畜禽泛基因组研究进展

doi:10.11843/j.issn.0366-6964.2023.09.001

摘要/Abstract

摘要： 泛基因组是近些年来基因组研究领域出现的一个新名词,相较于单个线性参考基因组具有明显优势,能够有效解决参考基因组涵盖遗传信息有限的问题。随着测序技术的发展和对基因组的深入研究,泛基因组学相关研究也得到快速发展。本文综述了泛基因组学的发展历程、构建策略及其在畜禽上的研究现状,并对未来的应用趋势进行了展望,以期为畜禽泛基因组的深入研究提供参考。

关键词: 畜禽, 泛基因组, 核心基因, 可变基因, 结构变异

Abstract: As a study hotspot, pan-genome has frequently appeared in the genome field in recent years. Pan-genome had significant advantages compared to the single linear reference genome, and could effectively solve the problem of reference genome covering limited genetic information. Thanks to the fast pace at which sequencing technologies progress, pan-genome have been developed rapidly in recent years. Here, the development history and construction strategies of pan-genome were reviewed, as well as the study of livestock and poultry. Furthermore, the future application trend was propected, in order to provide reference for further study of pan-genome in livestock and poultry.

Key words: livestock and poultry, pan-genome, core genes, variable genes, structural variation

中图分类号:

S813.3

李珂, 王宇龙, 李栋, 史新娥, 杨公社, 于太永. 畜禽泛基因组研究进展[J]. 畜牧兽医学报, 2023, 54(9): 3595-3604.

LI Ke, WANG Yulong, LI Dong, SHI Xin'e, YANG Gongshe, YU Taiyong. Advances in Pan-genome Study of Livestock and Poultry[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3595-3604.

