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| 1 | The new chimeric chiron genes evolved essential roles in zebrafish embryonic development by regulating NAD+ levels显示文摘The origination of new genes is important for generating genetic novelties for adaptive evolution and biological diversity.However, their potential roles in embryonic development, evolutionary processes into ancient networks, and contributions to adaptive evolution remain poorly investigated. Here, we identified a novel chimeric gene family, the chiron family, and explored its genetic basis and functional evolution underlying the adaptive evolution of Danioninae fishes. The ancestral chiron gene originated through retroposition of nampt in Danioninae 48–54 million years ago(Mya) and expanded into five duplicates(chiron1–5) in zebrafish 1–4 Mya. The chiron genes(chirons) likely originated in embryonic development and gradually extended their expression in the testis. Functional experiments showed that chirons were essential for zebrafish embryo development. By integrating into the NAD^(+) synthesis pathway, chirons could directly catalyze the NAD^(+) rate-limiting reaction and probably impact two energy metabolism genes(nmnat 1 and naprt) to be under positive selection in Danioninae fishes. Together,these results mainly demonstrated that the origin of new chimeric chiron genes may be involved in adaptive evolution by integrating and impacting the NAD^(+) biosynthetic pathway. This coevolution may contribute to the physiological adaptation of Danioninae fishes to widespread and varied biomes in Southeast Asian. | Chengchi Fang Xiaoni Gan Chengjun Zhang Shunping He | 2021 | Science China(Life Sciences)2021，64，11： | 1 |
| 2 | 3D landscape reorganization in response to feeding preferences adaptation in the youngest split Gymnocypris fish显示文摘Divergence in feeding preference is one of the main mechanisms that lead to the emergence of new species.However,little is known about the underlying genetic mechanism of feeding preference adaptation,especially in the three-dimensional(3D)chromatin organization regulation.Gymnocypris eckloni scoliostomus(GS)and G.eckloni eckloni(GE)are two sister species of G.eckloni(Cyprinidae:Schizothoracinae:Gymnocypris). | Ning Sun Cheng Wang Wenqi Lv Xiaoni Gan Liandong Yang Shunping He Chengchi Fang | 2023 | Journal of Genetics and Genomics2023，50，4： | 0 |
| 3 | Pseudo-chromosome–length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation显示文摘High hydrostatic pressure,low temperature,and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments.Here,we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel(MAE,Ilyophis brunneus,captured below a depth of 3,500 m)by using Illumina,Pac Bio,and Hi-C sequencing.We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes.The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes.Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species,European eel,~111.9 Mya and experienced a rapid evolution.The genome evolutionary analyses primarily revealed the following:(i)under high hydrostatic pressure,the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability;ACOX1 may enhance the fluidity of cell membrane and maintain transport activity;the expansion of ABCC12 gene family may enhance the integrity of DNA;(ii)positively selected HARS likely maintain the transcription ability at low temperatures;and(iii)energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and m TOR signaling pathways. | Jie Chen Honghui Zeng Wenqi Lv Ning Sun Cheng Wang Wenjie Xu Mingliang Hu Xiaoni Gan Lisheng He Shunping He Chengchi Fang | 2023 | Science China(Life Sciences)2023，66，6： | 0 |
| 4 | Improved genome assembly of Chinese sucker(Myxocyprinus asiaticus)provides insights into the identification and characterization of pharyngeal teeth related maker genes in Cyprinoidei显示文摘The Chinese sucker,Myxocyprinus asiaticus(M.asiaticus,Catostomidae,Cypriniformes),is the only living species of Catostomidae in Asia.There are more than 75 species of this family in North America.The fossil record of this group dates back to the early Eocene.As the Chinese sucker is located at the base of the Cyprinoidei phylogeny,this species is also important in clarifying the evolutionary relationships within Cyprinoidei.Here,we assembled a high-quality genome of the Chinese sucker,contig N50(40.26 Mb),which is nearly ten times longer than the previous version(4.19 Mb).Phylogenetic analysis identified that Chinese sucker together with Cyprinidae groups are paraphyletic with respect to Cobitoidea.The specific whole genome duplication event of the Chinese sucker was estimated to have occurred~25.9 million years ago.Analysis of population historical changes indicated a trend of reduction for the Chinese sucker and T.tibetana.Since Dlx genes play a key role in Cypriniformes pharyngeal teeth development,we conducted a genome-wide identification of Dlx genes,and found that these genes were doubled in whole genome duplication events,followed by the loss of specific copies.Transcriptome results showed that the expression levels of these paralogous genes were similar.This genomic resource provides useful information for the protection of Chinese sucker and functional study of Dlx genes. | Xin Liu Honghui Zeng Cheng Wang Jing Bo Xiaoni Gan Chengchi Fang Shunping He | 2022 | Water Biology and Security2022，1，3： | 0 |
| 5 | Sympatric or micro-allopatric speciation in a glacial lake?Genomic islands support neither显示文摘Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation.One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence,wherein divergent DNA segments are interspersed with low-divergence segments.Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow.Sympatric divergence of endemic fishes is known from isolated saline,crater,postglacial,and ancient lakes.Two morphologically distinct cyprinid fishes,Gymnocypris eckloni scoliostomus(GS)and G.eckloni eckloni(GE),in a small glacial lake on the Qinghai-Tibet Plateau,Lake Sunmcuo,match the biogeographic criteria of sympatric speciation.In this study,we examined genome-wide variation in 46individuals from these two groups.The divergence time between the GS and GE lineages was estimated to be 20-60 Kya.We identified 54 large genomic islands(≥100 kb)of speciation,which accounted for 89.4%of the total length of all genomic islands.These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes.Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation,they were too large to support the hypothesis of sympatric speciation.Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands(as small as a few kilobases in size).Thus,the observed pattern is consistent with the extensive evidence on parapatric speciation,in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation.We suggest that many,if not most,of the reported cases of sympatric speciation are likely to be micro-parapatric speciation. | Ning Sun Liandong Yang Fei Tian Honghui Zeng Ziwen He Kai Zhao Cheng Wang Minghui Meng Chenguang Feng Chengchi Fang Wenqi Lv Jing Bo Yongtao Tang Xiaoni Gan Zuogang Peng Yiyu Chen Shunping He | 2022 | National Science Review2022，9，12： | 0 |
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