Publications by authors named "Shaohong Feng"

11 Publications

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A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes.

Genome Res 2021 Mar 6;31(3):497-511. Epub 2021 Jan 6.

MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.

Emu and other ratites are more informative than any other birds in reconstructing the evolution of the ancestral avian or vertebrate karyotype because of their much slower rate of genome evolution. Here, we generated a new chromosome-level genome assembly of a female emu, and estimated the tempo of chromosome evolution across major avian phylogenetic branches, by comparing it to chromosome-level genome assemblies of 11 other bird and one turtle species. We found ratites exhibited the lowest numbers of intra- and inter-chromosomal changes among birds since their divergence with turtles. The small-sized and gene-rich emu microchromosomes have frequent inter-chromosomal contacts that are associated with housekeeping genes, which appears to be driven by clustering their centromeres in the nuclear interior, away from the macrochromosomes in the nuclear periphery. Unlike nonratite birds, only less than one-third of the emu W Chromosome regions have lost homologous recombination and diverged between the sexes. The emu W is demarcated into a highly heterochromatic region (WS0) and another recently evolved region (WS1) with only moderate sequence divergence with the Z Chromosome. WS1 has expanded its inactive chromatin compartment, increased chromatin contacts within the region, and decreased contacts with the nearby regions, possibly influenced by the spreading of heterochromatin from WS0. These patterns suggest that alteration of chromatin conformation comprises an important early step of sex chromosome evolution. Overall, our results provide novel insights into the evolution of avian genome structure and sex chromosomes in three-dimensional space.
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http://dx.doi.org/10.1101/gr.271569.120DOI Listing
March 2021

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals.

Gigascience 2021 Jan;10(1)

MOE Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.

Background: Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques.

Results: A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination.

Conclusions: Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.
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http://dx.doi.org/10.1093/gigascience/giaa142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7787181PMC
January 2021

Dense sampling of bird diversity increases power of comparative genomics.

Authors:
Shaohong Feng Josefin Stiller Yuan Deng Joel Armstrong Qi Fang Andrew Hart Reeve Duo Xie Guangji Chen Chunxue Guo Brant C Faircloth Bent Petersen Zongji Wang Qi Zhou Mark Diekhans Wanjun Chen Sergio Andreu-Sánchez Ashot Margaryan Jason Travis Howard Carole Parent George Pacheco Mikkel-Holger S Sinding Lara Puetz Emily Cavill Ângela M Ribeiro Leopold Eckhart Jon Fjeldså Peter A Hosner Robb T Brumfield Les Christidis Mads F Bertelsen Thomas Sicheritz-Ponten Dieter Thomas Tietze Bruce C Robertson Gang Song Gerald Borgia Santiago Claramunt Irby J Lovette Saul J Cowen Peter Njoroge John Philip Dumbacher Oliver A Ryder Jérôme Fuchs Michael Bunce David W Burt Joel Cracraft Guanliang Meng Shannon J Hackett Peter G Ryan Knud Andreas Jønsson Ian G Jamieson Rute R da Fonseca Edward L Braun Peter Houde Siavash Mirarab Alexander Suh Bengt Hansson Suvi Ponnikas Hanna Sigeman Martin Stervander Paul B Frandsen Henriette van der Zwan Rencia van der Sluis Carina Visser Christopher N Balakrishnan Andrew G Clark John W Fitzpatrick Reed Bowman Nancy Chen Alison Cloutier Timothy B Sackton Scott V Edwards Dustin J Foote Subir B Shakya Frederick H Sheldon Alain Vignal André E R Soares Beth Shapiro Jacob González-Solís Joan Ferrer-Obiol Julio Rozas Marta Riutort Anna Tigano Vicki Friesen Love Dalén Araxi O Urrutia Tamás Székely Yang Liu Michael G Campana André Corvelo Robert C Fleischer Kim M Rutherford Neil J Gemmell Nicolas Dussex Henrik Mouritsen Nadine Thiele Kira Delmore Miriam Liedvogel Andre Franke Marc P Hoeppner Oliver Krone Adam M Fudickar Borja Milá Ellen D Ketterson Andrew Eric Fidler Guillermo Friis Ángela M Parody-Merino Phil F Battley Murray P Cox Nicholas Costa Barroso Lima Francisco Prosdocimi Thomas Lee Parchman Barney A Schlinger Bette A Loiselle John G Blake Haw Chuan Lim Lainy B Day Matthew J Fuxjager Maude W Baldwin Michael J Braun Morgan Wirthlin Rebecca B Dikow T Brandt Ryder Glauco Camenisch Lukas F Keller Jeffrey M DaCosta Mark E Hauber Matthew I M Louder Christopher C Witt Jimmy A McGuire Joann Mudge Libby C Megna Matthew D Carling Biao Wang Scott A Taylor Glaucia Del-Rio Alexandre Aleixo Ana Tereza Ribeiro Vasconcelos Claudio V Mello Jason T Weir David Haussler Qiye Li Huanming Yang Jian Wang Fumin Lei Carsten Rahbek M Thomas P Gilbert Gary R Graves Erich D Jarvis Benedict Paten Guojie Zhang

Nature 2020 11 11;587(7833):252-257. Epub 2020 Nov 11.

