506:
over an
Illumina-only assembly. Another plant genome that was recently published that used long reads in combination with short reads is the improved assembly of the apple genome. In this project a hybrid approach was used, combining different data types from sequencing technologies. The sequences used came from: PacBio RS II, Illumina paired-end reads (PE) and Illumina mate- pair reads (MP). As a first step an assembly from Illumina paired-end reads was performed using a well-known de novo assembly software SOAPdevo. Then using a hybrid assembly pipeline DBG2OLC. the contigs obtained at the first step and the long reads from PacBio were combined. The assembly was then polished with the help of Illumina paired-end reads by mapping them to the contigs using BWA-MEM. By mapping the mate-pair reads on the corrected contigs they scaffold the assembly. Further BioNano optical mapping analysis with a total length of 649.7 Mb, were used in the hybrid assembly pipeline together with the scaffolds obtained from the previous step. The resulting scaffolds were anchored to a genetic map constructed from 15,417 single-nucleotide
455:, 2010, an economically important tropical fruit tree crop and the primary source of cocoa. The genome was sequenced in a consortium, "The International Cocoa Genome Sequencing consortium (ICGS) " and produced a total of 17.6 million 454 single end reads, 8.8 million 454 paired-end reads, 398.0 million Illumina paired-end reads and about 88,000 Sanger BAC reads. First by using genome assembly software, Newbler, an assembly was produced with 25,912 contigs and 4,792 scaffolds from the reads obtained from Roche/454 and Sanger raw data. This had a total length of 326.9 Mb, which represents 76% of the estimated genome size. The Illumina reads were used to complement the
25:
126:(NGS), and therefore most plant genome assemblies available that used NGS alone are highly fragmented, contain large numbers of contigs, and genome regions are not finished. Highly repetitive sequences, often larger than 10kbp, are the main challenge in plants. Most of the chromosomal sequences are produced by the activity of
391:
Sanger technology on ABI3730x1 sequencers. To assemble the reads, Arachne, 2002, a software designed to analyze reads obtained from both ends of plasmid clones, was used. In total 6.2 million paired-end tag reads were produced. The software produced 20.784 contigs that were combined into 3,830 supercontigs, having an
510:(SNPs) markers. For better understanding of the number and diversity of genes that were identified, ribonucleic acid RNA-seq, were used. The resulted genome has a dimension of 643.2 Mb getting closer to the estimated genome size than the previous published assembly and a smaller number of protein-coding- genes.
423:
Due to its relatively cheap cost in comparison to previous methods, most of the recent plant genomes were sequenced and assembled using data from NGS (next-generation- sequencing) technology. In general the NGS data are used in combination with Sanger
Sequencing technology or long-reads obtained from
390:
The draft genome of grapevine is the fourth genome published for a flowering plant and the first from a fruit crop. The sequences of the genome were obtained from different types of libraries, like plasmids, fosmids and BACs. All the data were generated by paired-end sequencing of cloned insert using
352:
Sanger clone-by-clone strategy has the advantage of working in small units, which reduces the complexity and computational requirements, as well as minimized problems associated with the misassembly of highly repetitive DNA and therefore is an attractive solution in assembling plant genomes and other
270:
With BAC, the genome is first split into smaller pieces with the location recorded. The pieces of DNA are then inserted into BAC clones that are further multiplied by inserting them into bacterial cells that grow very fast. These pieces are further fragmented into overlapping smaller pieces that are
209:
database and contains resources for a reduced number of sequenced plant species (45, Oct. 2017). It mainly provides genome sequences, gene models, functional annotations and polymorphic loci. For some of the plant species, additional information is provided including population structure, individual
505:
having a genome size estimated at 989 Mb. For this, a 60× coverage of the genome was generated, with 20% of the reads larger than 20 kb. Data were assembled using PacBio's hierarchical genome assembly process (HGAP), and showed that long-read assemblies revealed a 63-fold improvement in contig size
365:
sequencing technology there is no order for the fragments that are sequenced. The DNA is randomly sheared and cloned fragments are sequenced and assembled using computational methods. This technology reduced the cost and the time associated with construction of the maps and relies on computational
220:
Plant Genome DataBase Japan (PGDBj) is a website that contains information related to genomes of model and crop plants from databases. It has three main components: ortholog db, DNA marker and linkage map db, and plant resource db, where multiple plant resources accumulated by different institutes
189:), began in September 1997, when scientists from many nations agreed to an international collaboration to sequence the rice genome, forming "The International Rice Genome Sequencing Project" (IRGSP). At an estimated size between 400 and 430 Mb, approximatively four times larger in dimensions than
