Liu Q, Xiong G, Wang Z, Wu Y, Tu T, Schwarzacher T, Heslop-Harrison JS. 2024. Chromosome-level genome assembly of the diploid oat species Avena longiglumis. Scientific Data 11: 412. https://doi.org/10.1038/s41597-024-03248-6 Abstract: ALO-Genome

Two years since we released the sequence assembly, annotation and preprint of the Avena longiglumis (an A genome, diploid, 2n=2x=14, wild oat species), the assembly is now published formally. The assembly is available from figshare as chromosome fasta files and gff annotation file, https://figshare.com/s/34d0c099e42eb39a05e2 and Genbank/NCBI as ASM3006302v1 GCA_030063025.1 at https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=4500 .

The diploid wild oat Avena longiglumis has nutritional and adaptive traits which are
valuable for common oat (A. sativa) breeding. The combination of Illumina, Nanopore and Hi-C data allowed us to assemble a high-quality chromosome-level genome of A. longiglumis (ALO), evidenced by contig N50 of 12.68 Mb with 99% BUSCO completeness for the assembly size of 3,960.97 Mb. A total of 40,845 protein-coding genes were annotated. The assembled genome was composed of 87.04% repetitive DNA sequences. Dotplots of the genome assembly (PI657387) with two published ALO genomes were compared to indicate the conservation of gene order and equal expansion of all syntenic blocks among three genome assemblies. Two recent whole-genome duplication events were characterized in genomes of diploid Avena species. These findings provide new knowledge for the genomic features of A. longiglumis, give information about the species diversity, and will accelerate the functional genomics and breeding studies in oat and related cereal crops.

The paper about the assembly, much more biology, and comparative information is presented in the unrefereed BioRXiv preprint: Liu Q, Yuan H, Li M, Wang Z, Cui D, Ye Y, Sun Z, Tan X, Schwarzacher T, Heslop-Harrison JS. 2022. Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses. BioRXiv. 2022 Feb 10:2022-02. https://www.biorxiv.org/content/10.1101/2022.02.09.479819v1 https://doi.org/10.1101/2022.02.09.479819

In the interim, we have also assembled and published the mitochondrial genome sequence assembly from Avena longiglumis, showing the multipartite structure of the 548,445 bp long genome, Liu Q, Yuan H, Xu J, Cui D, Xiong G, Schwarzacher T, Heslop-Harrison JS. The mitochondrial genome of the diploid oat Avena longiglumis. BMC Plant Biology. 2023 Apr 26;23(1):218. https://link.springer.com/article/10.1186/s12870-023-04217-8 doi.org/10.1186/s12870-023-04217-8 

In another manuscript, we use the assembly data to study the events of chromosome evolution and genome expansion from the inferred ancestral grass karyotype to oats, Avena: Liu Q, Ye L, Li M, Wang Z, Xiong G, Ye Y, Tu T, Schwarzacher T, Heslop-Harrison JS. Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena. BMC Plant Biology. 2023 Dec 8;23(1):627. doi.org/10.1186/s12870-023-04644-7

About the same time as our assembly was uploaded, two other Avena longiglumis assemblies were also published – allowing not only cross-validation of the assemblies of these 500,000,000 bp long chromosomes, but also identifying structural variations between the different genotypes.

We have discussed the remarkable preponderance of large terminal inter-chromosomal translocations between Avena chromosomes in several of our manuscripts, where they occur both between chromosomes within a genome and between genomes. For example, in work with Paulina Tomaszewska, Tomaszewska P, Schwarzacher T, Heslop-Harrison JS. Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids. Frontiers in Plant Science. 2022 Nov 22;13:1026364. doi: 10.3389/fpls.2022.1026364

First author Professor Qing Liu adds this summary in Chinese:

绘制燕麦野生种基因密码图谱

燕麦曾是土耳其安纳托利亚地区小麦田中的杂草，在三千多年前被驯化，其基因组遗传多样性丰富，表现为基因组较大 (12.6 Gb, 6x)，具有类似马赛克的染色体镶嵌结构，导致燕麦染色体结构变异的进化事件知之甚少，而其二倍体野生种基因数量相似，是燕麦抗逆、适应性状的基因宝库。为此，珍稀濒危植物保育研究组刘青团队，采用基因组学技术，组装燕麦野生种基因组序列，开展比较基因组学研究，研究结果加深人们对燕麦基因组起源的认识。

