Genomics of the origin and evolution of Citrus

Abstract

Genomics of the origin and evolution of CitrusGuohong albert Wu 1 , Javier Terol 2 , Victoria ibanez 2 , antonio López-García 2 , estela Pérez-román 2 , carles borredá 2 , concha Domingo 2 , francisco r. Tadeo 2 , Jose carbonell-caballero 3 , roberto alonso 3 , franck curk 4 , Dongliang Du 5 , Patrick Ollitrault 6 , Mikeal L. roose 7 , Joaquin Dopazo 3,8 , frederick G. Gmitter Jr 5 , Daniel S. rokhsar 1,9,10 & Manuel Talon 2The genus Citrus and related genera (Fortunella, Poncirus, Eremocitrus and Microcitrus) belong to the angiosperm subfamily Aurantioideae of the Rutaceae family, which is widely distributed across the monsoon region from west Pakistan to north-central China and south through the East Indian Archipelago to New Guinea and the Bismarck Archipelago, northeastern Australia, New Caledonia, Melanesia and the western Polynesian islands 1 . Native habitats of citrus and related genera roughly extend throughout this broad area (Extended Data Fig. 1a and Supplementary Table 1), although the geogra phical origin, timing and dispersal of citrus species across southeast Asia remain unclear. A major obstacle to resolving these uncertainties is our poor understanding of the genealogy of complex admixture in cultivated citrus, as has recently been shown 2 . Some citrus are clonally propagated apomictically 3 through nucellar embryony, that is, the development of non-sexual embryos originating in the maternal nucellar tissue of the ovule, and this natural process may have been co-opted during domestication; grafting is a relatively recent phenomenon 4 . Both modes of clonal propagation have led to the domestication of fixed (desirable) genotypes, including interspecific hybrids, such as oranges, limes, lemons, grapefruits and other types.Under this scenario, it is not surprising that the current chaotic citrus taxonomy-based on long-standing, conflicting proposals 5,6 -requires a solid reformulation consistent with a full understanding of the hybrid and/or admixture nature of cultivated citrus species. Here we analyse genome sequences of diverse citrus to characterize the diversity and evolution of citrus at the species level and identify citrus admixtures and interspecific hybrids. We further examine the network of relatedness among mandarins and sweet orange, as well as the pattern of the introgression of pummelos among mandarins for clues to the early stages of citrus domestication. Diversity and evolution of the genus CitrusTo investigate the genetic diversity and evolutionary history of citrus, we analysed the genomes of 58 citrus accessions and two outgroup genera (Poncirus and Severinia) that were sequenced to high coverage, including recently published sequences 2,3,7 as well as 30 new genome sequences described here. For our purpose, we do not include accessions related by somatic mutations. These sequences represent a diverse sampling of citrus species, their admixtures and hybrids (Supplementary Tables 2, 3 and Supplementary Notes 1, 2). Our collection includes accessions from eight previously unsequ...

Occurrence of prophage and historical perspectives associated with the dissemination of huanglongbing in mainland China

“…It could also be attributed to seedling introductions from multiple provinces, including Sichuan, Guangdong, Zhejiang and Hunan in the 1960s to 1970s (Yunnan Citrus Huanglongbing Research Group, 1981, Investigation report on citrus yellowing in Yunnan province, unpublished). Yunnan, as one region of origin of contemporary citrus species (Wu et al , ), is more likely to be a region of origin for HLB in HAR. Potentially, the incursion of HLB in Yunnan was through introductions of seedlings from border countries, such as Laos, Myanmar, Vietnam or Thailand (Bové, ), which are geographically close to Xishuangbanna.…”

Phyllosticta citricarpa and sister species of global importance to Citrus

“…Since the fifth century BC, the movement of citrus plants from Asia, where citrus and CBS disease are endemic, occurred to countries around the Mediterranean Sea (Mabberley, 2004;Nicolosi, 2007;Ramon-Laca, 2003;Wu et al, 2018). Phyllosticta spp.…”

“…Phyllosticta citrichinaensis, P. citriasiana and P. citrimaxima were found only in Asia, and the endophyte P. citribraziliensis has been reported only in South America (Glienke et al, 2011;Guarnaccia et al, 2017a;Wang et al, 2012;Wikee et al, 2013b;Wulandari et al, 2009). Current knowledge about the distribution of these Phyllosticta species reveals that most of them are present in Asia, where citrus originated (Wu et al, 2018). However, several incursions have occurred along with the global establishment of citrus cultivation and given the long-range dispersal of these species via infected citrus plant propagation material, it would be expected that P. citricarpa and/ or other Phyllosticta species may be present in many citrus-producing countries.…”

Association between blooming time and climatic adaptation in Prunus mume

“…Next‐generation sequencing (NGS) technologies are faster and cheaper than Sanger sequencing, which is frequently used in plant studies and allows for a deeper genome variant analysis (Deschamps & Campbell, ; Jackson, Iwata, Lee, Schmutz, & Shoemaker, ). So far, genome sequencing and evolutionary genetics have provided information about the origin, evolution (Ellegren, ; Sedivy, Wu, & Hanzawa, ; Velasco, Hough, Aradhya, & Ross‐Ibarra, ; Wu, Terol, et al, ; Yu et al, ), and domestication (Akagi, Hanada, Yaegaki, Gradziel, & Tao, ; Myles et al, ; Qiu et al, ; Velasco et al, ; Wu, Wang, et al, ). The first 237M long genomic map of P. mume was constructed in 2012, and the actual size of the genome of P. mume was estimated to be about 280M.…”