500:
RS 2). In general, long reads from TGS have relatively high error rates (~10% on average) and therefore repeated sequencing of the same DNA fragments is required. The price of such technology is still quite high and therefore is generally used in combination with short reads from NGS. One of the
440:
reads in combination with Sanger sequences. 72.2-fold genome coverage high quality base pairs were generated from which 3.9-fold coverage was provided from Sanger and the
Illumina GA reads provided 68.3-fold coverage. From this two assemblies were produced based on the sequencing technology. The
398:
The anchorage of the supercontigs along the genome was performed first by joining supercontigs together using paired BAC end sequences. The resulting ultracontigs and the remained supercontigs were then aligned along the genetic map of the genome. Later improvements of this strategy enabled the
310:
positions and orientations. End sequences from 47,788 BAC clones were used to extend contigs from anchored BACs and to select a minimum tiling path. A total of 1,569 clones found in minimum tiling path were selected and sequenced. Direct PCR products were used to clone remaining gaps, and YACs
337:), is the last plant genome project primarily based on Sanger BAC-by-BAC strategy. The genome size of Maize, 2.3 Gb and 10 chromosomes, is significantly larger than that of rice and Arabidopsis. To assemble the genome of maize a set of 16,848 minimally overlapping BAC clones derived
196:
Between 2000 and 2008 in total 10 plant genomes were published while in 2012 alone, 13 plant genomes were published. Since then the number was constantly increasing, and now more than 400 plant genomes are available in the NCBI genome database, of which 72 were re-annotated .
496:(TGS) some of the limitations from previous methods of sequencing and assembling plant genomes have started to be addressed. This technology is characterized by the parallel sequencing of single molecules of DNA, that results in sequences up to 54 kbp length (
513:
The use of long reads in the plant genome assemblies became more popular, for reducing the number of scaffolds and increasing the quality of the genome by improving the assembly and coverage in regions that are not clearly defined by NGS assembly.
449:(367 Mb). A genetic map was constructed to anchor the assembled genome. 72.8% of the assembled sequences were successfully anchored onto the seven chromosomes. Another plant genome that combined NGS with Sanger sequencing was the genome of
459:
assembly, by aligning the short reads on the cocoa genome assembly using the SOAP software. A similar strategy that combined NGS reads and Sanger
Sequencing was used for other important plant species like the first published apple genome
353:
complex eukaryotic genomes. The main disadvantages of this method are the costs and the resources required. The cost of the first plant genome assemblies was estimated between 70 million dollars and 200 million dollars per assembly.
348:
and sequences from libraries with methyl-filtered DNA (libraries that uses the knowledge that the bases in genic sequences tends to be less heavily methylated than those in non-genic regions) and high C0 t techniques.
224:
PlantsDB is a resource for analysing and storing genetic and genomic information from various plants, and offers tools to query these data and to perform comparative analysis with the help of in-house tools.
943:
Flavell RB, Gale MD, O'dell M, Murphy G, Moore G, Lucas H (1993). "Molecular organization of genes and repeats in the large cereal genomes and implications for the isolation of genes by chromosome walking".
271:
placed into a vector and then sequenced. The small pieces are then assembled into contigs by overlapping them. Next, using the map from the first step the contigs are assembled back into the chromosomes.
142:(LTR) retrotransposons are predominant and constitute from 15% to 90% of the genome. Polyploidy is another challenge in assembling a plant genome, and it is estimated that ~80% of plants are polyploids.
274:
The first complete plant genome assembly (also the first plant genome published) that used this type of technique was
Arabidopsis thaliana, in 2000. Different large-insert libraries like BACs,
176:) has convenient traits, such as a small nuclear genome (135Mbp) and a short generation time (8 weeks from seed to seed). The genome has five chromosomes reflecting approximately 4% of the
251:
In general, for sequencing and assembling large and complex genomes like plants, different strategies are used, based on the technologies available at that time when the project started.
441:
resulting contigs were compared between them, resulting in a total length of the assembled genome of 243.5 Mb. The result is about 30% smaller than the genome size estimated by
2448:
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. (June 2013). "Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data".
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1181:
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46:
33:
1232:
Bolser D, Staines DM, Pritchard E, Kersey P (2016). "Ensembl Plants: Integrating Tools for
Visualizing, Mining, and Analyzing Plant Genomics Data".
315:
sequences. The resulting sequenced regions were 115.4 Mb of the 125 Mb predicted size of the genome and a total of 25,498 of protein-coding genes.
