Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

/pdf/genome-sequence-and-analysis-of-the-tuber-crop-potato-3bzwxev7ko.pdf

Genome sequence and analysis of the tuber crop potato.

We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

/pdf/the-genome-of-the-mesopolyploid-crop-species-brassica-rapa-54ka2hnfpp.pdf

The genome of the mesopolyploid crop species Brassica rapa

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

http://science.sciencemag.org/content/sci/345/6199/950.full.pdf

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

/pdf/sequencing-of-allotetraploid-cotton-gossypium-hirsutum-l-acc-3aex1man4n.pdf

Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species rarely occur in nature mainly due to reproductive barriers but how such hurdles can be overcome is largely unknown. xBrassicoraphanus is a fertile intergeneric allopolyploid synthesized between Brassica rapa and Raphanus sativus in the Brassicaceae family. Genomes of B. rapa and R. sativus are diverged enough to suppress synapsis formation between non-homologous progenitor chromosomes during meiosis, and we found that both genomes reside in the single nucleus of xBrassicoraphanus without genome loss or rearrangement. Expressions of syntenic orthologs identified in B. rapa and R. sativus were adjusted to a hybrid nuclear environment of xBrassicoraphanus, which necessitates reconfiguration of transcription network by rewiring cis-trans interactions. B. rapa coding sequences have a higher level of gene-body methylation than R. sativus, and such methylation asymmetry is maintained in xBrassicoraphanus. B. rapa-originated transposable elements were transcriptionally silenced in xBrassicoraphanus, rendered by gain of CHG methylation in trans via small RNAs derived from the same sequences of R. sativus subgenome. Our work proposes that not only transcription compatibility but also a certain extent of genome divergence supports hybrid genome stabilization, which may explain great diversification and expansion of angiosperms during evolution.

https://www.biorxiv.org/content/biorxiv/early/2021/09/28/2021.09.28.462158.full.pdf

A merger between compatible but divergent genomes supports allopolyploidization in the Brassicaceae family

We identified BAC clones which harbor DNAs derived from the B. rapa organelle genomes by in silico mapping of 80,292 B. rapa BAC end sequences on the Arabidopsis organelle genomes and subsequent insert size estimation and fingerprinting. A total of 1,048 putative chloroplast genome-derived BAC clones (2.6%) were identified. Fingerprinting and sequencing revealed that many of them represented the entire chloroplast genome (about 150 kb). Meanwhile, only 59 putative mitochondrial genome-derived BACs (0.15%) were identified and most of them showed rare agreement between the in silico map and fingerprinting. We sequenced BAC clone KBrB042G11 (42G11) and compared it to the mitochondrial genome of B. napus and A. thaliana which showed dynamic rearrangement events. The order of 33 orthologous genes was collinear between the 42G11 BAC and its counterpart in B. napus. Five distinctive rearrangements and two InDels were identified between these two closely related species and the rearrangements were related to the occurrence of small tandem repeat sequences. Sequences of the 33 orthologous genes in the homoeologous regions of B. napus and B. rapa were almost 100% identical. Gene orders showed no colinearity between Arabidopsis and Brassica even though 31 orthologous genes shared high sequence similarity with p-values over 1E-32. FISH analysis using the identified BAC revealed a large chloroplast genome insertion in the pericentromeric region of chromosome (chr.) 4 of B. rapa.

In silico-selection of Brassica rapa organelle genome-derived BACs using their end sequences and sequence level comparative analysis of the 124 kb mitochondrial genome sequences in the family Brassicaceae

Beom-Seok Park

Papers

A merger between compatible but divergent genomes supports allopolyploidization in the Brassicaceae family

In silico-selection of Brassica rapa organelle genome-derived BACs using their end sequences and sequence level comparative analysis of the 124 kb mitochondrial genome sequences in the family Brassicaceae