Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

Abstract

Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete 1-4. Here we report referencegrade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3-79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques. Compared with previous assembled draft genomes 1,3 , these genome sequences show considerable improvements in contiguity and completeness for regions with high content of repeats such as centromeres. Comparative genomics analyses identify extensive structural variations that probably occurred after polyploidization, highlighted by large paracentric/pericentric inversions in 14 chromosomes. We constructed an introgression line population to introduce favorable chromosome segments from G. barbadense to G. hirsutum, allowing us to identify 13 quantitative trait loci associated with superior fiber quality. These resources will accelerate evolutionary and functional genomic studies in cotton and inform future breeding programs for fiber improvement. Cotton represents the largest source of natural textile fibers in the world. Over 90% of annual fiber production comes from allotetraploid cotton (G. hirsutum and G. barbadense), which originated from an allopolyplodization event approximately 1-2 million year ago, followed by millennia of asymmetric subgenome selection 5,6. G. hirsutum is cultivated all over the world because of its high yield and G. barbadense is prized for its superior fiber quality. To cultivate G. hirsutum that produces longer, finer and stronger fibers, one approach is to introduce the superior fiber traits from G. barbadense into G. hirsutum. A genomics-enabled breeding strategy requires a detailed and robust understanding of genomic organization. Genomic feature G. hirsutum G. barbadense

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

“…We have reported a highly contiguous genome assembly of B. juncea variety Varuna, an oleiferous type belonging to the Indian gene pool of mustard, using long-read SMRT sequencing and optical mapping. The B. juncea assembly reported here has given contig N50 value of >5Mb, comparable to the other recent SMRT based genome assemblies [9][10][11][12][13][14] . We found recursive optical mapping with three different labeling reactions to be highly useful for correcting mis-assemblies.…”

“…Recent genome sequencing efforts have relied exclusively on high coverage SMRT sequencing, both for the de-novo genome assemblies and for improving earlier assembled draft genomes that used the second-generation technologies [8][9][10][11][12][13] . Amongst the Brassica species -assembly of B. rapa Chiifu has been improved by additional data from ~57x SMRT sequencing, BioNano optical mapping, and Hi-C reads 14 .…”

Comparison ofArachis monticolawith Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut

“…Besides, there are several large inversions in A03, A07, A09, B05, and B10 of A. monticola , which are not observed in A. hypogaea , suggesting the possible introgression events occurred from wild diploids to cultivated A. hypogaea (Figures S2a and S3a, Supporting Information). These large inversions are present with discrete chromatin interactions around breakpoints by mapping Hi‐C links between species (Figures S2b and S3b, Supporting Information), and similar Hi‐C interaction maps have been used to identify large‐scale chromosomal rearrangements in tetraploid cotton . The differences between the A and B subgenomes of the wild and cultivated peanuts and their respective diploids may lead to the debate about the origin of tetraploid peanuts, which is more likely resolved in this study …”

TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

“…Frequent gaps and breaks in repetitive sequence are inherent to short-read assemblies. In fact, long-read assemblies with contig N50s exceeding scaffold N50s of short-read assemblies have been obtained in other plant and animal species [56-58]. Thus, we propose to improve our Illumina-based scaffolding and gap-filling methodology by integrating long-read sequencing into TRITEX in the future.…”