263:
for each chromosome before the sequencing, and rely on libraries made from large-insert clones. The most common type of large-insert clone is the
1123:
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, et al. (March 2000). "The genome sequence of
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The C. elegans
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1504:"Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model"
232:
that integrates plant sequence data and comparative genomic methods, and performs evolutionary analysis within the green plant lineage (
532:"Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage"
283:
1429:
1388:
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1249:
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501:
first plant genome that used long-reads from TGS, Pacific
Biosciences in combination with short reads from NGS was the genome of
392:
240:
264:
114:
and repetitive elements than species from other kingdoms. One of the most complex plant genome assemblies available is that of
1330:
Nakaya A, Ichihara H, Asamizu E, Shirasawa S, Nakamura Y, Tabata S, Hirakawa H (2017). "Plant Genome DataBase Japan (PGDBJ)".
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2611:"DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies"
1863:
493:
425:
287:
279:
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38:
295:
806:
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275:
849:
Lanciano S, Carpentier MC, Llauro C, Jobet E, Robakowska-Hyzorek D, Lasserre E, et al. (February 2017).
2715:
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401:
362:
299:
169:
127:
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a total of 3,401 mapped clones in a minimum tiling path were selected from the physical map and assembled.
1140:
507:
165:
1273:
Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, et al. (November 2016).
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2622:
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1995:
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156:
139:
1982:
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630:
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497:
467:
383:
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2532:
2473:
2404:
Lee H, Gurtowski J, Yoo S, Nattestad M, Marcus S, Goodwin S, McCombie WR, Schatz M (2016-04-13).
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1002:
831:
739:
696:
1702:
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, et al. (September 2007).
583:"The C-value enigma in plants and animals: a review of parallels and an appeal for partnership"
530:
Moreau H, Verhelst B, Couloux A, Derelle E, Rombauts S, Grimsley N, et al. (August 2012).
2648:
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2013:
1964:
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1416:. Methods in Molecular Biology. Vol. 1533. Humana Press, New York, NY. pp. 183–200.
1394:
1384:
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1236:. Methods in Molecular Biology. Vol. 1374. Humana Press, New York, NY. pp. 115–140.
1206:
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994:
957:
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882:
851:"Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants"
823:
788:
731:
661:
612:
563:
345:
151:
1704:"The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla"
1453:
Van Bel M, Silvestri F, Weitz EM, Kreft L, Botzki A, Coppens F, Vandepoele K (January 2022).
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2666:
Li H (2013). "Aligning sequence reads, clone sequences and assembly contigs with BWA- MEM".
2638:
2630:
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2563:
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2457:
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2003:
1954:
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1375:. Methods in Molecular Biology. Vol. 1533. New York, NY: Humana Press. pp. 33–44.
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1198:
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1089:
1044:
986:
949:
917:
900:
Michael TP, VanBuren R (April 2015). "Progress, challenges and the future of crop genomes".
872:
862:
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770:
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602:
594:
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446:
291:
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from combinations of physical and genetic map were selected and sequenced. The assembly on
2710:
2433:
van Deynze A (2015). "Using spinach to compare technologies for whole genome assemblies".
451:
407:
206:
131:
2031:
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, et al. (January 2010).
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size. The genome was sequenced and annotated by the Arabidopsis Genome Initiative (AGI).
2626:
2382:
2329:
2129:
Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, et al. (February 2011).
2048:
1999:
1950:
1835:
1778:
1763:"The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)"
1719:
1667:
1620:
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1290:
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The genome of plants can vary in their structure and complexity from small genomes like
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2313:
1795:
1762:
1528:
1503:
1479:
1454:
1307:
1274:
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Meyers LA, Levin DA (June 2006). "On the abundance of polyploids in flowering plants".
877:
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783:
759:"Repetitive DNA and next-generation sequencing: computational challenges and solutions"
758:
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135:
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91:
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was performed in addition with external information data. The data was obtained from
233:
2552:"SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler"
2536:
2257:
1593:
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Vandepoele K (2017). "A Guide to the PLAZA 3.0 Plant Comparative Genomic Database".
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243:(TAIR) maintains a web database of the "model higher plant Arabidopsis Thaliana ".
185:
177:
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1628:
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Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, et al. (April 2008).
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647:
115:
103:
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Swan KA, Curtis DE, McKusick KB, Voinov AV, Mapa FA, Cancilla MR (July 2002).
1519:
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119:
79:
1025:"Analysis of the genome sequence of the flowering plant Arabidopsis thaliana"
548:
1843:
1819:
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1202:
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106:(15 Mbp). to very large and complex genomes that have typically much higher
90:(deoxyribonucleic acid) fragments that are obtained from different types of
83:
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2587:
2568:
2528:
2469:
2355:
2298:
2249:
2208:
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2017:
1968:
1935:"Genome sequencing and analysis of the model grass Brachypodium distachyon"
1919:
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1058:
998:
929:
886:
827:
792:
735:
665:
616:
567:
130:(MGEs) in the plant genomes. MGEs are divided into two classes: class I or
24:
2314:"The tomato genome sequence provides insights into fleshy fruit evolution"
2271:
Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, et al. (January 2013).
