Victor Albert analyzes “reference genome” to trace evolutionary traits of Litchi chinensis

Victor Albert.

Victor Albert, PhD, Empire Innovation Professor, Department of Biological Sciences

Victor A. Albert, PhD, Empire Innovation Professor, Department of Biological Sciences, along with a large international team from China, the U.S., Singapore, France and Canada, are co-authors of a study recently published in Nature Genetics. Their research not only adds new chapters to the history of the lychee, it also provides an in-depth look at flowering time, a hugely important trait in agriculture. “Early-maturing lychees versus late-maturing lychees came from different places and were domesticated independently,” says Dr. Albert, “This, by itself, is an interesting story, but we also wanted to know what causes these differences. Why do these varieties fruit and flower at different times?” By comparing the DNA of many lychee varieties, the team identified a genetic variant that could be used to create a simple test for identifying early- and late-blooming lychee plants. Read the news story by Charlotte Hsu.

Research News

Lychee genome tells colorful story about colorful tropical fruit

Lychee fruits growing in Shenzhen, China.

Lychee fruits growing in Shenzhen, China. In a new study, scientists report sequencing and analyzing the genomes of wild and cultivated lychee varieties. Photo: Huicong Wang

By CHARLOTTE HSU

Published January 5, 2022

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headshot of Victor Albert.
“Like a puzzle, we’re piecing together the history of what humans did with lychee. ”
Victor Albert, Empire Innovation Professor
Department of Biological Sciences

They’re prickly on the outside, sweet on the inside and beloved for their iconic pink shells and pearly, fragrant fruit. In the U.S., you might encounter them as a flavorful ingredient in bubble tea, ice cream or a cocktail. You can also peel them and eat them fresh.

Lychees have been grown in China since ancient times, with records of cultivation dating back about 2,000 years. Fresh lychees were an object of such desire that in the Tang Dynasty, one emperor set up a dedicated horse relay to deliver the fruits to the imperial court from harvests made far to the south.

Now, scientists have used genomics to peer even deeper into the lychee’s history. And in the process, they’ve uncovered insights that could help shape the species’ future, too.

“Lychee is an important tropical agricultural crop in the Sapindaceae (maple and horse chestnut) family, and it is one of the most economically significant fruit crops grown in eastern Asia, especially so to the yearly income of farmers in southern China,” says Jianguo Li, professor in the South China Agricultural University (SCAU) College of Horticulture and a senior author of the study. “By sequencing and analyzing wild and cultivated lychee varieties, we were able to trace the origin and domestication history of lychee. We demonstrated that extremely early- and late-maturing cultivars were derived from independent human domestication events in Yunnan and Hainan, respectively.”

Additionally, “We identified a specific genetic variant, a deleted stretch of genetic material, that can be developed as a simple biological marker for screening of lychee varieties with different flowering times, contributing importantly to future breeding programs,” adds Rui Xia, professor in the same college at SCAU and another senior author of the research.

“Like a puzzle, we’re piecing together the history of what humans did with lychee,” notes UB evolutionary biologist Victor Albert, also a senior author of the study. “These are the main stories our research tells: the origins of lychee, the idea that there were two separate domestications and the discovery of a genetic deletion that we think causes different varieties to fruit and flower at different times.”

The study, published on Jan. 3 in Nature Genetics, was led by SCAU in collaboration with a large international team from China, the U.S., Singapore, France and Canada.

Domesticated more than once

Lychee fruits.

Lychee fruits. Photo: Haibin Sun

To conduct the study, scientists produced a high-quality “reference genome” for a popular lychee cultivar called Feizixiao and compared its DNA to that of other wild and farmed varieties. All the cultivars belong to the same species, Litchi chinensis.

The research shows that the lychee tree, Litchi chinensis, was likely domesticated more than once. Wild lychees originated in Yunnan in southwestern China, spread east and south to Hainan Island, and then were domesticated independently in each of these two locations, the analysis suggests.

In Yunnan, people began cultivating very early-flowering varieties, and in Hainan, late-blooming varieties that bear fruit later in the year. Eventually, interbreeding between cultivars from these two regions led to hybrids, including varieties like Feizixiao, that remain extremely popular today.

The exact timing of these events is uncertain. For instance, the study suggests that one milestone, the evolutionary split between L. chinensis populations in Yunnan and Hainan, which took place before domestication, could have occurred around 18,000 years ago. But that is only an estimate; other solutions are possible. Still, the analysis provides a fascinating look at the evolutionary history of lychees and their link with humans.

Simple test could tell when tree will flower

The study not only adds new chapters to the history of the lychee; it also provides an in-depth look at flowering time, a hugely important trait in agriculture.

“Early-maturing lychees versus late-maturing lychees came from different places and were domesticated independently,” says Albert, Empire Innovation Professor of Biological Sciences, College of Arts and Sciences. “This, by itself, is an interesting story, but we also wanted to know what causes these differences. Why do these varieties fruit and flower at different times?”

By comparing the DNA of many lychee varieties, the team identified a genetic variant that could be used to create a simple test for identifying early- and late-blooming lychee plants.

The variant is a deletion — a chunk of missing DNA — that lies near two genes associated with flowering, and may help to control the activity of one or both of them.

Yunnan cultivars that bloom very early have the deletion, inheriting it from both parents. Hainan varieties that mature late do not have it at all. And Feizixiao — a hybrid with nearly equal amounts of DNA from each of the two regional populations — is “heterozygous” for the deletion, meaning that it has only one copy inherited from one parent. This makes sense, as Feizixiao flowers early, but not extremely early.

