Graph construction method impacts variation representation and analyses in a bovine super-pangenome DOI Creative Commons
Alexander S. Leonard, Danang Crysnanto, Xena Marie Mapel

и другие.

Genome biology, Год журнала: 2023, Номер 24(1)

Опубликована: Май 22, 2023

Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, consequently downstream analyses, is largely unknown.We create multi-species super-pangenomes using pggb, cactus, minigraph with the Bos taurus reference sequence eleven haplotype-resolved assemblies taurine indicine cattle, bison, yak, gaur. We recover 221 k nonredundant structural variations (SVs) pangenomes, of which 135 (61%) are common all three. SVs derived assembly-based calling show high agreement consensus calls (96%), validate only a small proportion private each graph. Pggb also incorporate base-level variation, approximately 95% exact matches assembly-derived calls, significantly improves edit rate when realigning compared minigraph. use three investigate 9566 variable number tandem repeats (VNTRs), finding 63% identical predicted repeat counts in graphs, while can over or underestimate count given its approximate coordinate system. examine highly VNTR locus that unit copy impacts expression proximal genes non-coding RNA.Our findings indicate good between pangenome methods individual strengths weaknesses need be considered analysing different types variants assemblies.

Язык: Английский

A draft human pangenome reference DOI Creative Commons
Wen‐Wei Liao, Mobin Asri, Jana Ebler

и другие.

Nature, Год журнала: 2023, Номер 617(7960), С. 312 - 324

Опубликована: Май 10, 2023

Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic sequences 1,115 gene duplications relative to existing reference GRCh38. Roughly 90 additional derived variation. Using our analyse short-read data reduced small variant discovery errors by 34% increased number detected per haplotype 104% compared with GRCh38-based workflows, which enabled typing vast majority sample.

Язык: Английский

Процитировано

598
A graph-based genome and pan-genome variation of the model plant Setaria DOI Creative Commons
Qiang He,

Sha Tang,

Hui Zhi

и другие.

Nature Genetics, Год журнала: 2023, Номер 55(7), С. 1232 - 1242

Опубликована: Июнь 8, 2023

Abstract Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the pan-genome by assembling 110 representative genomes from worldwide collection. The composed 73,528 gene families, which 23.8%, 42.9%, 29.4% 3.9% are core, soft dispensable private genes, respectively; 202,884 nonredundant structural variants were also detected. characterization pan-genomic suggests their importance during foxtail millet domestication improvement, as exemplified identification yield SiGW3 , where 366-bp presence/absence promoter variant accompanies expression variation. We developed graph-based genome performed large-scale genetic studies 68 traits 13 environments, identifying potential genes improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection editing accelerate under climatic conditions.

Язык: Английский

Процитировано

111
The integrated genomics of crop domestication and breeding DOI Creative Commons
Xuehui Huang, Sanwen Huang, Bin Han

и другие.

Cell, Год журнала: 2022, Номер 185(15), С. 2828 - 2839

Опубликована: Май 27, 2022

Язык: Английский

Процитировано

101
A comprehensive overview of cotton genomics, biotechnology and molecular biological studies DOI

Xingpeng Wen,

Zhiwen Chen, Zuoren Yang

и другие.

Science China Life Sciences, Год журнала: 2023, Номер 66(10), С. 2214 - 2256

Опубликована: Март 6, 2023

Язык: Английский

Процитировано

86
Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding DOI Creative Commons
Yaoyao Wu, Dawei Li, Yong Hu

и другие.

Cell, Год журнала: 2023, Номер 186(11), С. 2313 - 2328.e15

Опубликована: Май 1, 2023

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to seed-reproducing diploid. Historical accumulation of deleterious mutations in genomes has hindered development elite inbred lines and hybrids. Utilizing whole-genome phylogeny 92 Solanaceae its sister clade species, we employ an evolutionary strategy identify mutations. The deep reveals genome-wide landscape highly constrained sites, comprising ∼2.4% genome. Based on diploid diversity panel, infer 367,499 variants, which 50% occur at non-coding 15% synonymous sites. Counterintuitively, with relatively high homozygous burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion inferred increases genomic-prediction accuracy yield by 24.7%. Our study generates insights into incidence properties their far-reaching consequences breeding.

Язык: Английский

Процитировано

58
Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons DOI Creative Commons
Shangkun Jin, Zegang Han, Yan Hu

и другие.