1109:
2550:
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. (December 2012).
1738:
598:
429:
312:
260:
2337:
2222:
Wang K, Wang Z, Li F, Ye W, Wang J, Song G, et al. (October 2012).
2088:
Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, et al. (December 2009).
2057:
2032:
2008:
1983:
1959:
1934:
1933:
The International Brachypodium Initiative; et al. (February 2010).
1820:"The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)"
1786:
1728:
1703:
259:
Clone-by-clone sequencing strategies are based on the construction of a
2519:
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502:
412:
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376:
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107:
71:
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774:
727:
2418:
2405:
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2089:
1275:"Gramene Database: Navigating Plant Comparative Genomics Resources"
714:
Shendure J, Ji H (October 2008). "Next-generation DNA sequencing".
2672:
1676:
1651:
461:
341:
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were constructed. The physical maps were integrated together with
173:
75:
2183:"The genome of the domesticated apple (Malus × domestica Borkh.)"
369:
A considerable number of important plant genomes like grapevine (
2687:
1984:"The Sorghum bicolor genome and the diversification of grasses"
286:(TACs) were combined to assemble the genome. From clones with
87:
18:
1652:"US firm's bid to sequence rice genome causes stir in Japan"
632:"Sequencing and assembly of the 22-gb loblolly pine genome"
2224:"The draft genome of a diploid cotton Gossypium raimondii"
193:, rice has the smallest of the major cereal crop genomes.
2688:"Bionano: Transforming the Way the World Sees the Genome"
387:) were sequenced and assembled with Sanger WGS strategy.
2406:"Third-generation sequencing and the future of genomics"
1886:"High-throughput gene mapping in Caenorhabditis elegans"
395:
value of 64kb. Supercontigs had a total size of 498 Mb.
160:, was finished in 2000, being the third multicellular
979:
Evolution; International Journal of Organic Evolution
333:
One of the most important crops in the world, maize (
213:
Gramene is an online web database resource for plant
2273:"The draft genome of sweet orange (Citrus sinensis)"
1023:The Arabidopsis Genome Initiative (December 2000).
2609:Ye C, Hill CM, Wu S, Ruan J, Ma ZS (August 2016).
436:), was one of the plant genomes that used the NGS
217:and pathway analysis based on Ensembl technology.
183:The initiative for sequencing the genome of rice (
172:. Arabidopsis, unlike other plants' genomes (e.g.
2033:"Genome sequence of the palaeopolyploid soybean"
2090:"The genome of the cucumber, Cucumis sativus L"
284:transformation-competent artificial chromosomes
8:
2435:Plant & Animal Genomics XXIII Conference
757:Treangen TJ, Salzberg SL (November 2011).
2671:
2642:
2577:
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2007:
1958:
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948:. Dordrecht: Springer. pp. 199–213.
876:
866:
782:
655:
606:
557:
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210:genotypes, linkage, and phenotype data.
124:next-generation- sequencing technologies
49:of all important aspects of the article.
522:
318:To sequence and assemble the genome of
45:Please consider expanding the lead to
2312:Tomato Genome Consortium (May 2012).
2176:
2174:
1697:
1695:
1551:
1549:
1547:
1176:
1174:
1172:
1018:
1016:
228:PLAZA is another online resource for
7:
290:, by comparison of the patterns and
326:), the same strategy was used. For
122:using only short reads provided by
14:
472:), draft genome of sweet orange (
357:Sanger whole-genome shotgun (WGS)
78:species, which is assembled into
902:Current Opinion in Plant Biology
808:Theoretical and Applied Genetics
445:of isolated nuclei stained with
311:allowed the characterization of
288:restriction fragment fingerprint
241:Arabidopsis Information Resource
150:The first complete plant genome
23:
2131:"The genome of Theobroma cacao"
1866:from the original on 2023-05-29
478:) and the domesticated tomato (
265:bacterial artificial chromosome
37:may be too short to adequately
47:provide an accessible overview
1:
2391:10.1080/14772000.2015.1099575
1629:10.1016/j.tplants.2010.10.005
1155:10.1126/science.287.5461.2185
1094:10.1126/science.282.5396.2012
2371:Systematics and Biodiversity
1422:10.1007/978-1-4939-6658-5_10
954:10.1007/978-94-011-1510-0_16
868:10.1371/journal.pgen.1006630
1381:10.1007/978-1-4939-6658-5_2
1340:10.1007/978-1-4939-6658-5_3
1242:10.1007/978-1-4939-3167-5_6
648:10.1534/genetics.113.159715
581:Gregory TR (January 2005).
