A complex interplay of evolutionary forces continues to shape ancient co-occurring symbiont genomes

Vasquez, Yumary; Bennett, Gordon M.

doi:10.1016/j.isci.2022.104786

Cited by 11 publications

(15 citation statements)

References 137 publications

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“…Based on observations made by researchers at one of the public junior high schools in Yogyakarta, it is known that that this application has not been used, even though this application has advantages that can make students better understand the concept of the existing material [46]- [50]. This is in accordance with several studies using mindfulness that have been carried out where maps are able to improve students' conceptual understanding abilities [51]- [55]. Because of these advantages, the researcher intends to conduct research to determine the analysis of the need for using mind map applications to improve students' conceptual understanding abilities.…”

Section: Introduction Human Development By Humanizing Humanssupporting

confidence: 66%

I Mind Map Application Needs Analysis to Improve Students’ Mathematical Concept Understanding Ability

Pertiwi

Khuzaini

Beneditha³

et al. 2022

JOAW

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The ability to understand concepts is the mastery of the material in which students recognize, know, and are able to re-express concepts in a form that is easier to understand. However, students’ conceptual understanding skills still tend to be low. So it takes teaching materials that integrate these abilities. For this reason, this study aims to analyze the need for teaching materials based on mind map applications to improve students’ conceptual understanding skills. A mind map is a mind map in the form of a diagram that visually describes ideas, concepts, information, or other things. This type of research is descriptive qualitative. The research was conducted in one of the public junior high schools in Yogyakarta. The subjects in this study were 32 students of class IXA. Data collection techniques used interviews, concept understanding ability tests, and preliminary study questionnaires. While the data analysis technique uses the Miles and Huberman model which consists of data collection, data reduction, data presentation, and drawing conclusions. The results showed that teachers had not implemented mind map-assisted learning, students’ conceptual understanding abilities tended to be low, students were interested in learning using mind map applications because students could develop ways of thinking and make them more active during learning

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Section: Introduction Human Development By Humanizing Humanssupporting

confidence: 66%

I Mind Map Application Needs Analysis to Improve Students’ Mathematical Concept Understanding Ability

Pertiwi

Khuzaini

Beneditha³

et al. 2022

JOAW

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“…In Oliarus , despite a more robust functional role than Sulcia , Vidania has a smaller genome and lower GC content overall, which is consistent with previous results ( Bennett and Mao 2018 ). These genomic differences are likely a result of relaxed selection on Sulcia related to the acquisition of Vidania with a robust set of nutritional provisioning genes ( Bennett and Mao 2018 ; Vasquez and Bennett 2022 ).…”

Section: Resultsmentioning

confidence: 99%

“…While Sulcia exhibits extremely low substitution rates between the two host species, its partner endosymbionts Vidania and Purcelliella have much higher substitution rates. This pattern appears to be highly conserved among Auchenorrhyncha hosts that harbor Sulcia and one or two of its partner endosymbionts ( Vasquez and Bennett 2022 ). Additionally, for Purcelliella , we see variation in the rates of molecular evolution between cave and surface host cixiid species.…”

Section: Discussionmentioning

confidence: 99%

“…In the later stages, symbionts continue to lose nonessential genes at a much slower pace, often conserving key biological functions and genomic synteny for long periods of evolutionary time ( Latorre and Manzano-Marin 2017 ; McCutcheon et al 2019 ). However, essential genes are still often lost from these tiny genomes even among closely related host species likely resulting from strong genetic drift ( Chong et al 2019 ; Vasquez and Bennett 2022 ). Gene functions that are lost can be compensated for by several processes such as horizontal gene transfer of host-encoded homologs ( Hansen and Moran 2014 ; Sloan et al 2014 ), the acquisition of new co-endosymbionts ( McCutcheon et al 2009 ; Sheffer et al 2020 ; Dial et al 2021 ), or senior symbiont replacement by junior endosymbionts ( Clayton et al 2012 ; Toenshoff et al 2012 ; Koga and Moran 2014 ; Sudakaran et al 2017 ; Chong and Moran 2018 ; Mao and Bennett 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Genomic Comparisons Reveal Selection Pressure and Functional Variation Between Nutritional Endosymbionts of Cave-Adapted and Epigean Hawaiian Planthoppers

