Gene-rich germline-restricted chromosomes in black-winged fungus gnats evolved through hybridization.
Gene-rich germline-restricted chromosomes in black-winged fungus gnats evolved through hybridization.
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DOI：
10.1371/journal.pbio.3001559
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发表时间：
2022-03
期刊：
影响因子：
9.8
通讯作者：
Ross L
中科院分区：
文献类型：
--
作者：
Hodson CN;Jaron KS;Gerbi S;Ross L
生殖系限制性DNA已经在多种动物类群中进化，并且在几种脊椎动物分支、线虫和苍蝇中发现。在这些谱系中，部分染色体或整个染色体在发育早期从体细胞中消除，将基因组的部分限制在种系中。很少有人知道为什么生殖限制性DNA已经进化，特别是在苍蝇，其中3个不同的家庭，摇蚊科，Cecidomyiidae和Sciaridae，携带生殖限制性染色体（GRC）。我们进行了gnatBradysia（Sciara）coprophila（双翅目：Sciaridae），其中有2个大的生殖系限制的“L”染色体的GRCs的基因组分析。我们对B的基因组进行了测序和组装。利用体细胞和种系组织之间的序列覆盖率和k-mer频率的差异来鉴定GRC序列并将其与基因组中的其他染色体进行比较。我们发现B.嗜粪菌大，基因丰富，并且在基因组中的其它染色体上具有许多具有不同同源物的基因。我们还发现在我们测序的群体中存在2个不同的GRCs。GRC基因在序列上与另一个双翅目（Cecidomyiidae）的基因比与Sciaridae的同源基因更相似。这一意外的发现表明，这些染色体可能是通过与相关谱系杂交而出现在Sciaridae中的。这些结果提供了一个基础，从它来回答许多问题的进化GRC在Sciaridae，如如何杂交事件导致GRC和这些染色体上的功能是什么导致他们被限制在种系。生殖系限制性染色体从所有体细胞组织中消除，同时保留在生殖系中。这项对真菌蚊蚋中这些染色体的进化起源的研究表明，它们与不同家族的苍蝇最相似，这表明这些特殊染色体的古老异源多倍化起源。
Germline-restricted DNA has evolved in diverse animal taxa and is found in several vertebrate clades, nematodes, and flies. In these lineages, either portions of chromosomes or entire chromosomes are eliminated from somatic cells early in development, restricting portions of the genome to the germline. Little is known about why germline-restricted DNA has evolved, especially in flies, in which 3 diverse families, Chironomidae, Cecidomyiidae, and Sciaridae, carry germline-restricted chromosomes (GRCs). We conducted a genomic analysis of GRCs in the fungus gnat Bradysia (Sciara) coprophila (Diptera: Sciaridae), which has 2 large germline-restricted “L” chromosomes. We sequenced and assembled the genome of B. coprophila and used differences in sequence coverage and k-mer frequency between somatic and germline tissues to identify GRC sequence and compare it to the other chromosomes in the genome. We found that the GRCs in B. coprophila are large, gene rich, and have many genes with divergent homologs on other chromosomes in the genome. We also found that 2 divergent GRCs exist in the population we sequenced. GRC genes are more similar in sequence to genes from another Dipteran family (Cecidomyiidae) than to homologous genes from Sciaridae. This unexpected finding suggests that these chromosomes likely arose in Sciaridae through hybridization with a related lineage. These results provide a foundation from which to answer many questions about the evolution of GRCs in Sciaridae, such as how this hybridization event resulted in GRCs and what features on these chromosomes cause them to be restricted to the germline. Germ-line restricted chromosomes are eliminated from all somatic tissues while being retained in the germline. This study of the evolutionary origin of such chromosomes in fungus gnats reveals that they are most similar to a fly of a different family, suggesting an ancient allopolyploidization origin for these peculiar chromosomes.
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