494:third-generation sequencing
426:third generation sequencing
280:yeast artificial chromosome
2732:
419:Next-generation sequencing
1299:10.1016/j.cpb.2016.12.005
922:10.1016/j.pbi.2015.02.002
693:10.1007/s11032-009-9357-9
296:polymerase chain reaction
276:P1 artificial chromosomes
205:EnsemblPlants is part of
1826:(Submitted manuscript).
1650:Saegusa A (April 1999).
1414:Plant Genomics Databases
1373:Plant Genomics Databases
1332:Plant Genomics Databases
763:Nature Reviews. Genetics
549:10.1186/gb-2012-13-8-r74
70:represents the complete
1844:10.1126/science.1128691
1609:Trends in Plant Science
1578:10.1126/science.1178534
1520:10.1093/database/baw018
1203:10.1126/science.1068275
402:Brachypodium distachyon
164:genome published after
128:mobile genetic elements
2569:10.1186/2047-217X-1-18
1459:Nucleic Acids Research
492:With the emergence of
16:Genomic plant sequence
1279:Current Plant Biology
255:Sanger clone-by-clone
140:long- terminal repeat
68:plant genome assembly
1471:10.1093/nar/gkab1024
1234:Plant Bioinformatics
716:Nature Biotechnology
481:Solanum lycopersicum
428:. The genome of the
230:comparative genomics
215:comparative genomics
157:Arabidopsis thaliana
2627:2016NatSR...631900Y
2383:2016SyBio..14....1B
2338:10.1038/nature11119
2330:2012Natur.485..635T
2058:10.1038/nature08670
2049:2010Natur.463..178S
2009:10.1038/nature07723
2000:2009Natur.457..551P
1960:10.1038/nature08747
1951:2010Natur.463..763T
1836:2006Sci...313.1596T
1830:(5793): 1596–1604.
1787:10.1038/nature06856
1779:2008Natur.452..991M
1729:10.1038/nature06148
1720:2007Natur.449..463J
1668:1999Natur.398..545S
1621:2011TPS....16...77F
1570:2009Sci...326.1112S
1564:(5956): 1112–1115.
1465:(D1): D1468–D1474.
1291:2016CPBio...7...10G
1195:2002Sci...296...92G
1137:2000Sci...287.2185.
1131:(5461): 2185–2195.
1086:1998Sci...282.2012.
1080:(5396): 2012–2018.
1041:2000Natur.408..796T
914:2015COPB...24...71M
384:Populus trichocarpa
381:), and cottonwood (
247:Assembly strategies
2615:Scientific Reports
2462:10.1038/nmeth.2474
820:10.1007/BF00222197
681:Molecular Breeding
599:10.1093/aob/mci009
134:, and class II or
110:, higher rates of
2635:10.1038/srep31900
2324:(7400): 635–641.
2234:(10): 1098–1103.
2100:(12): 1275–1281.
2043:(7278): 178–183.
1994:(7229): 551–556.
1945:(7282): 763–768.
1902:10.1101/gr.208902
1773:(7190): 991–996.
1714:(7161): 463–467.
1035:(6814): 796–815.
946:Chromosomes Today
722:(10): 1135–1145.
469:Gossypium Raimond
64:
63:
2723:
2696:
2695:
2684:
2678:
2677:
2675:
2663:
2657:
2656:
2646:
2606:
2600:
2599:
2581:
2571:
2547:
2541:
2540:
2522:
2512:
2503:(7): 1099–1106.
2488:
2482:
2481:
2445:
2439:
2438:
2430:
2424:
2423:
2421:
2401:
2395:
2394:
2366:
2360:
2359:
2349:
2309:
2303:
2302:
2292:
2268:
2262:
2261:
2243:
2219:
2213:
2212:
2202:
2178:
2169:
2168:
2150:
2126:
2120:
2119:
2109:
2085:
2079:
2078:
2060:
2028:
2022:
2021:
2011:
1979:
1973:
1972:
1962:
1930:
1924:
1923:
1913:
1896:(7): 1100–1105.
1881:
1875:
1874:
1872:
1871:
1815:
1809:
1808:
1798:
1758:
1752:
1751:
1741:
1731:
1699:
1690:
1689:
1679:
1647:
1641:
1640:
1604:
1598:
1597:
1553:
1542:
1541:
1531:
1499:
1493:
1492:
1482:
1450:
1444:
1443:
1409:
1403:
1402:
1368:
1362:
1361:
1327:
1321:
1320:
1310:
1270:
1264:
1263:
1229:
1223:
1222:
1189:(5565): 92–100.
