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果蝇黏附基因位于短重复序列附近的基因拷贝数的更高进化动态。

Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences.

机构信息

Université Paris Cité, CNRS, Institut Jacques Monod, 75013, Paris, France.

Department of Biological Sciences, Columbia University, New York city, New York, USA.

出版信息

BMC Ecol Evol. 2024 Feb 2;24(1):18. doi: 10.1186/s12862-023-02178-y.

DOI:10.1186/s12862-023-02178-y
PMID:38308233
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10835880/
Abstract

BACKGROUND

During evolution, genes can experience duplications, losses, inversions and gene conversions. Why certain genes are more dynamic than others is poorly understood. Here we examine how several Sgs genes encoding glue proteins, which make up a bioadhesive that sticks the animal during metamorphosis, have evolved in Drosophila species.

RESULTS

We examined high-quality genome assemblies of 24 Drosophila species to study the evolutionary dynamics of four glue genes that are present in D. melanogaster and are part of the same gene family - Sgs1, Sgs3, Sgs7 and Sgs8 - across approximately 30 millions of years. We annotated a total of 102 Sgs genes and grouped them into 4 subfamilies. We present here a new nomenclature for these Sgs genes based on protein sequence conservation, genomic location and presence/absence of internal repeats. Two types of glue genes were uncovered. The first category (Sgs1, Sgs3x, Sgs3e) showed a few gene losses but no duplication, no local inversion and no gene conversion. The second group (Sgs3b, Sgs7, Sgs8) exhibited multiple events of gene losses, gene duplications, local inversions and gene conversions. Our data suggest that the presence of short "new glue" genes near the genes of the latter group may have accelerated their dynamics.

CONCLUSIONS

Our comparative analysis suggests that the evolutionary dynamics of glue genes is influenced by genomic context. Our molecular, phylogenetic and comparative analysis of the four glue genes Sgs1, Sgs3, Sgs7 and Sgs8 provides the foundation for investigating the role of the various glue genes during Drosophila life.

摘要

背景

在进化过程中，基因可能会经历复制、丢失、倒位和基因转换。为什么某些基因比其他基因更具动态性，这一点我们还不太理解。在这里，我们研究了编码粘性蛋白的几个 Sgs 基因（构成动物在变态过程中黏附的生物胶）在果蝇种系中是如何进化的。

结果

我们检查了 24 种果蝇的高质量基因组组装，以研究在大约 3000 万年的时间里，存在于黑腹果蝇中的 4 个粘性基因（Sgs1、Sgs3、Sgs7 和 Sgs8）在果蝇属中的进化动态。我们总共注释了 102 个 Sgs 基因，并将它们分为 4 个子家族。我们根据蛋白质序列的保守性、基因组位置以及内部重复的存在/缺失，提出了这些 Sgs 基因的新命名法。我们发现了两种类型的粘性基因。第一类（Sgs1、Sgs3x、Sgs3e）显示出少数基因丢失，但没有发生复制、局部倒位或基因转换。第二类（Sgs3b、Sgs7、Sgs8）则表现出多个基因丢失、基因复制、局部倒位和基因转换事件。我们的数据表明，后一组基因附近存在短的“新胶”基因可能加速了它们的进化。

结论

我们的比较分析表明，粘性基因的进化动态受到基因组背景的影响。我们对 Sgs1、Sgs3、Sgs7 和 Sgs8 这四个粘性基因的分子、系统发育和比较分析为研究不同粘性基因在果蝇生活中的作用提供了基础。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/ad5c031b888b/12862_2023_2178_Fig11_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/6e4f890eeed5/12862_2023_2178_Fig1_HTML.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/41a1f0907255/12862_2023_2178_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/f74a34b7013b/12862_2023_2178_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/9617806c4711/12862_2023_2178_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/e120470eef65/12862_2023_2178_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/57a795e5375b/12862_2023_2178_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/8739f37a2887/12862_2023_2178_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/c985db37d52b/12862_2023_2178_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/ad5c031b888b/12862_2023_2178_Fig11_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/6e4f890eeed5/12862_2023_2178_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/4fc0657d005d/12862_2023_2178_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/187c6f0d1d83/12862_2023_2178_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/41a1f0907255/12862_2023_2178_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/f74a34b7013b/12862_2023_2178_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/9617806c4711/12862_2023_2178_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/e120470eef65/12862_2023_2178_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/57a795e5375b/12862_2023_2178_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/8739f37a2887/12862_2023_2178_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/c985db37d52b/12862_2023_2178_Fig10_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ea2/10835880/ad5c031b888b/12862_2023_2178_Fig11_HTML.jpg

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