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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...genes in which one haplotype exhibits complete coverage, whereas the other shows partial coverage. In contrast, fully identical homologous gene pairs—those with both identical lengths and amino acid sequences—accounted for only 6.5% (1027 pairs). These results suggest that there is a certain degree...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...coefficient. (C) Phylogenetic tree of representative Gypsy RT protein segments longer than 100 amino acids. Green circles highlight crown nodes of identified families with bootstrap support values of 75 or more. (D) Genomic occurrence of the four identified Gypsy clades in the T. panzhihuanense .On the 17...
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Method: Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics
- Alexey Vorobev,
- Marion Dupouy,
- Quentin Carradec,
- Tom O. Delmont,
- Anita Annamalé,
- Patrick Wincker,
- and Eric Pelletier
Genome Res. April 2020 30: 647-659; Published in Advance March 23, 2020, doi:10.1101/gr.253070.119
...at least 50 amino acids (Fig. 2).Segregation of the Bathycoccus ecotypesTo assess the potential of the MGT approach to segregate closely related biological entities, we focused on the MGTs highly similar to the reference transcriptomes of Bathycoccus prasinos. Bathycoccus is a genus of green algae from...
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Research: Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
- Isabela Gerdes Gyuricza,
- Joel M. Chick,
- Gregory R. Keele,
- Andrew G. Deighan,
- Steven C. Munger,
- Ron Korstanje,
- Steven P. Gygi,
- and Gary A. Churchill
Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
...filtering, the age-pQTL hotspot on Chromosome 3 includes 208 proteins, and the Chromosome 12 hotspot includes 194 proteins (Supplemental Fig. S9; Supplemental Data S12).View larger version: In this window In a new window Figure 5. Genetic mapping reveals genomic hotspots of age-interactive QTL. (A) Age...
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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
....93% average pairwise identity with the 2004 assembly in regions that are comparable (Supplemental Table S3). The main Cryptosporidium subtyping marker, the 60 kDa surface protein (gp60 locus subtype IIa), shows four amino acid differences (two in the serine repeat region) between CpIA and CpIRef (Supplemental...
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Method: Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants
- Dongqing Shi,
- Jun Wu,
- Haibao Tang,
- Hao Yin,
- Hongtao Wang,
- Ran Wang,
- Runze Wang,
- Ming Qian,
- Juyou Wu,
- Kaijie Qi,
- Zhihua Xie,
- Zhiwen Wang,
- Xiang Zhao,
- and Shaoling Zhang
Genome Res. November 2019 29: 1889-1899; Published in Advance October 24, 2019, doi:10.1101/gr.251033.119
...window Figure 3. Mosaic assembly of Pbr017687.1 in the reference . Four base pairs in yellow only matched haplotype A, and 4 bp in red only matched haplotype B. Five of these eight sequences result in differences in amino acid sequence. (N) Redundant sequences in the reference.Mutations caused...
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LETTER: Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network
- Jochen Förster,
- Iman Famili,
- Patrick Fu,
- Bernhard Ø. Palsson,
- and Jens Nielsen
Genome Res. February 1, 2003 13: 244-253; doi:10.1101/gr.234503
...for biomass precursor and amino acid production by the network were evaluated. During the reconstruction process, a number of decisions on each reaction needed to be taken (Fig. 1 ). Is an enzyme present in the organism? Which reaction catalyzes the enzyme, and what is the stoichiometry of that reaction...
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Research: Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection
- Simon R. Harris,
- Carl Robinson,
- Karen F. Steward,
- Katy S. Webb,
- Romain Paillot,
- Julian Parkhill,
- Matthew T.G. Holden,
- and Andrew S. Waller
Genome Res. September 2015 25: 1360-1371; Published in Advance July 9, 2015, doi:10.1101/gr.189803.115
...to regulate virulence factors, including capsule, in S. pyogenes (Grahamet al. 2002). Both isolates shared a second SNP in csrS, which is predicted to result in a Leu257Phe amino acid substitution in addition to one nonsense mutation and a further 40 nonsynonymous mutations elsewhere in the (Supplemental...
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Research: Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
- Yoko Arimizu,
- Yumi Kirino,
- Mitsuhiko P. Sato,
- Koichi Uno,
- Toshio Sato,
- Yasuhiro Gotoh,
- Frédéric Auvray,
- Hubert Brugere,
- Eric Oswald,
- Jacques G. Mainil,
- Kelly S. Anklam,
- Dörte Döpfer,
- Shuji Yoshino,
- Tadasuke Ooka,
- Yasuhiro Tanizawa,
- Yasukazu Nakamura,
- Atsushi Iguchi,
- Tomoko Morita-Ishihara,
- Makoto Ohnishi,
- Koichi Akashi,
- Tetsuya Hayashi,
- and Yoshitoshi Ogura
Genome Res. September 2019 29: 1495-1505; Published in Advance August 22, 2019, doi:10.1101/gr.249268.119
...the analyses. Finally, 884 strains were used for further analyses and are listed in Supplemental Table S1.Detection of virulence genesPresence of non-LEE effectors was analyzed by TBLASTN search (>50% identity and >50% coverage) using amino acid sequences as query. Other virulence genes were identified using...
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LETTER: Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model
- Natalie C. Duarte,
- Markus J. Herrgård,
- and Bernhard Ø. Palsson
Genome Res. July 2004 14: 1298-1309; Published in Advance June 14, 2004, doi:10.1101/gr.2250904
.... The highest false prediction rates were obtained for genes involved in quinone biosynthesis (45.3%), followed by phospholipid biosynthesis (39.3%) and branched chain amino acid biosynthesis (37.5%). Subsystems with high false prediction rates also included oxidative phosphorylation (31.4%), mirroring...

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