1178:
1167:
1166:
1148:
1120:
1114:
1113:
1069:
1063:
1062:
1052:
1050:10.1038/35048692
1020:
1011:
1010:
991:10.1554/05-629.1
985:(6): 1198–1206.
974:
968:
967:
940:
934:
933:
897:
891:
890:
880:
870:
846:
840:
839:
803:
797:
796:
786:
754:
748:
747:
711:
705:
704:
676:
670:
669:
659:
627:
621:
620:
610:
587:Annals of Botany
578:
572:
571:
561:
551:
527:
488:Third-generation
447:propidium iodide
132:retrotransposons
72:genomic sequence
59:
56:
50:
27:
19:
2731:
2730:
2726:
2725:
2724:
2722:
2721:
2720:
2701:
2700:
2699:
2692:bionanogenomics
2686:
2685:
2681:
2665:
2664:
2660:
2608:
2607:
2603:
2549:
2548:
2544:
2510:10.1038/ng.3886
2497:Nature Genetics
2490:
2489:
2485:
2447:
2446:
2442:
2432:
2431:
2427:
2403:
2402:
2398:
2368:
2367:
2363:
2311:
2310:
2306:
2290:10.1038/ng.2472
2277:Nature Genetics
2270:
2269:
2265:
2241:10.1038/ng.2371
2228:Nature Genetics
2221:
2220:
2216:
2193:(10): 833–839.
2187:Nature Genetics
2180:
2179:
2172:
2135:Nature Genetics
2128:
2127:
2123:
2094:Nature Genetics
2087:
2086:
2082:
2030:
2029:
2025:
1981:
1980:
1976:
1932:
1931:
1927:
1890:Genome Research
1883:
1882:
1878:
1869:
1867:
1817:
1816:
1812:
1760:
1759:
1755:
1701:
1700:
1693:
1649:
1648:
1644:
1606:
1605:
1601:
1555:
1554:
1545:
1501:
1500:
1496:
1452:
1451:
1447:
1432:
1411:
1410:
1406:
1391:
1370:
1369:
1365:
1350:
1329:
1328:
1324:
1272:
1271:
1267:
1252:
1231:
1230:
1226:
1180:
1179:
1170:
1146:10.1.1.549.8639
1122:
1121:
1117:
1071:
1070:
1066:
1022:
1021:
1014:
976:
975:
971:
964:
942:
941:
937:
899:
898:
894:
861:(2): e1006630.
848:
847:
843:
805:
804:
800:
775:10.1038/nrg3117
756:
755:
751:
728:10.1038/nbt1486
713:
712:
708:
678:
677:
673:
629:
628:
624:
580:
579:
575:
529:
528:
524:
520:
490:
475:Citrus sinensis
463:Malus domestica
452:Theobroma cacao
434:Cucumis sativus
421:
408:Sorghum bicolor
359:
257:
249:
203:
170:D. melanogaster
148:
136:DNA transposons
100:
60:
54:
51:
44:
32:This article's
28:
17:
12:
11:
5:
2729:
2727:
2719:
2718:
2716:Bioinformatics
2713:
2703:
2702:
2698:
2697:
2679:
2658:
2601:
2542:
2483:
2456:(6): 563–569.
2450:Nature Methods
2440:
2425:
2419:10.1101/048603
2396:
2361:
2304:
2263:
2214:
2200:10.1038/ng.654
2170:
2148:10.1038/ng.736
2141:(2): 101–108.
2121:
2107:10.1038/ng.475
2080:
2023:
1974:
1925:
1876:
1810:
1753:
1691:
1642:
1599:
1543:
1494:
1445:
1430:
1404:
1389:
1363:
1348:
1322:
1265:
1250:
1224:
1168:
1115:
1064:
1012:
969:
962:
935:
892:
841:
814:(2): 157–165.
798:
749:
706:
687:(4): 553–570.
671:
642:(3): 875–890.
622:
593:(1): 133–146.