China National GeneBank, BGI-Shenzhen, Shenzhen, China.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity. Sparse taxon sampling has previously been proposed to confound phylogenetic inference, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
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http://dx.doi.org/10.1038/s41586-020-2873-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759463PMC
November 2020

Progressive Cactus is a multiple-genome aligner for the thousand-genome era.

Nature 2020 11 11;587(7833):246-251. Epub 2020 Nov 11.

UC Santa Cruz Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA.

New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies. For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far.
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http://dx.doi.org/10.1038/s41586-020-2871-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7673649PMC
November 2020

Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet.

Curr Biol 2020 01 12;30(1):108-114.e5. Epub 2019 Dec 12.

Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Dr. Aiguader 88, 08003 Barcelona, Spain. Electronic address:

As the only endemic neotropical parrot to have recently lived in the northern hemisphere, the Carolina parakeet (Conuropsis carolinensis) was an iconic North American bird. The last surviving specimen died in the Cincinnati Zoo in 1918 [1]. The cause of its extinction remains contentious: besides excessive mortality associated to habitat destruction and active hunting, their survival could have been negatively affected by its range having become increasingly patchy [2] or by the exposure to poultry pathogens [3, 4]. In addition, the Carolina parakeet showed a predilection for cockleburs, an herbaceous plant that contains a powerful toxin, carboxyatractyloside, or CAT [5], which did not seem to affect them but made the birds notoriously toxic to most predators [3]. To explore the demographic history of this bird, we generated the complete genomic sequence of a preserved specimen held in a private collection in Espinelves (Girona, Spain), as well as of a close extant relative, Aratinga solstitialis. We identified two non-synonymous genetic changes in two highly conserved proteins known to interact with CAT that could underlie a specific dietary adaptation to this toxin. Our genomic analyses did not reveal evidence of a dramatic past demographic decline in the Carolina parakeet; also, its genome did not exhibit the long runs of homozygosity that are signals of recent inbreeding and are typically found in endangered species. As such, our results suggest its extinction was an abrupt process and thus likely solely attributable to human causes.
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http://dx.doi.org/10.1016/j.cub.2019.10.066DOI Listing
January 2020

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.

Nat Ecol Evol 2019 05 1;3(5):834-844. Epub 2019 Apr 1.

MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China.

Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.
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http://dx.doi.org/10.1038/s41559-019-0850-1DOI Listing
May 2019

The Genomic Footprints of the Fall and Recovery of the Crested Ibis.

Curr Biol 2019 01 10;29(2):340-349.e7. Epub 2019 Jan 10.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China. Electronic address:

Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of endangered species [1-4]. However, factors such as outbreeding depression [5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management programs. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [7, 8]. We extend this approach to its natural conclusion, by characterizing the complete genomic sequences of modern and historic population samples of the crested ibis (Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinction. Though its once tiny population has today recovered to >2,000 individuals [9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymorphisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.
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http://dx.doi.org/10.1016/j.cub.2018.12.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345625PMC
January 2019

Author Correction: Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours.

Nat Ecol Evol 2018 09;2(9):1514

China National Genebank, BGI -Shenzhen, Shenzhen, China.

In the version of this Article originally published, there were some errors in the affiliations: Stephen J. O'Brien's affiliations were incorrectly listed as 8,9; they should have been 7,9. Affiliation 3 was incorrectly named the Institute of Cytology and Genetics of the Russian Academy of Sciences; it should have read Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences. Affiliation 4 was incorrectly named the Institute of Molecular and Cell Biology of the Russian Academy of Sciences; it should have read Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences. These have now been corrected.
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http://dx.doi.org/10.1038/s41559-018-0664-6DOI Listing
September 2018

Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours.

Nat Ecol Evol 2018 09 6;2(9):1479-1491. Epub 2018 Aug 6.

China National Genebank, BGI -Shenzhen, Shenzhen, China.

Strains of red fox (Vulpes vulpes) with markedly different behavioural phenotypes have been developed in the famous long-term selective breeding programme known as the Russian farm-fox experiment. Here we sequenced and assembled the red fox genome and re-sequenced a subset of foxes from the tame, aggressive and conventional farm-bred populations to identify genomic regions associated with the response to selection for behaviour. Analysis of the re-sequenced genomes identified 103 regions with either significantly decreased heterozygosity in one of the three populations or increased divergence between the populations. A strong positional candidate gene for tame behaviour was highlighted: SorCS1, which encodes the main trafficking protein for AMPA glutamate receptors and neurexins and suggests a role for synaptic plasticity in fox domestication. Other regions identified as likely to have been under selection in foxes include genes implicated in human neurological disorders, mouse behaviour and dog domestication. The fox represents a powerful model for the genetic analysis of affiliative and aggressive behaviours that can benefit genetic studies of behaviour in dogs and other mammals, including humans.
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http://dx.doi.org/10.1038/s41559-018-0611-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6663081PMC
September 2018

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

Genes (Basel) 2018 Jun 20;9(6). Epub 2018 Jun 20.

Department of Animal Science, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

The genome of a red fox () was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.
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http://dx.doi.org/10.3390/genes9060308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027122PMC
June 2018

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication.

BMC Genomics 2015 Jun 5;16:431. Epub 2015 Jun 5.

CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650223, China.

Background: Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.

Results: We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits.

Conclusion: Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.
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http://dx.doi.org/10.1186/s12864-015-1606-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455334PMC
June 2015