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Research: The Chinese longsnout catfish genome provides novel insights into the feeding preference and corresponding metabolic strategy of carnivores
- Yulong Liu,
- Gang Zhai,
- Jingzhi Su,
- Yulong Gong,
- Bingyuan Yang,
- Qisheng Lu,
- Longwei Xi,
- Yutong Zheng,
- Jingyue Cao,
- Haokun Liu,
- Junyan Jin,
- Zhimin Zhang,
- Yunxia Yang,
- Xiaoming Zhu,
- Zhongwei Wang,
- Gaorui Gong,
- Jie Mei,
- Zhan Yin,
- Rodolphe E. Gozlan,
- Shouqi Xie,
- and Dong Han
Genome Res. July 2024 34: 981-996; Published in Advance August 9, 2024, doi:10.1101/gr.278476.123
...et al. 2016; Kasumyan 2019). The sense of taste is important in the differentiation of feeding preferences and feeding habits (Kasumyan 2019; Jiao et al. 2021). Taste is perceived via the taste receptor signaling pathway (including genes such as tas1rs) in the taste buds (Bruch et al. 1988; Bachmanov...
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LETTER: Comparative genomic analysis identifies an evolutionary shift of vomeronasal receptor gene repertoires in the vertebrate transition from water to land
- Peng Shi and
- Jianzhi Zhang
Genome Res. February 2007 17: 166-174; Published in Advance January 8, 2007, doi:10.1101/gr.6040007
...for vomeronasal and olfactory receptors become more significant when smaller gene families are also used in generating the distribution of r . Qualitatively similar results are obtained when we use the cutoff size of 20 genes, but the number of gene families left (125) for analysis becomes too small to give...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...of ZNFs but also that of other expansive gene families. We therefore used olfactory receptors as a control case; olfactory receptors are membrane proteins known to turn over rapidly across species but are not expected to interact physically with TEs. In a sample of representative species from 103...
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Resource: A single-cell transcriptome atlas of the maturing zebrafish telencephalon
- Shristi Pandey,
- Anna J. Moyer,
- and Summer B. Thyme
Genome Res. April 2023 33: 658-671; Published in Advance April 18, 2023, doi:10.1101/gr.277278.122
...for all clusters. For example, Pallium_01 and Pallium_04 both cluster near the basolateral amygdala and anterior olfactory neurons (Fig. 4C,D), unrelated to their expected cell types from anatomical analysis (Ganz et al. 2014; Porter and Mueller 2020), and do not share obvious marker genes with single...
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LETTER: Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity
- James P. Noonan,
- Jane Grimwood,
- Jeremy Schmutz,
- Mark Dickson,
- and Richard M. Myers
Genome Res. March 2004 14: 354-366; doi:10.1101/gr.2133704
..., immunoglobulin and T-cell receptor gene clusters, generate the enormous range of antigen recognition molecules required to mount an effective immune response in an environment of multiple, rapidly evolving pathogens (for review, see Flajnik 2002 ). Olfactory receptor gene clusters provide the molecular means...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...the association between PCNEs and synteny conservation with high resolution. For these analyses, and all further analyses presented in this article, we have removed all olfactory receptor genes from our gene sets because their extensive tandem duplication can dominate whole comparisons (for further discussion...
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Research: The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus
- Li Ren,
- Wuhui Li,
- Qinbo Qin,
- He Dai,
- Fengming Han,
- Jun Xiao,
- Xin Gao,
- Jialin Cui,
- Chang Wu,
- Xiaojing Yan,
- Guoliang Wang,
- Guiming Liu,
- Jia Liu,
- Jiaming Li,
- Zhong Wan,
- Conghui Yang,
- Chun Zhang,
- Min Tao,
- Jing Wang,
- Kaikun Luo,
- Shi Wang,
- Fangzhou Hu,
- Rurong Zhao,
- Xuming Li,
- Min Liu,
- Hongkun Zheng,
- Rong Zhou,
- Yuqin Shu,
- Yude Wang,
- Qinfeng Liu,
- Chenchen Tang,
- Wei Duan,
- and Shaojun Liu
Genome Res. November 2019 29: 1805-1815; Published in Advance October 24, 2019, doi:10.1101/gr.249805.119
...contraction events associated with nine biological process categories related to bone development and skeletal muscle function (Supplemental Table S11), and 69 genes in expansion events were related to the detection of chemical stimuli in olfactory perception (GO:0050911). These factors might contribute...
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LETTER: Species-Specific Class I Gene Expansions Formed the Telomeric 1 Mb of the Mouse Major Histocompatibility Complex
- Toyoyuki Takada,
- Attila Kumánovics,
- Claire Amadou,
- Masayasu Yoshino,
- Elsy P. Jones,
- Maria Athanasiou,
- Glen A. Evans,
- and Kirsten Fischer Lindahl
Genome Res. April 1, 2003 13: 589-600; doi:10.1101/gr.975303
...the telomeric 1 Mb is rich in olfactory receptor genes and contains just two functional class I genes, H2-M3 and H2-M2 ( Amadou et al. 1999 ). Here we report the finished sequence of the class I-rich part of the H2-M region. RESULTS Genomic Sequencing of the Centromeric H2-M Region We previously constructed...
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LETTER: Transcriptional Regulation of the Stem Cell Leukemia Gene (SCL) — Comparative Analysis of Five Vertebrate SCL Loci
- Berthold Göttgens,
- Linda M. Barton,
- Michael A. Chapman,
- Angus M. Sinclair,
- Bjarne Knudsen,
- Darren Grafham,
- James G.R. Gilbert,
- Jane Rogers,
- David R. Bentley,
- and Anthony R. Green
Genome Res. May 1, 2002 12: 749-759; doi:10.1101/gr.45502
...of NFI-binding sites and cloning of NFI-cDNAs suggest a regulatory role for NFI transcription factors in olfactory neuron gene expression. Brain Res. Mol. Brain Res. 72 : 65 – 79 . ↵ Beckers J. , Gerard M. , Duboule D. ( 1996 ) Transgenic analysis of a potential Hoxd-11 limb regulatory element present...
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Resource: Coelacanth genomes reveal signatures for evolutionary transition from water to land
- Masato Nikaido,
- Hideki Noguchi,
- Hidenori Nishihara,
- Atsushi Toyoda,
- Yutaka Suzuki,
- Rei Kajitani,
- Hikoyu Suzuki,
- Miki Okuno,
- Mitsuto Aibara,
- Benjamin P. Ngatunga,
- Semvua I. Mzighani,
- Hassan W.J. Kalombo,
- Kawilarang W.A. Masengi,
- Josef Tuda,
- Sadao Nogami,
- Ryuichiro Maeda,
- Masamitsu Iwata,
- Yoshitaka Abe,
- Koji Fujimura,
- Masataka Okabe,
- Takanori Amano,
- Akiteru Maeno,
- Toshihiko Shiroishi,
- Takehiko Itoh,
- Sumio Sugano,
- Yuji Kohara,
- Asao Fujiyama,
- and Norihiro Okada
Genome Res. October 2013 23: 1740-1748; Published in Advance July 22, 2013, doi:10.1101/gr.158105.113
...and/or a slow rate of evolution. We found a substantial number of genes that encode olfactory and pheromone receptors with features characteristic of tetrapod receptors for the detection of airborne ligands. We also found that limb enhancers of bmp7 and gli3 , both of which are essential for limb...
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