Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

First author: Jae Young Choi; Affiliations: New York University (纽约大学): New York, USA

Corresponding author: Michael D. Purugganan

The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group’s evolutionary history is not fully resolved. To address these gaps, we use long-read nanopore sequencing and assemble the genomes of two circum-basmati rice varieties. We generate two high-quality, chromosome-level reference genomes that represent the 12 chromosomes of Oryza. The assemblies show a contig N50 of 6.32 Mb and 10.53 Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies, we characterize structural variations segregating across circum-basmati genomes. We discover repeat expansions not observed in japonica—the rice group most closely related to circum-basmati—as well as the presence and absence variants of over 20 Mb, one of which is a circum-basmati-specific deletion of a gene regulating awn length. We further detect strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow has its greatest effect on chromosome 10, causing both structural variation and single-nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, and Iran/Pakistan. The availability of high-quality reference genomes allows functional and evolutionary genomic analyses providing genome-wide evidence for gene flow between circum-aus and circum-basmati, describes the nature of circum-basmati structural variation, and reveals the presence/absence variation in this important and iconic rice variety group.

香米是亚洲水稻的一个类群，包含许多标志性的品种，在印度次大陆上广泛种植。除了其经济和文化重要性。香米目前还缺乏一个高质量的参考基因组，以及该类群的演化历史也不清楚。为了填补这些空白，作者基于长read纳米孔测序组装了两个香米品种的基因组，一个是来自巴基斯坦的Basmati，另一个是来自伊朗的Dom Sufid。作者组装了两个高质量的、染色体水平的参考基因组，与稻属植物一样含12条染色体。其中，Basmati品种的组装contig N50为6.32Mb，而Dom Sufid品种的组装contig N50为10.53Mb。基于这两个基因组，作者鉴定了印度香米不同品种间的结构变异。作者在印度香米鉴定到了与其最近缘的水稻品种粳稻中所没有的重复序列的扩张，另外还有超过20Mb的“存在/缺失”变异，其中一个印度香米特异的基因删除，与稻芒的长度相关。作者进一步检测了basmati与aus两个水稻类群之间的群体混合信号（p.s. aus是来一种自孟加拉国的水稻品种）。该基因流对于10号染色体具有非常大的影响，造成了结构变异和单核苷酸多态性，使得全基因的历史演化出现了偏离。最后，对于78个香米品种的群体基因组分析显示存在三个按照地理种源分布的遗传群体，分别分布在不丹/尼泊尔、印度/孟加拉国/缅甸以及伊朗/巴基斯坦。本文提供高质量基因组是的功能和演化基因组研究成为可能，同时也为aus和basmati两个水稻类群之间的基因流提供了全基因组的证据，并且鉴定了香米基因组中的结构变异，揭示了在该具标志性且珍贵的水稻品种的“存在/缺失”变异。

通讯：Michael D. Purugganan (https://www.york.ac.uk/biology/research/plant-biology/ian-a-graham/)

个人简介：1985年，菲律宾大学，学士；1986年，哥伦比亚大学，硕士；1993年，佐治亚大学，博士。

研究方向：植物适应的演化基因组学与生态基因组学；植物驯化遗传学；生物的多细胞性演化与社会性行为研究。

doi: https://doi.org/10.1186/s13059-020-1938-2

Journal: Genome Biology

Published date: February 05, 2020