参考文献

[1] GREEN E D,WATSON J D,COLLINS F S.Human genome project:twenty-five years of big biology[J].Nature, 2015,526(7571):29-31.
[2] TETTELIN H,MASIGNANI V,CIESLEWICZ M J,et al.Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae:implications for the microbial "pan-genome"[J].Proc Natl Acad Sci U S A,2005, 102(39):13950-13955.
[3] HOGG J S,HU F Z,JANTO B,et al.Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains[J]. Genome Biol, 2007,8(6):R103.
[4] BOISSY R,AHMED A,JANTO B,et al.Comparative supragenomic analyses among the pathogens Staphylococcus aureus,Streptococcus pneumoniae,and Haemophilus influenzae using a modification of the finite supragenome model[J].BMC Genomics,2011,12:187.
[5] 唐蝶,周倩.植物基因组组装技术研究进展[J].生物技术通报,2021,37(6):1-12.
TANG D,ZHOU Q.Research advances in plant genome assembly[J].Biotechnology Bulletin,2021,37(6):1-12.(in Chinese)
[6] GOLICZ A A,BAYER P E,BHALLA P L,et al.Pangenomics comes of age:from bacteria to plant and animal applications[J].Trends Genet,2020,36(2):132-145.
[7] BROCKHURST M A,HARRISON E,HALL J P J,et al.The ecology and evolution of pangenomes[J].Curr Biol,2019,29(20):R1094-R1103.
[8] LEI L,GOLTSMAN E,GOODSTEIN D,et al.Plant pan-genomics comes of age[J].Annu Rev Plant Biol,2021, 72:411-435.
[9] BONNICI V,MARESI E,GIUGNO R.Challenges in gene-oriented approaches for pangenome content discovery[J].Brief Bioinform,2021,22(3):bbaa198.
[10] SHERMAN R M,SALZBERG S L.Pan-genomics in the human genome era[J].Nat Rev Genet,2020,21(4):243-254.
[11] GORDON S P,CONTRERAS-MOREIRA B,WOODS D P,et al.Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure[J].Nat Commun,2017,8(1):2184.
[12] HOLT K E,WERTHEIM H,ZADOKS R N,et al.Genomic analysis of diversity,population structure,virulence, and antimicrobial resistance in Klebsiella pneumoniae,an urgent threat to public health[J].Proc Natl Acad Sci U S A,2015,112(27):E3574-E3581.
[13] DORON S,MELAMED S,OFIR G,et al.Systematic discovery of antiphage defense systems in the microbial pangenome[J].Science,2018,359(6379):eaar4120.
[14] PETIT-HOUDENOT Y,FUDAL I.Complex interactions between fungal avirulence genes and their corresponding plant resistance genes and consequences for disease resistance management[J].Front Plant Sci,2017,8:1072.
[15] 边培培,张禹,姜雨.泛基因组:高质量参考基因组的新标准[J].遗传,2021,43(11):1023-1037.
BIAN P P,ZHANG Y,JIANG Y.Pan-genome:setting a new standard for high-quality reference genomes[J]. Hereditas (Beijing),2021,43(11):1023-1037.(in Chinese)
[16] ZHAO Q,FENG Q,LU H Y,et al.Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice[J].Nat Genet,2018,50(2):278-284.
[17] GOLICZ A A,BAYER P E,BARKER G C,et al.The pangenome of an agronomically important crop plant Brassica oleracea[J].Nat Commun,2016,7(1):13390.
[18] MEDINI D,DONATI C,TETTELIN H,et al.The microbial pan-genome[J].Curr Opin Genet Dev,2005,15(6):589-594.
[19] MARRONI F,PINOSIO S,MORGANTE M.Structural variation and genome complexity:is dispensable really dispensable?[J].Curr Opin Plant Biol,2014,18:31-36.
[20] MUZZI A,DONATI C.Population genetics and evolution of the pan-genome of Streptococcus pneumoniae[J]. Int J Med Microbiol,2011,301(8):619-622.
[21] DONATI C,HILLER N L,TETTELIN H,et al.Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species[J].Genome Biol,2010,11(10):R107.
[22] 李金明.高通量测序技术[M].北京:科学出版社,2018.
LI J M.High-throughput Sequencing[M].Beijing:Science Press,2018.(in Chinese)
[23] PUIGBÒ P,LOBKOVSKY A E,KRISTENSEN D M,et al.Genomes in turmoil:quantification of genome dynamics in prokaryote supergenomes[J].BMC Biol,2014,12:66.
[24] READ B A,KEGEL J,KLUTE M J,et al.Pan genome of the phytoplankton Emiliania underpins its global distribution[J].Nature,2013,499(7457):209-213.
[25] MORGANTE M,DEPAOLI E,RADOVIC S.Transposable elements and the plant pan-genomes[J].Curr Opin Plant Biol,2007,10(2):149-155.
[26] LI R Q,LI Y R,ZHENG H C,et al.Building the sequence map of the human pan-genome[J].Nat Biotechnol,2010,28(1):57-63.
[27] GOODWIN S,MCPHERSON J D,MCCOMBIE W R.Coming of age:ten years of next-generation sequencing technologies[J].Nat Rev Genet,2016,17(6):333-351.
[28] READ B A,KEGEL J,KLUTE M J,et al.Pan genome of the phytoplankton Emiliania underpins its global distribution[J].Nature,2013,499(7457):209-213.
[29] JARVIS E D,MIRARAB S,ABERER A J,et al.Whole-genome analyses resolve early branches in the tree of life of modern birds[J].Science,2014,346(6215):1320-1331.
