Positive selection drives the evolution of a primate bitter taste receptor gene

Dong, Xiaoyan; Liang, Qiufang; Li, Jiaping; Feng, Pingping

doi:10.1002/ece3.7440

Cited by 6 publications

(7 citation statements)

References 43 publications

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“…Such sites are likely linked to the critically functional regions of the receptors. Just as it was found in the previous studies, for example, in T2R1, the positively selected sites are concentrated on the first and second extracellular loops (EL1, EL2) in ligand binding (Dong et al, 2021). In T2R16, the positively selected sites are fewer, which may be related to primates.…”

Section: Ta B L Esupporting

confidence: 68%

The evolution of bitter taste receptor gene in primates: Gene duplication and selection

Feng,

Liang,

et al. 2023

Ecology and Evolution

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Bitter taste perception plays an important role in preventing animals from digesting poisonous and harmful substances. In primates, especially the Cercopithecidae species, most species feed on plants; thus, it is reasonable to speculate that most of the bitter taste receptor genes (T2Rs) of primates are under purifying selection to maintain the functional stability of bitter taste perception. Gene duplication has happened in T2Rs frequently, and what will be the fate of T2Rs copies is another question we are concerned about. To answer these questions, we selected the T2Rs of primates reported in another study and conducted corresponding selective pressure analyses to determine what kind of selective pressure was acting on them. Further, we carried out selective pressure analyses on gene copies and their corresponding ancestors by considering several possible situations. The results showed that among the 25 gene groups examined here, 15 groups are subject to purifying selection and others are under relaxed selection, with many positively selected sites detected. Gene copies existed in several groups, but only some groups (clade1_a1‐b2, clade1_c‐c2, clade1_d1‐d3, clade1_f1‐f2, T2R10, T2R13, and T2R42) have positively selected sites, inferring that they may have some relation to functional divergence. Taken together, T2Rs in primates are under diverse selective pressures, and most gene copies are subject to the same selective pressures. In such cases, the copies may be just to keep the function conservative, and more copies can increase the quantity of the bitter taste receptor, raise the efficiency of bitter substance recognition, and finally enhance the fitness of feeding during the evolutionary course of primates. This study can improve our understanding of T2Rs evolution in primates.

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Section: Ta B L Esupporting

confidence: 68%

The evolution of bitter taste receptor gene in primates: Gene duplication and selection

Feng,

Liang,

et al. 2023

Ecology and Evolution

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“…This is why insectivorous lizards and geckos have such a high number of T2R genes, which are needed for these species to recognize poisonous substances from insects by the perception of bitter taste. The selection pressure on the extracellular, transmembrane and intracellular regions of T2Rs was found to be different in some primates and mammals, and without exception, the extracellular region was favored by positive selection pressure, while the transmembrane region and intracellular region was more favored by purifying selection (Shi et al 2003;Strotmann et al 2011;Dong et al 2021). In sauropsids, we analyzed the selection pressure in extracellular, transmembrane and intracellular regions by the paired YN00 model, which still showed the same pattern as above.…”

Section: Discussionmentioning

confidence: 93%

Chromosome-level genome assembly provides insights into adaptive evolution of chromosome and important traits in the geckoGekko japonicus