573:
536:Genome Biology
521:
519:
516:
489:
486:
443:flow cytometry
420:
417:
399:sequencing of
358:
355:
256:
253:
248:
245:
202:
199:
147:
144:
112:heterozygosity
99:
96:
62:
61:
41:the key points
31:
29:
22:
15:
13:
10:
9:
6:
4:
3:
2:
2728:
2717:
2714:
2712:
2709:
2708:
2706:
2693:
2689:
2683:
2680:
2674:
2669:
2662:
2659:
2654:
2650:
2645:
2640:
2636:
2632:
2628:
2624:
2620:
2616:
2612:
2605:
2602:
2597:
2593:
2589:
2585:
2580:
2575:
2570:
2565:
2561:
2557:
2553:
2546:
2543:
2538:
2534:
2530:
2526:
2521:
2516:
2511:
2506:
2502:
2498:
2494:
2487:
2484:
2479:
2475:
2471:
2467:
2463:
2459:
2455:
2451:
2444:
2441:
2436:
2429:
2426:
2420:
2415:
2411:
2407:
2400:
2397:
2392:
2388:
2384:
2380:
2376:
2372:
2365:
2362:
2357:
2353:
2348:
2343:
2339:
2335:
2331:
2327:
2323:
2319:
2315:
2308:
2305:
2300:
2296:
2291:
2286:
2282:
2278:
2274:
2267:
2264:
2259:
2255:
2251:
2247:
2242:
2237:
2233:
2229:
2225:
2218:
2215:
2210:
2206:
2201:
2196:
2192:
2188:
2184:
2177:
2175:
2171:
2166:
2162:
2158:
2154:
2149:
2144:
2140:
2136:
2132:
2125:
2122:
2117:
2113:
2108:
2103:
2099:
2095:
2091:
2084:
2081:
2076:
2072:
2068:
2064:
2059:
2054:
2050:
2046:
2042:
2038:
2034:
2027:
2024:
2019:
2015:
2010:
2005:
2001:
1997:
1993:
1989:
1985:
1978:
1975:
1970:
1966:
1961:
1956:
1952:
1948:
1944:
1940:
1936:
1929:
1926:
1921:
1917:
1912:
1907:
1903:
1899:
1895:
1891:
1887:
1880:
1877:
1865:
1861:
1857:
1853:
1849:
1845:
1841:
1837:
1833:
1829:
1825:
1821:
1814:
1811:
1806:
1802:
1797:
1792:
1788:
1784:
1780:
1776:
1772:
1768:
1764:
1757:
1754:
1749:
1745:
1740:
1739:11577/2430527
1735:
1730:
1725:
1721:
1717:
1713:
1709:
1705:
1698:
1696:
1692:
1687:
1683:
1678:
1677:10.1038/19123
1673:
1669:
1665:
1662:(6728): 545.
1661:
1657:
1653:
1646:
1643:
1638:
1634:
1630:
1626:
1622:
1618:
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1600:
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1591:
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1583:
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1567:
1563:
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1548:
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1539:
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1521:
1517:
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1498:
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1481:
1476:
1472:
1468:
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1449:
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1441:
1437:
1433:
1431:9781493966561
1427:
1423:
1419:
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1390:9781493966561
1386:
1382:
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1364:
1359:
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1349:9781493966561
1345:
1341:
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1296:
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1288:
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1276:
1269:
1266:
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1253:
1251:9781493931668
1247:
1243:
1239:
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1200:
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1169:
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1160:
1156:
1152:
1147:
1142:
1138:
1134:
1130:
1126:
1119:
1116:
1111:
1107:
1103:
1099:
1095:
1091:
1087:
1083:
1079:
1075:
1068:
1065:
1060:
1056:
1051:
1046:
1042:
1038:
1034:
1030:
1026:
1019:
1017:
1013:
1008:
1004:
1000:
996:
992:
988:
984:
980:
973:
970:
965:
963:9789401046602
959:
955:
951:
947:
939:
936:
931:
927:
923:
919:
915:
911:
907:
903:
896:
893:
888:
884:
879:
874:
869:
864:
860:
856:
855:PLOS Genetics
852:
845:
842:
837:
833:
829:
825:
821:
817:
813:
809:
802:
799:
794:
790:
785:
780:
776:
772:
768:
764:
760:
753:
750:
745:
741:
737:
733:
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721:
717:
710:
707:
702:
698:
694:
690:
686:
682:
675:
672:
667:
663:
658:
653:
649:
645:
641:
637:
633:
626:
623:
618:
614:
609:
604:
600:
596:
592:
588:
584:
577:
574:
569:
565:
560:
555:
550:
545:
541:
537:
533:
526:
523:
517:
515:
511:
509:
508:polymorphisms
504:
499:
495:
487:
485:
483:
482:
477:
476:
471:
470:
465:
464:
458:
454:
453:
448:
444:
439:
435:
431:
427:
418:
416:
414:
410:
409:
404:
403:
396:
394:
388:
386:
385:
380:
379:
378:Carica papaya
374:
373:
372:Vitis Vinifer
367:
364:
356:
354:
350:
347:
343:
338:
336:
331:
329:
325:
321:
316:
314:
309:
305:
301:
300:physical maps
297:
293:
292:hybridization
289:
285:
281:
277:
272:
268:
266:
262:
254:
252:
246:
244:
242:
237:
235:
234:Viridiplantae
231:
226:
222:
218:
216:
211:
208:
207:EnsemblGenome
200:
198:
194:
192:
188:
187:
181:
179:
175:
171:
167:
163:
159:
158:
153:
145:
143:
141:
138:. In plants,
137:
133:
129:
125:
121:
117:
116:loblolly pine
113:
109:
105:
97:
95:
93:
89:
85:
81:
77:
73:
69:
58:
48:
42:
40:
35:
30:
26:
21:
20:
2691:
2682:
2661:
2621:(1): 31900.
