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| 1 | Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library显示文摘Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes,however,the utility of this technology for complex plant genomes is unproven.We evaluated the technology for this purpose by sequencing the 3.5-gigabase(Gb)diploid pepper(Capsicum annuum)genome with a single Linked-Read library.Plant genomes,including pepper,are characterized by long,highly similar repetitive sequences.Accordingly,significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus.With a phased assembly approach,we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion.The Supernova software generated a highly ordered,more contiguous sequence assembly than all currently available C.annuum reference genomes.Over 83%of the final assembly was anchored and oriented using four publicly available de novo linkage maps.A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly.The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and nonpungent peppers,as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes.The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes.This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction. | Amanda M.Hulse-Kemp Shamoni Maheshwari Kevin Stoffel Theresa A.Hill David Jaffe Stephen R.Williams Neil Weisenfeld Srividya Ramakrishnan Vijay Kumar Preyas Shah Michael C.Schatz Deanna M.Church Allen Van Deynze | 2018 | Horticulture Research2018，5，1： | 4 |
| 2 | Enzyme immunoassay based survey of precipitation and surface water for the presence of atrazine, metolachlor and 2,4-D显示文摘 | J. C. Hall T. D. Van Deynze J. Struger C. H. Chan | 1993 | Journal of Environmental Science and Health, Part B1993，，5： | 1 |
| 3 | Diversity in conserved genes in tomato显示文摘 | Van Deynze A Stoffel K Buell C R | 2007 | BMC Genomics2007，8，： | 1 |
| 4 | The inheritance of seed colour and vernalization requirement in Brassica napus using doubled haploid populations显示文摘 | Van Deynze A E Peter K P | 1994 | Euphytica1994，74，： | 1 |
| 5 | The inheritance of'seed colour and vernalization requirement in Brassica napus Using Doubled Haploid Population 显示文摘 | Deynze A V Dawls K | 1994 | Euphytica1994，74，： | 1 |
| 6 | Molecular genetic maps for chromosome 1 in Triticeae species and their relation to chromosomes in rice and oats显示文摘 | van Deynze AE Dubcovsky J Gill KS | 1995 | Genome1995，38，： | 1 |
| 7 | Moleculargenetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat 显示文摘 | Van Deynze A E Dubcovsky J Gill KS | 1995 | Genome1995，38，： | 1 |
| 8 | Sampling nucleotide di- versity in cotton显示文摘 | van Deynze A Stoffel K Lee M | 2009 | BMC Plant Biology2009，9，1： | 1 |
| 9 | Molecular mapping of wheat, Homoeologous group 2显示文摘 | Nelson JC van Deynze AE Autrique E | 1995 | C enome1995，38，： | 1 |
| 10 | Molecular mapping of wheat, Homoeologous group 3显示文摘 | Nelson JC van Deynze AE Autrique E | 1995 | Genome1995，38，： | 1 |
| 11 | Molecular mapping of when, major genes and rearrangements in homoeologous groups 4, 5 and 7显示文摘 | Nelson JC Sorrells ME van Deynze AE | 1995 | Genetics1995，141，： | 1 |
| 12 | Tolerance of switchgrass to extreme soil moisture stress: Ecological implications显示文摘 | Jacob N. Barney J. Jeremiah Mann Guy B. Kyser Eduardo Blumwald Allen Van Deynze Joseph M. DiTomaso | 2009 | Plant Science2009，，6： | 1 |
| 13 | The inheritance of seed colour and vernalization requirement in Brassica napus using doubled haploid populations 显示文摘 | Van Deynze A E Peter K P | 1994 | Euphytica1994，74，： | 1 |
| 14 | Temperature effects on seed colour in black and yellow-seeded rapeseed显示文摘 | Deynze | 1993 | Canadian Journal of Plannt Science1993，73，2： | 1 |
| 15 | Temperature effects on seed color in black - and yellow - seeded rapeseed 显示文摘 | Van Deynze A E Beversdorf W D Pauls K P | 1993 | Can J Plant Sci1993，73，： | 1 |
| 16 | The identification of restriction fragment length polymorphisms linked to seed colour genes in Brassica napus显示文摘 | Van Deynze A E Landry B S Pauls K P | 1995 | Genome1995，38，： | 1 |
| 17 | The inheritance of seed colour and vernalization requirement in Brassica napus using doubled haploid populations显示文摘 | Van Deynze A Pauls K P | 1994 | Euphytica1994，74，： | 1 |
| 18 | Molecular mapping of wheat: maior genes and rearrangements in homoeologous groups 4,5, and 7显示文摘 | NELSON J C SORRELLS M E VAN DEYNZE A E LU Y H ATKINSON M BERNARD M LEROY P FARIS J D ANDERSON J A | 1995 | Genetics1995，141，： | 1 |
| 19 | Molecular-genetic maps for group 1 chromosome of Triticeae species and their relation to chromosomes in rice and oat显示文摘 | VAN DEYNZE A E DUBCOVSKY J GILL K S NELSON J C SORRELLS M E DVORAK J | 1995 | Genome1995，38，： | 1 |
| 20 | Molecular mapping of wheat homoeologous group 2显示文摘 | Nelson J C Van Deynze A E | 1995 | Genome1995，38，： | 1 |
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