Molecular Plant, Год журнала: 2023, Номер 16(4), С. 678 - 693

Опубликована: Фев. 9, 2023

Structural variations (SVs) have long been described as being involved in the origin, adaption, and domestication of species. However, underlying genetic genomic mechanisms are poorly understood. Here, we report a high-quality genome assembly Gossypium barbadense acc. Tanguis, landrace that is closely related to formation extra-long-staple (ELS) cultivated cotton. An SV-based pan-genome (Pan-SV) was then constructed using total 182 593 non-redundant SVs, including 2236 inversions, 97 398 insertions, 82 959 deletions from 11 assembled genomes allopolyploid The utility this Pan-SV demonstrated through population structure analysis genome-wide association studies (GWASs). Using segregation mapping populations produced crossing ELS cotton along with an GWAS, certain SVs responsible for speciation, domestication, improvement tetraploid cottons were identified. Importantly, some presently identified associated yield fiber quality had not previous SNP-based GWAS. In particular, 9-bp insertion or deletion found associate elimination interspecific reproductive isolation between hirsutum G. barbadense. Collectively, study provides new insights into genome-wide, gene-scale linked important agronomic traits major crop species highlights importance during

Язык: Английский

Процитировано

49
A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range DOI Creative Commons
Qichao Lian, Bruno Hüettel,

Birgit Walkemeier

и другие.

Nature Genetics, Год журнала: 2024, Номер 56(5), С. 982 - 991

Опубликована: Апрель 11, 2024

Abstract Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation diverse environments, developed into powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from global species range. We found that genomic colinearity is very conserved, even among geographically genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare typically only single accession. This indicates the karyotype quasi-fixed arms counter-selected. Centromeric regions display higher structural dynamics, divergences core centromeres account most size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being all 40% appearing be dispensable, including 18% private accession, indicating unexplored genic diversity. These new will empower future genetic research.

Язык: Английский

Процитировано

48
A second update to the checklist of the vascular flora alien to Italy DOI
Gabriele Galasso, Fabio Conti, Lorenzo Peruzzi

и другие.

Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, Год журнала: 2024, Номер 158(2), С. 297 - 340

Опубликована: Март 3, 2024

Critical and updated alien species inventories are crucial to properly manage contrast biological invasions. After 6 years, a second update the inventory of vascular flora Italy is presented. It provides details on occurrence at administrative regional level and, for first time, floristic data San Marino. The checklist includes 1782 taxa (1673 species, 28 subspecies, 69 hybrids 12 cultivar groups not attributable specific binomial), distributed in 786 genera 159 families; 2 lycophytes, 13 ferns fern allies, 37 gymnosperms 1730 angiosperms. Among these, 154 archaeophytes 1628 neophytes. currently established 899 (649 naturalized 250 invasive), while 796 casual aliens, 1 assessed, 38 have been confirmed recent times, 4 considered extinct or possibly country, 40 doubtfully occurring Italy, unknown distribution 110 reported by mistake be excluded national level. This allows establish an up-to-date number (10,023) constituting whole (either native alien) Italian flora.

Язык: Английский

Процитировано

46
Technology-enabled great leap in deciphering plant genomes DOI
Lingjuan Xie, Xiaojiao Gong, Kun Yang

и другие.

Nature Plants, Год журнала: 2024, Номер 10(4), С. 551 - 566

Опубликована: Март 20, 2024

Язык: Английский

Процитировано

35
A simple and efficient in planta transformation method based on the active regeneration capacity of plants DOI Creative Commons

Guoguo Mei,

Ao Chen,

Yaru Wang

и другие.

Plant Communications, Год журнала: 2024, Номер 5(4), С. 100822 - 100822

Опубликована: Янв. 21, 2024

Plant genetic transformation strategies serve as essential tools for the engineering and advanced molecular breeding of plants. However, complicated operational protocol low efficiency current restrict modification most plant species. This paper describes development a Regenerative Activity-dependent in Planta Injection Delivery (RAPID) method based on active regeneration capacity In this method, Agrobacterium tumefaciens was delivered to meristems via injection inducing transfected nascence tissues. Stable transgenic plants were obtained by subsequent vegetative propagation positive The successfully applied with strong capacity, including different genotypes sweet potato (Ipomoea batatas), (Solanum tuberosum), bayhops pes-caprae). Compared traditional methods, RAPID has markedly high efficiency, shorter duration, does not require tissue culture procedures. therefore overcomes limitations methods achieving rapid planta transformation, can be potentially wide range species that are capable regeneration.

Язык: Английский

Процитировано

33