2618:
2614:
2604:
2559:
2555:
2545:
2500:
2496:
2486:
2453:
2449:
2443:
2434:
2428:
2409:
2399:
2374:
2370:
2364:
2321:
2317:
2307:
2283:(1): 59–66.
2280:
2276:
2266:
2231:
2227:
2217:
2190:
2186:
2138:
2134:
2124:
2097:
2093:
2083:
2040:
2036:
2026:
1991:
1987:
1977:
1942:
1938:
1928:
1893:
1889:
1879:
1868:. Retrieved
1827:
1823:
1813:
1770:
1766:
1756:
1711:
1707:
1659:
1655:
1645:
1615:(2): 77–88.
1612:
1608:
1602:
1561:
1557:
1511:
1507:
1497:
1462:
1458:
1448:
1413:
1407:
1372:
1366:
1331:
1325:
1282:
1278:
1268:
1233:
1227:
1186:
1182:
1128:
1124:
1118:
1077:
1073:
1067:
1032:
1028:
982:
978:
972:
945:
938:
905:
901:
895:
858:
854:
844:
811:
807:
801:
769:(1): 36–46.
766:
762:
752:
719:
715:
709:
684:
680:
674:
639:
635:
625:
590:
586:
576:
539:
535:
525:
512:
491:
480:
474:
468:
462:
450:
433:
422:
406:
400:
397:
389:
382:
377:
371:
368:
360:
351:
339:
334:
332:
328:Oryza sativa
327:
323:
320:Oryza sativa
319:
317:
306:to identify
304:genetic maps
273:
269:
258:
250:
238:
227:
223:
219:
212:
204:
195:
190:
186:Oryza sativa
184:
182:
178:human genome
155:
149:
101:
94:technology.
67:
65:
52:
36:
34:lead section
2556:GigaScience
2520:10449/42064
466:), cotton (
375:), papaya (
366:resources.
191:A. thaliana
120:chromosomes
104:green algae
80:chromosomes
2705:Categories
2412:: 048603.
1870:2023-06-19
1514:: baw018.
542:(8): R74.
518:References
298:(PCR) the
282:(YAC) and
166:C. elegans
162:eukaryotic
154:, that of
146:Assemblies
92:sequencing
84:organelles
82:and other
2673:1303.3997
2562:(1): 18.
2478:205421576
1285:: 10–15.
1141:CiteSeerX
1007:198156503
908:: 71–81.
484:) genome
201:Databases
98:Structure
86:by using
55:June 2024
39:summarize
2653:27573208
2588:23587118
2537:24690391
2529:28581499
2470:23644548
2377:(1): 1.
2356:22660326
2299:23179022
2258:38495587
2250:22922876
2209:20802477
2157:21186351
2116:19881527
2067:20075913
2018:19189423
1969:20148030
1920:12097347
1864:Archived
1852:16973872
1805:18432245
1748:17721507
1686:10217128
1637:21081278
1594:21433160
1586:19965430
1538:26989150
1508:Database
1489:34747486
1440:27987171
1399:27987163
1358:27987164
1317:28713666
1260:26519403
1211:11935018
1163:10731132
1059:11130711
999:16892970
930:25703261
887:28212378
836:20591213
828:24173886
793:22124482
736:18846087
701:29239452
666:24653210
636:Genetics
617:15596463
568:22925495
438:Illumina
430:cucumber
335:Zea mays
324:japonica
313:telomere
152:assembly
2644:5004134
2623:Bibcode
2596:2681931
2579:3626529
2410:bioRxiv
2379:Bibcode
2347:3378239
2326:Bibcode
2165:4685532
2075:4372224
2045:Bibcode
1996:Bibcode
1947:Bibcode
1860:7717980
1832:Bibcode
1824:Science
1796:2836516
1775:Bibcode
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