[30] LI Y H,ZHOU G Y,MA J X,et al.De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits[J].Nat Biotechnol,2014,32(10):1045-1052.
[31] CHEN F,SONG Y F,LI X J,et al.Genome sequences of horticultural plants:past,present,and future[J].Hortic Res,2019,6:112.
[32] LAM E T,HASTIE A,LIN C,et al.Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly[J].Nat Biotechnol,2012,30(8):771-776.
[33] MASCHER M,MUEHLBAUER G J,ROKHSAR D S,et al.Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)[J].Plant J,2013,76(4):718-727.
[34] BURTON J N,ADEY A,PATWARDHAN R P,et al.Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions[J].Nat Biotechnol,2013,31(12):1119-1125.
[35] KAPLAN N,DEKKER J.High-throughput genome scaffolding from in vivo DNA interaction frequency[J].Nat Biotechnol,2013,31(12):1143-1147.
[36] SONG J M,GUAN Z L,HU J L,et al.Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus[J].Nat Plants,2020,6(1):34-45.
[37] JEBB D,HUANG Z X,PIPPEL M,et al.Six reference-quality genomes reveal evolution of bat adaptations[J]. Nature,2020,583(7817):578-584.
[38] MAMIDI S,HEALEY A,HUANG P,et al.A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci[J].Nat Biotechnol,2020,38(10):1203-1210.
[39] GERDOL M,MOREIRA R,CRUZ F,et al.Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel[J].Genome Biol,2020,21(1):275.
[40] QIN P,LU H W,DU H L,et al.Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations[J].Cell,2021,184(13):3542-3558.e16.
[41] QIAO Q,EDGER P P,XUE L,et al.Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)[J].Proc Natl Acad Sci USA,2021,118(45):e2105431118.
[42] HUANG G,WU Z G,PERCY R G,et al.Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution[J].Nat Genet,2020,52(5):516-524.
[43] LI J Y,YUAN D J,WANG P C,et al.Cotton pan-genome retrieves the lost sequences and genes during domestication and selection[J].Genome Biol,2021,22(1):119.
[44] WANG M J,LI J Y,QI Z Y,et al.Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium[J].Nat Genet,2022,54(12):1959-1971.
[45] HOOPES G,MENG X X,HAMILTON J P,et al.Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity[J].Mol Plant,2022,15(3):520-536.
[46] TANG D,JIA Y X,ZHANG J Z,et al.Genome evolution and diversity of wild and cultivated potatoes[J].Nature, 2022,606(7914):535-541.
[47] TONG X L,HAN M J,LU K P,et al.High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation[J].Nat Commun,2022,13(1):5619.
[48] GOLICZ A A,BATLEY J,EDWARDS D.Towards plant pangenomics[J].Plant Biotechnol J,2016,14(4):1099-1105.
[49] HURGOBIN B,EDWARDS D.SNP discovery using a pangenome:has the single reference approach become obsolete?[J]. Biology,2017,6(4):21.
[50] HU Z Q,SUN C,LU K C,et al.EUPAN enables pan-genome studies of a large number of eukaryotic genomes[J]. Bioinformatics,2017,33(15):2408-2409.
[51] SUN C,HU Z Q,ZHENG T Q,et al.RPAN:rice pan-genome browser for~3000 rice genomes[J].Nucleic Acids Res,2017,45(2):597-605.
[52] GAO L,GONDA I,SUN H H,et al.The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor[J].Nat Genet,2019,51(6):1044-1051.
[53] WANG W S,MAULEON R,HU Z Q,et al.Genomic variation in 3,010 diverse accessions of Asian cultivated rice[J].Nature,2018,557(7703):43-49.
[54] HÜBNER S,BERCOVICH N,TODESCO M,et al.Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance[J].Nat Plants,2019,5(1):54-62.
[55] ALONGE M,WANG X G,BENOIT M,et al.Major impacts of widespread structural variation on gene expression and crop improvement in Tomato[J].Cell,2020,182(1):145-161.e23.
[56] GOLICZ A A,BAYER P E,BARKER G C,et al.The pangenome of an agronomically important crop plant Brassica oleracea[J].Nat Commun,2016,7:13390.
[57] LI R Q,ZHU H M,RUAN J,et al.De novo assembly of human genomes with massively parallel short read sequencing[J].Genome Res,2010,20(2):265-272.
[58] HIRSCH C N,FOERSTER J M,JOHNSON J M,et al.Insights into the maize pan-genome and pan-transcriptome[J].Plant Cell,2014,26(1):121-135.
[59] JAYAKODI M,PADMARASU S,HABERER G,et al.The barley pan-genome reveals the hidden legacy of mutation breeding[J].Nature,2020,588(7837):284-289.
[60] WALKOWIAK S,GAO L L,MONAT C,et al.Multiple wheat genomes reveal global variation in modern breeding[J]. Nature,2020,588(7837):277-283.
[61] AGABA M,ISHENGOMA E,MILLER W C,et al.Giraffe genome sequence reveals clues to its unique morphology and physiology[J].Nat Commun,2016,7(1):11519.
