Acta Veterinaria et Zootechnica Sinica ›› 2023, Vol. 54 ›› Issue (9): 3595-3604.doi: 10.11843/j.issn.0366-6964.2023.09.001
• REVIEW • Previous Articles Next Articles
LI Ke, WANG Yulong, LI Dong, SHI Xin'e, YANG Gongshe, YU Taiyong*
Received:
2023-02-06
Published:
2023-09-22
CLC Number:
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.
[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. |
[1] | WANG Yaxin, WANG Jing, TIAN Xuekai, YANG Gongshe, YU Taiyong. Application of Multi-omics Technology in the Study of Important Economic Traits of Livestock and Poultry [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1842-1853. |
[2] | XU Tingting, QI Fenfang, HUANG Shihui, NIU Xi, LI Sheng, RAN Xueqin, WANG Jiafu, XIE Jian. Study of the Polymorphisms of Structural Variation and the Expression of MAP3K4 gene in Xiang Pig [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 5046-5055. |
[3] | XIA Chunqiu, WAN Fachun, LIU Lei, SHEN Weijun, XIAO Dingfu. Valine: Biological Function and Application in Livestock and Poultry Diets [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4502-4513. |
[4] | ZONG Wencheng, WANG Ligang, SONG Chengyi, WANG Lixian, ZHANG Longchao. Advances of Structural Variation in Pig Genome [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(9): 2833-2844. |
[5] | GUO Haikang, WAN Fachun, SHEN Weijun, WANG Zuo. Research Progress and Related Regulation Technology on Bacterial Quorum Sensing in the Gastro-intestinal Tract of Livestock and Poultry [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(6): 1678-1688. |
[6] | SHU Ze, WANG Lixian, WANG Ligang. Research Progress of Alternative Splicing and Its Application in Livestock and Poultry Breeding [J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(12): 2911-2920. |
[7] | HU Jing-jie,GUO Xin,LI Ren-wei,GONG Dao-qing,DU Sheng-ming. Pathogenesis Study of Important Pathogens in Livestock and Poultry:An Introduction to a Major Project of National Natural Science Foundation of China [J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2014, 45(12): 2088-2090. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||