Genome Sequencing and Assembly by Long Reads in Plants

Li, Changsheng; Lin, Feng; An, Dong; Wang, Wen-Qin; Rui, Huang

doi:10.3390/genes9010006

Cited by 97 publications

(83 citation statements)

References 66 publications

(104 reference statements)

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“…The accuracy of genome sequencing and assembly of complex genomes is affected by different factors ranging from plant material availability to genome size, GC content, repeat content, ploidy level, sequencing technology, and bioinformatic software [19][20][21][22] . Long-read sequencing technologies, such as those of Pacific Biosciences or Oxford Nanopore Technologies, are currently used for reconstructing Mb-long chromosome sequences or both haplotypes of highly heterozygous genomes [23][24][25][26][27] . Short-read sequencing is less expensive, provides more coverage with the same investment and thus more sequence accuracy, but it leads to more fragmented assemblies.…”

Section: Discussionmentioning

confidence: 99%

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Scalabrin

Toniutti²,

Gaspero

et al. 2020

Sci Rep

118

111

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the genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to lowfrequency derived alleles and highly negative values of Taijma's D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-toeast geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.

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Section: Discussionmentioning

confidence: 99%

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Scalabrin

Toniutti²,

Gaspero

et al. 2020

Sci Rep

118

111

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show abstract

“…Its genome and annotation updates help future research on functional genomics, and also help breeders to simplify their work and enrich the genomics resources of barley. The generation of Tibetan hulless barley high-quality reference genomes also demonstrates the superiority of PacBio long reads sequencing technology for larger genome assembly[50]. Although the genome has a long contig, the scaffold is still a bit short at the state-of-art of the current genome assembly, mainly because of the complexity and data volume of the scaffolding mate-pair library is relatively few.…”

Section: Discussionmentioning

confidence: 99%

Improved high-quality genome assembly and annotation of Tibetan hulless barley

Tashi

Zeng

Li³

et al. 2018

Preprint

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AbstractBackgroundThe Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called “Qingke” in Chinese and “Ne” in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The Tibetan hulless barley in China has about 3500 years of cultivation history, mainly produced in Tibet, Qinghai, Sichuan, Yunnan and other areas. In addition, Tibetan hulless barley has rich nutritional value and outstanding health effects, including the beta glucan, dietary fiber, amylopectin, the contents of trace elements, which are higher than any other cereal crops.FindingsHere, we reported an improved high-quality assembly of Tibetan hulless barley genome with 4.0 Gb in size. We employed the falcon assembly package, scaffolding and error correction tools to finish improvement using PacBio long reads sequencing technology, with contig and scaffold N50 lengths of 1.563Mb and 4.006Mb, respectively, representing more continuous than the original Tibetan hulless barley genome nearly two orders of magnitude. We also re-annotated the new assembly, and reported 61,303 stringent confident putative protein-coding genes, of which 40,457 is HC genes. We have developed a new Tibetan hulless barley genome database (THBGD) to download and use friendly, as well as to better manage the information of the Tibetan hulless barley genetic resources.ConclusionsThe availability of new Tibetan hulless barley genome and annotations will take the genetics of Tibetan hulless barley to a new level and will greatly simplify the breeders effort. It will also enrich the granary of the Tibetan people.

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“…The model, known as 'U's triangle has three diploid species -B. rapa (AA, n=10), B. nigra (BB, n=8) and B. oleracea (CC, n=9) on the nodes and three allotetraploids -B. juncea (AABB, n=18), B. napus (AACC, n=19) and B. carinata (BBCC, n=17) at the coordinates. B. rapa was the first of the six species to be sequenced 2 followed by B. oleracea 3 The long-read third generation technologies such as SMRT sequencing by PacBio and Nanopore sequencing combined with long-range scaffolding technologies have significantly improved genome assemblies providing higher levels of contiguity and more extensive coverage of repeat sequences, transposable elements, centromeric and telomeric regions 6,7 .…”

Section: Introductionmentioning

confidence: 99%

A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

Paritosh

Yadava

Singh

et al. 2019

Preprint

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Brassica juncea (AABB; genome size ~920 Mb), commonly referred to as mustard, is a natural allopolyploid of two diploid species -B. rapa (AA) and B. nigra (BB). We report a highly contiguous genome assembly of an oleiferous type of B. juncea variety Varuna, an archetypical Indian gene pool line of mustard, with ~100x PacBio single-molecule real-time (SMRT) reads providing contigs with an N50 value of >5Mb. Assembled contigs were corrected and scaffolded with BioNano optical mapping. Three different linkage maps containing a large number of GBS markers were developed and used to anchor scaffolds/contigs to the 18 linkage groups of B. juncea. The resulting chromosome-scale assembly is a significant improvement over the previous draft assembly of B. juncea Tumida, a vegetable type of mustard. The assembled genome was characterized for transposons, centromeric repeats, gene content, and gene block associations. Both A and B genomes contain highly fragmented gene block arrangements. In comparison to the A genome, the B genome contains a significantly higher content of LTR/Gypsy retrotransposons, distinct centromeric repeats and a large number of B. nigra specific gene clusters that break the gene collinearity between the A and the B genomes. The genome assembly reported here will provide a fillip to the breeding work on oleiferous types of mustard that are grown extensively in the dry land areas of South Asia and elsewhere.

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Genome Sequencing and Assembly by Long Reads in Plants

Cited by 97 publications

References 66 publications

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm

Improved high-quality genome assembly and annotation of Tibetan hulless barley

A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

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