[62] JIAO W B,SCHNEEBERGER K.Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics[J].Nat Commun,2020,11(1):989.
[63] SUN C,HUANG J X,WANG Y,et al.Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits[J].Mol Biol Evol,2021,38(2):486-501.
[64] DANILEVICZ M F,TAY FERNANDEZ C G,MARSH J I,et al.Plant pangenomics:approaches,applications and advancements[J].Curr Opin Plant Biol,2020,54:18-25.
[65] TAO Y F,JORDAN D R,MACE E S.A graph-based pan-genome guides biological discovery[J].Mol Plant,2020,13(9):1247-1249.
[66] BAYER P E,GOLICZ A A,SCHEBEN A,et al.Plant pan-genomes are the new reference[J].Nat Plants,2020, 6(8):914-920.
[67] GARRISON E,SIRÉN J,NOVAK A M,et al.Variation graph toolkit improves read mapping by representing genetic variation in the reference[J].Nat Biotechnol,2018,36(9):875-879.
[68] LI H,FENG X W,CHU C.The design and construction of reference pangenome graphs with minigraph[J]. Genome Biol,2020,21(1):265.
[69] PATEN B,EARL D,NGUYEN N,et al.Cactus:Algorithms for genome multiple sequence alignment[J].Genome Res,2011,21(9):1512-1528.
[70] LIU Y,DU H L,LI P C,et al.Pan-genome of wild and cultivated soybeans[J].Cell,2020,182(1):162-176.e13.
[71] ZHANG X H,LIU T J,WANG J L,et al.Pan-genome of Raphanus highlights genetic variation and introgression among domesticated,wild,and weedy radishes[J].Mol Plant,2021,14(12):2032-2055.
[72] CAI X,CHANG L C,ZHANG T T,et al.Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa[J].Genome Biol,2021,22(1):166.
[73] ZHOU Y,ZHANG Z Y,BAO Z G,et al.Graph pangenome captures missing heritability and empowers tomato breeding[J].Nature,2022,606(7914):527-534.
[74] VARSHNEY R K,ROORKIWAL M,SUN S,et al.A chickpea genetic variation map based on the sequencing of 3,366 genomes[J].Nature,2021,599(7886):622-627.
[75] LARSON G,DOBNEY K,ALBARELLA U,et al.Worldwide phylogeography of wild boar reveals multiple centers of pig domestication[J].Science,2005,307(5715):1618-1621.
[76] GROENEN M A M,ARCHIBALD A L,UENISHI H,et al.Analyses of pig genomes provide insight into porcine demography and evolution[J].Nature,2012,491(7424):393-398.
[77] LI M Z,CHEN L,TIAN S L,et al.Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies[J].Genome Res,2017,27(5):865-874.
[78] TIAN X M,LI R,FU W W,et al.Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data[J].Sci China Life Sci,2020,63(5):750-763.
[79] JIANG Y F,WANG S,WANG C L,et al.Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs[J].iScience,2023,26(3):106119.
[80] CRYSNANTO D,PAUSCH H.Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery[J].Genome Biol,2020,21(1):184.
[81] CRYSNANTO D,LEONARD A S,FANG Z H,et al.Novel functional sequences uncovered through a bovine multiassembly graph[J].Proc Natl Acad Sci U S A,2021,118(20):e2101056118.
[82] GONG M,YANG P,FANG W W,et al.Building a cattle pan-genome using more de novo assemblies[J].J Genet Genomics,2022,49(9):906-908.
[83] TALENTI A,POWELL J,HEMMINK J D,et al.A cattle graph genome incorporating global breed diversity[J]. Nat Commun,2022,13(1):910.
[84] LEONARD A S,CRYSNANTO D,FANG Z H,et al.Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies[J].Nat Commun,2022,13(1):3012.
[85] ZHOU Y,YANG L,HAN X T,et al.Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations,providing new insights into their diversity and evolutionary history[J].Genome Res,2022,32(8):1585-1601.
[86] LI R,FU W W,SU R,et al.Towards the complete goat pan-genome by recovering missing genomic segments from the reference genome[J].Front Genet,2019,10:1169.
[87] LI R,GONG M,ZHANG X M,et al.The first sheep graph pan-genome reveals the spectrum of structural variations and their effects on different tail phenotypes[J/OL].bioRxiv,2021,doi:10.1101/2021.12.22.472709.
[88] ZHANG G J,LI C,LI Q Y,et al.Comparative genomics reveals insights into avian genome evolution and adaptation[J].Science,2014,346(6215):1311-1320.
[89] LOVELL P V,WIRTHLIN M,WILHELM L,et al.Conserved syntenic clusters of protein coding genes are missing in birds[J].Genome Biol,2014,15(12):565.
[90] WANG K J,HU H F,TIAN Y D,et al.The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size[J].Mol Biol Evol,2021,38(11):5066-5081.
[91] LI M,SUN C J,XU N Y,et al.De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on microchromosomes and subtelomeric regions[J].Mol Biol Evol,2022,39(4):msac066.