Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes [version 1; peer review: 2 approved with reservations]

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding genes, 8 rRNA genes and 48 tRNA genes. Using the cp genome assembly as

[1]  R. Mwanga,et al.  Gene Pool Subdivision of East African Sweetpotato Parental Material , 2018, Crop science.

[2]  M. Rausher,et al.  Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia , 2018, Current Biology.

[3]  Richard G. F. Visser,et al.  De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences , 2017, Front. Plant Sci..

[4]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[5]  D. Haak,et al.  Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data , 2017, BMC Genomics.

[6]  Y. Sakakibara,et al.  Genome sequence and analysis of the Japanese morning glory Ipomoea nil , 2016, Nature Communications.

[7]  Patrick Mardulyn,et al.  NOVOPlasty: de novo assembly of organelle genomes from whole genome data. , 2016, Nucleic acids research.

[8]  H. Daniell,et al.  Chloroplast genomes: diversity, evolution, and applications in genetic engineering , 2016, Genome Biology.

[9]  Dmitry Antipov,et al.  plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data , 2016, bioRxiv.

[10]  Peer Bork,et al.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees , 2016, Nucleic Acids Res..

[11]  G. C. Yencho,et al.  ‘NASPOT 12 O’ and ‘NASPOT 13 O’ Sweetpotato , 2016 .

[12]  Sang-Choon Lee,et al.  Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species , 2015, Scientific Reports.

[13]  Lang Yan,et al.  Analyses of the Complete Genome and Gene Expression of Chloroplast of Sweet Potato [Ipomoea batata] , 2015, PloS one.

[14]  A. Kotorashvili,et al.  Complete chloroplast DNA sequences of Zanduri wheat (Triticum spp.) , 2015, Genetic Resources and Crop Evolution.

[15]  Sara Goodwin,et al.  Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome , 2015, bioRxiv.

[16]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

[17]  Shilin Chen,et al.  High-accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy. , 2014, The New phytologist.

[18]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[19]  Aaron A. Klammer,et al.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.

[20]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[21]  Xiaowu Wang,et al.  Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology , 2012, Front. Plant Sci..

[22]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[23]  D. McKey,et al.  Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces , 2011, Molecular ecology.

[24]  Wenqin Wang,et al.  High-Throughput Sequencing of Three Lemnoideae (Duckweeds) Chloroplast Genomes from Total DNA , 2011, PloS one.

[25]  G. C. Yencho,et al.  ‘NASPOT 11’, a Sweetpotato Cultivar Bred by a Participatory Plant-breeding Approach in Uganda , 2011 .

[26]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[27]  R. Mwanga,et al.  'NASPOT 7', 'NASPOT 8', 'NASPOT 9 O', 'NASPOT 10 O', and 'Dimbuka-Bukulula' sweetpotato. , 2009 .

[28]  T. Mockler,et al.  Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology , 2008, Nucleic acids research.

[29]  A. Kanagaraj,et al.  The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron , 2008, Theoretical and Applied Genetics.

[30]  P. E. Abidin,et al.  Release of Two Orange-fleshed Sweetpotato Cultivars, ‘SPK004’ (‘Kakamega’) and ‘Ejumula’, in Uganda , 2007 .

[31]  Ralph Bock,et al.  OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes , 2007, Current Genetics.

[32]  J. Boore,et al.  Bmc Plant Biology , 2007 .

[33]  J. Tomkins,et al.  Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes , 2007, Theoretical and Applied Genetics.

[34]  Joey Shaw,et al.  Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. , 2007, American journal of botany.

[35]  R. Jansen,et al.  The complete nucleotide sequence of the coffee (Coffea arabica L.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms. , 2007, Plant biotechnology journal.

[36]  Mihai Pop,et al.  Minimus: a fast, lightweight genome assembler , 2007, BMC Bioinformatics.

[37]  R. Jansen,et al.  The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms , 2006, BMC Plant Biology.

[38]  Sonja Siljak-Yakovlev,et al.  The origin and evolution of sweet potato (Ipomoea batatas Lam.) and its wild relatives through the cytogenetic approaches. , 2006, Plant science : an international journal of experimental plant biology.

[39]  Amit Dhingra,et al.  Rapid and accurate pyrosequencing of angiosperm plastid genomes , 2006, BMC Plant Biology.

[40]  J. Tomkins,et al.  Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes , 2006, Theoretical and Applied Genetics.

[41]  P. E. Abidin,et al.  Adaptation and stability analysis of sweet potato varieties for low-input systems in Uganda , 2005 .

[42]  T. Wood,et al.  Complete Chloroplast Genome Sequence of Glycine max and Comparative Analyses with other Legume Genomes , 2005, Plant Molecular Biology.

[43]  S. Wyman,et al.  Automatic annotation of organellar genomes with DOGMA , 2004 .

[44]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[45]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[46]  G. C. Yencho,et al.  Release of Six Sweetpotato Cultivars ('NASPOT 1∑ to 'NASPOT 6∑ ) in , 2003 .

[47]  Sabine Cornelsen,et al.  Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[48]  E. Carey,et al.  Release of Five Sweetpotato Cultivars in Uganda , 2001 .

[49]  Mei Sun,et al.  Genetic diversity and relationships of sweetpotato and its wild relatives in Ipomoea series Batatas (Convolvulaceae) as revealed by inter-simple sequence repeat (ISSR) and restriction analysis of chloroplast DNA , 2000, Theoretical and Applied Genetics.

[50]  F. Takaiwa,et al.  The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression , 1986, The EMBO journal.

[51]  H. Kössel,et al.  Cotranscription and processing of 23S, 4.5S and 5S rRNA in chloroplasts from Zea mays. , 1984, Nucleic acids research.

[52]  James B. Hicks,et al.  A plant DNA minipreparation: Version II , 1983, Plant Molecular Biology Reporter.

[53]  P. Dukes,et al.  ‘Resisto’ Sweet Potato , 1983, HortScience.

[54]  G. C. Yencho,et al.  Sweetpotato ( Ipomoea batatas L.) , 2017 .

[55]  G. C. Yencho,et al.  Advances in sweetpotato breeding from 1992 to 2012. , 2015 .

[56]  R. Jarret,et al.  Phylogenetics and diversification of morning glories (tribe Ipomoeeae, Convolvulaceae) based on whole plastome sequences. , 2014, American journal of botany.

[57]  Songnian Hu,et al.  An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform , 2011, Plant Methods.

[58]  A. Sandelius,et al.  The chloroplast : interactions with the environment , 2010 .

[59]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[60]  E. Mace,et al.  A high-throughput DNA extraction protocol for tropical molecular breeding programs , 2007, Plant Molecular Biology Reporter.

[61]  Huanming Yang,et al.  A Comparison of Rice Chloroplast Genomes , 2004 .