduced sequence contains an exon, it may be inserted near existing exons, resulting in an exon shuffling event. Assuming RNA pol II transcription and normal post-transcriptional processing, two ormore exons in the transduced sequencemay bemerged and reinserted, resulting...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...region indicated with dashed rectangles in the upper plot. MHC-I, MHC-II and APG are marked and labeled individually, with the width of rectangles corresponding to gene lengths. Maximum relative expression: the maximum fraction of total MHC-I expression (FPKM) attributable to a sequence across all RNA...
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LETTER: Comparative Analysis of Gene-Expression Patterns in Human and African Great Ape Cultured Fibroblasts
- Mazen W. Karaman,
- Marlys L. Houck,
- Leona G. Chemnick,
- Shailender Nagpal,
- Daniel Chawannakul,
- Dominick Sudano,
- Brian L. Pike,
- Vincent V. Ho,
- Oliver A. Ryder,
- and Joseph G. Hacia
Genome Res. July 2003 13: 1619-1630; doi:10.1101/gr.1289803
...blot analysis ( LAMP1, AKAP2 , and SPTLC1 ) ( Fig. 2C ; Suppl. Fig. 1) were caused by sequence differences between African great ape transcripts and the probes in the microarray (Suppl. Table 1). This is not unexpected, as mismatches between African great ape RNA samples and oligonucleotide probes...
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PERSPECTIVE: Comparing the human and chimpanzee genomes: Searching for needles in a haystack
- Ajit Varki and
- Tasha K. Altheide
Genome Res. December 2005 15: 1746-1758; doi:10.1101/gr.3737405
..., there are several caveats. For example, microarrays based on human oligonucleotide sequences may not accurately detect levels of expression in nonhuman primates nor detect significant alternative splicing of mRNAs ( Modrek and Lee 2002 ; Hsieh et al. 2003 ; Preuss et al. 2004 ; Steinmetz and Davis 2004...

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