Wang

Yue

et al. 2023

Preprint

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Gekko japonicus possess excellent flexible climbing and detoxification ability under insectivorous habits, and its chromosomes and the genetic evolutionary mechanisms behind these traits are still unclarified. Here, we assembled a chromosome-level genome of G. japonicus with a total size of 2.53 Gb contained in 19 pairs of chromosomes. The evolutionary breakpoint regions (EBRs) are significantly enriched for some repetitive elements compared to the rest of genome and the genes located in the EBRs are enriched in defense response pathway. G. japonicus specific gene families, expanded gene families and positively selected genes are mainly enriched in some pathways related to the immune, sensory and nervous systems. These results from comprehensive comparative genomics and evolutionary genomics analyses indicated that bitter taste receptor type 2 (T2Rs) expanded in different lineages by tandem gene duplication. The expansion and independent duplication events of T2Rs and positively selected branches were predominantly present in insectivorous species, suggests that T2Rs are associate with clearance of bitter toxins in gekkotans. Detoxification genes in detox and biosynthetic cytochrome P450 of G. japonicas have frequent duplication and loss events, suggests that they undergo more birth and death processes compared to biosynthesis type genes. Pro, Cys, Gly and Ser are the most abundant amino acids in 66 epidermis formation corneous beta proteins (CBPs) of G. japonicas, the abundance of Gly and Cys in CBPs implying significant effects on the flexibility and setae adhesiveness of gekkotans. Some thermosensitive thermoregulatory transient receptor potential channels under relaxed purifying selection or positive selection in G. japonicus, implying that one of the important factors improve the ability to adapt to climate change.

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“…For example, members of the cytochrome P450 monooxygenase gene superfamily are hypothesized to evolve in response to plant secondary compound composition (101), and have shown rapid evolution in folivorous mammals, including lemurs (71,102,103). Bitter taste receptor evolution may also play a key role in fine-tuning primate plant food selection (104)(105)(106). Differences in morphology are also likely to reflect differing physiological strategies.…”

Section: Discussionmentioning

confidence: 99%

Molecular adaptation to folivory and the conservation implications for Madagascar’s lemurs

Guevara

Greene

Blanco

et al. 2021

Preprint

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Folivory evolved independently at least three times over the last 40 million years among Madagascar's lemurs. Many extant lemuriform folivores exist in sympatry in Madagascar's remaining forests. These species avoid feeding competition by adopting different dietary strategies within folivory, reflected in behavioral, morphological, and microbiota diversity across species. These conditions make lemurs an ideal study system for understanding adaptation to leaf-eating. Most folivorous lemurs are also highly endangered. The significance of folivory for conservation outlook is complex. Though generalist folivores may be relatively well equipped to survive habitat disturbance, specialist folivores occupying narrow dietary niches may be less resilient. Characterizing the genetic bases of adaptation to folivory across species and lineages can provide insights into their differential physiology and potential to resist habitat change. We recently reported accelerated genetic change in RNASE1, a gene encoding an enzyme (RNase 1) involved in molecular adaptation in mammalian folivores, including various monkeys and sifakas (genus Propithecus; family Indriidae). Here, we sought to assess whether other lemurs, including phylogenetically and ecologically diverse folivores, might show parallel adaptive change in RNASE1 that could underlie a capacity for efficient folivory. We characterized RNASE1 in 21 lemur species representing all five families and members of the three extant folivorous lineages: 1) bamboo lemurs (family Lemuridae), 2) sportive lemurs (family Lepilemuridae), and 3) indriids (family Indriidae). We found pervasive sequence change in RNASE1 across all indriids, a dN/dS value > 3 in this clade, and evidence for shared change in isoelectric point, indicating altered enzymatic function. Sportive and bamboo lemurs, in contrast, showed more modest sequence change. The greater change in indriids may reflect a shared strategy emphasizing complex gut morphology and microbiota to facilitate folivory. This case study illustrates how genetic analysis may reveal differences in functional traits that could influence species' ecology and, in turn, their resilience to habitat change. Moreover, our results support the contention that not all primate folivores are built the same and highlight the need to avoid generalizations about dietary guild in considering conservation outlook, particularly in lemurs where such diversity in folivory has probably led to extensive specialization via niche partitioning.

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Positive selection drives the evolution of a primate bitter taste receptor gene

Cited by 6 publications

References 43 publications

The evolution of bitter taste receptor gene in primates: Gene duplication and selection

The evolution of bitter taste receptor gene in primates: Gene duplication and selection

Chromosome-level genome assembly provides insights into adaptive evolution of chromosome and important traits in the geckoGekko japonicus

Molecular adaptation to folivory and the conservation implications for Madagascar’s lemurs

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