近日，研究成果以“Chromosome-level genome assembly of the diploid oat species Avena longiglumis”为题，发表在国际期刊Scientific Data。研究团队通过基因组测序和组装，获得高质量的长颖燕麦 (Avena longiglumis, 2n = 2x = 14) 基因组3.85 Gb，注释40,845个蛋白质编码基因 (图1)，并获得耐盐的转录组数据，为燕麦耐盐基因的开发带来新启示。刘青副研究员 (第一作者) 和John Seymour Heslop Harrison教授为共同通讯作者，华南植物园涂铁要副研究员、已毕业博士研究生王梓维 (现为韶关学院英东生物与农业学院助理研究员)、硕士研究生熊圭参与该项工作。

比较基因组学研究发现，燕麦属野生种——长颖燕麦和异颖燕麦 (A. eriantha, 2n = 2x = 14) 的共线性区域高度保守；二倍体野生种染色体易位发生在近端粒50 Mb的区域 (图2)，六倍体燕麦也存在类似的基因组间易位；确定燕麦属发生过post-rho全基因组复制事件。该研究重构禾本科早熟禾亚科的进化史，为燕麦基因组辅助育种奠定重要的理论基础，将推动燕麦野生种质资源应用 (成果发表于BMC Plant Biology, 2023, 23:627)。

以上研究得到了国家自然科学基金 (32370402和32070359)、广东省基础与应用基础研究基金 (2021A1515012410)、中国科学院华南植物园海外知名学者项目 (Y861041001) 的资助。

论文链接：

Liu et al. Scientific Data, 2024, https://doi.org/10.1038/s41597-024-03248-6

Liu et al. BMC Plant Biology, 2023, https://doi.org/10.1186/s12870-023-04644-7

Mapping the genetic code of wild oat species

Oats were once a weed in wheat fields in the Anatolian region of Turkey and were domesticated more than 3,000 years ago. Their genomes are rich in genetic diversity, as shown by their large genomes (12.6 Gb, 6x) and mosaic-like chromosome mosaics. Little is known about the evolutionary events that lead to structural variation in oat chromosomes. However, the diploid wild species has a similar number of genes and is a genetic treasure house of oat stress resistance and adaptive traits. To this end, Liu Qing’s team from the Rare and Endangered Plant Conservation Research Group used genomics technology to assemble the genome sequence of wild oat species and conduct comparative genomics research. The research results deepened people’s understanding of the origin of the oat genome.

Recently, the research results were published in the international journal Scientific Data under the title “Chromosome-level genome assembly of the diploid oat species Avena longiglumis”. Through genome sequencing and assembly, the research team obtained a high-quality Avena longiglumis (Avena longiglumis, 2n = 2x = 14) genome of 3.85 Gb, annotated 40,845 protein-coding genes (Figure 1), and obtained salt-tolerant transcriptome data for The development of salt-tolerant genes in oats brings new revelations. Associate Researcher Liu Qing (first author) and Professor John Seymour Heslop Harrison are the co-corresponding authors. Associate Researcher Tu Tieyao of the South China Botanical Garden, graduated doctoral candidate Wang Ziwei (currently an assistant researcher at the Yingdong School of Biology and Agriculture, Shaoguan University), and Master’s student Xiong Gui participated in this work.

Comparative genomics studies have found that the collinear regions of wild species of oats—A. eriantha and A. eriantha, 2n = 2x = 14—are highly conserved; chromosomal translocations in diploid wild species occur at proximal telomeres A similar intergenomic translocation exists in the 50 Mb region (Fig. 2) in hexaploid oats; it is determined that a post-rho whole-genome duplication event occurred in the genus Oat. This study reconstructs the evolutionary history of the Poaceae subfamily Poaceae, lays an important theoretical foundation for genome-assisted breeding of oats, and will promote the application of oat wild germplasm resources (results published in BMC Plant Biology, 2023, 23:627).

The above research was funded by the National Natural Science Foundation of China (32370402 and 32070359), the Guangdong Basic and Applied Basic Research Fund (2021A1515012410), and the South China Botanical Garden Overseas Famous Scholars Project of the Chinese Academy of Sciences (Y861041001).

Paper link:

Liu et al. Scientific Data, 2024, https://doi.org/10.1038/s41597-024-03248-6

Liu et al. BMC Plant Biology, 2023, https://doi.org/10.1186/s12870-023-04644-7

图1 长颖燕麦基因组特征分析 (Scientific Data, 2024, 11:412)

图2早熟禾亚科代表种祖先核型重建 (BMC Plant Biology, 2023, 23:627)