Gossett

Porter

Vasquez³

et al. 2023

Genome Biology and Evolution

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Planthoppers in the family Cixiidae (Hempitera: Auchenorrhyncha: Fulgoromorpha) harbor a diverse set of obligate bacterial endosymbionts that provision essential amino acids and vitamins that are missing from their plant-sap diet. “Candidatus Sulcia muelleri”, and “Ca. Vidania fulgoroidea” have been associated with cixiid planthoppers since their origin within the Auchenorrhyncha, while “Ca. Purcelliella pentastirinorum” is a more recent endosymbiotic acquisition. Hawaiian cixiid planthoppers occupy diverse habitats including lava tube caves and shrubby surface landscapes, which offer different nutritional resources and environmental constraints. Genomic studies have focused on understanding the nutritional provisioning roles of cixiid endosymbionts more broadly, yet it is still unclear how selection pressures on endosymbiont genes might differ between cixiid host species inhabiting such diverse landscapes, or how variation in selection might impact symbiont evolution. In this study, we sequenced the genomes of Sulcia, Vidania, and Purcelliella isolated from both surface and cave-adapted planthopper hosts from the genus Oliarus. We found that nutritional biosynthesis genes were conserved in Sulcia and Vidania genomes in inter- and intra-host species comparisons. In contrast, Purcelliella genomes retain different essential nutritional biosynthesis genes between surface- and cave-adapted planthopper species. Finally, we see variation in selection pressures on symbiont genes both within and between host species suggesting that strong coevolution between host and endosymbiont is associated with different patterns of molecular evolution on a fine scale that may be associated with host diet.

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“…In extreme cases, genome size becomes so small, barely over 100 kilobases, that only functionally essential genes remain, including those involved in transcription, translation, and nutritional provisioning (Bennett and Moran, 2013). As these evolutionary processes proceed, even genes that seem essential in these tiny genomes can be lost over time (Vasquez and Bennett, 2022). Nevertheless, it is typically observed that the genomes of mutualistic endosymbionts establish a high level of synteny fairly early in their evolution (Patiño-Navarrete et al, 2013;Williams and Wernegreen, 2015;Chong et al, 2019) with some caveats (e.g., Sloan and Moran, 2013).…”

Section: Introductionmentioning

confidence: 99%

Genome comparison reveals inversions and alternative evolutionary history of nutritional endosymbionts in planthoppers (Hemiptera: Fulgoromorpha)

Deng

Bennett

Franco

et al. 2022

Preprint

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The evolutionary success of sap-feeding hemipteran insects in the suborder Auchenorrhyncha was enabled by nutritional contributions from their heritable endosymbiotic bacteria. However, the symbiont diversity, functions, and evolutionary origins in this large insect group have not been broadly characterized using genomic tools. In particular, the origins and relationships among ancient betaproteobacterial symbionts Vidania (in Fulgoromorpha) and Nasuia/Zinderia (in Cicadomorpha) are uncertain. Here, we characterized the genomes of Vidania and Sulcia from three Pyrops planthoppers (family Fulgoridae) to understand their metabolic functions and evolutionary histories. Like in previously characterized planthoppers, these symbionts share nutritional responsibilities, with Vidania providing seven out of ten essential amino acids. Sulcia lineages across the Auchenorrhyncha have a highly conserved genome but with multiple independent rearrangements occurring in an early ancestor of Cicadomorpha or Fulgoromorpha and in a few succeeding lineages. Genomic synteny was also observed within each of the betaproteobacterial symbiont genera Nasuia, Zinderia, and Vidania, but not across them, which challenges the expectation of a shared ancestry for these symbionts. The further comparison of other biological traits strongly suggests an independent origin of Vidania early in the planthopper evolution and possibly of Nasuia and Zinderia in their respective host lineages.

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A complex interplay of evolutionary forces continues to shape ancient co-occurring symbiont genomes

Cited by 11 publications

References 137 publications

I Mind Map Application Needs Analysis to Improve Students’ Mathematical Concept Understanding Ability

I Mind Map Application Needs Analysis to Improve Students’ Mathematical Concept Understanding Ability

Genomic Comparisons Reveal Selection Pressure and Functional Variation Between Nutritional Endosymbionts of Cave-Adapted and Epigean Hawaiian Planthoppers

Genome comparison reveals inversions and alternative evolutionary history of nutritional endosymbionts in planthoppers (Hemiptera: Fulgoromorpha)

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