“This is very useful for breeders. Because the lychee is perishable, flowering times have been important to extending the season for which the lychee is available in markets,” Albert says.

Sequencing lychee genome only the start

The team at SCAU initiated the lychee genome study as part of a bigger project that aims to greatly expand what we know about the DNA of important flowering plants within the same family, Sapindaceae.

Sapindaceae is a large family that includes many economically important plants,” Xia says. “So far, only a few of them, including lychee, longan, rambutan, yellowhorn and maple, have had their full genomes sequenced.”

“We, the College of Horticulture at SCAU, are working on a large collaborative project of sequencing more Sapindaceae species native to China and of economic importance, such as rambutan, sapindus (soapberries) and balloon vine, aiming at broad and thorough comparative genomics investigations for Sapindaceae genomics,” Xia adds. “The main research interests will be flowering, secondary metabolism leading to flavors and fragrances, flower and fruit development, among others.”

Senior authors on the Nature Genetics study are Rui Xia, Jianguo Li and Houbin Chen from SCAU; Ray Ming from the University of Illinois at Urbana-Champaign; and Victor Albert from UB. First authors are Guibing Hu, Junting Feng, Chengming Liu and Zhenxian Wu from SCAU; Xu Xiang from the Guangdong Academy of Agricultural Sciences; Jiabao Wang from the Chinese Academy of Tropical Agricultural Sciences; and Jarkko Salojärvi from the Nanyang Technological University.

Faculty Profile

  • Victor A. Albert

    PhD

    Victor A. Albert.

    Victor A. Albert

    PhD

    Victor A. Albert

    PhD

    Research Interests

    Plant evolutionary biology; development and genomics

    Education

    • A.B. and Sc.M., Biology, Brown University
    • Ph.D., Biology, University of North Carolina – Chapel Hill
    • Postdoctoral research, Uppsala University, Sweden

    Office Hours

    • By appointment

    Research Summary

    Victor Albert’s research employs genomic, developmental, and genetic approaches to understanding problems in plant evolutionary biology. Areas of current and recent interest include:

    - Genome sequencing and biodiversity "omics" analysis of tropical Southeast Asian flora, including the clove genus (Syzygium: Myrtaceae), tembusu tree (Cyrtophyllum: Gentianaceae), giant corpse lily (Amorphophallus titanum; Araceae), and Nepenthes pitcher plant (Nepenthaceae).

    - The genetic basis for convergent evolution and “adaptive” radiations of plant forms, for example in distantly related carnivorous plant lineages; this has included complete genome sequencing of the humped bladderwort, Utricularia gibba, butterwort species (Pinguicula), and other carnivorous plant species (e.g., Drosera - the sundews).

    - The role of mechanistic co-option in the evolution of carnivorous plant physiology, for example, by repurposing of pathogenesis-related gene functions.

    - Population genomic approaches to the study of interspecies admixture, local environmental adaptation, and the evolution of agriculturally important traits.

    - Genomics of the coffee plant; seeking evidence for factors underlying the massive diversification of its parent lineage in fruit types and secondary compound chemistries, and working toward better knowledge of traits important for developing agricultural systems.

    - Sequencing and characterization of the avocado and Amborella genomes, Amborella being the single sister species to all other flowering plants, and avocado lying near the base of angiosperm phylogeny; use these and other genomes in an attempt to uncover developmental regulatory mechanisms common to the “ancestral angiosperm”.

    - Reconstruction of whole-genome duplication history as it relates to the diversification of flowering plants, also the ancestral gene order for all angiosperms.

    - Evo-devo research on the evolution of reproductive development in flowering plants; topics include B-function MADS box genes and CYCLOIDEA-like genes; the former help specify petal identity, whereas the latter participate in the control of organ symmetry.

    Selected Publications

    • Chanderbali AS, Jin L, Xu Q, Zhang Y, Zhang J, Jian S, Carroll E, Sankoff D, Albert VA, Howarth DG, Soltis DE, Soltis, PS. Buxus and Tetracentron genomes help resolve eudicot genome history. Nature Communications 2022 13(1), 643.
    • Hu G, Feng J, Xiang X, Wang J, Salojärvi J, Liu C, Wu Z, Zhang J, Liang X, Jiang Z, Liu W, Ou L, Li J, Fan G, Mai Y, Chen C, Zhang X, Zheng J, Zhang Y, Peng H, Yao L, Wai CM, Luo X, Fu J, Tang H, Lan T, Lai B, Sun J, Wei Y, Li H, Chen J, Huang X, Yan Q, Liu X, McHale LK, Rolling W, Guyot R, Sankoff D, Zheng C, Albert VA, Ming R, Chen H, Xia R, Li J. Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars. Nat Genet. 2022 Jan 3. doi: 10.1038/s41588-021-00971-3.
    • Cervantes-Pérez SA, Yong-Villalobos L, Florez-Zapata N, Oropeza-Aburto A, Rico-Reséndiz F, Amasende-Morales I, Lan T, Martínez O, Vielle-Calzada JP, Albert VA, Herrera-Estrella L. Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba. Scientific Reports 11, 15725 (2021). doi: 10.1038/s41598-021-95054-y
    • Zhao Y, Broholm SK, Wang F, Rijpkema AS, Lan T, Albert VA, Teeri TH, Elomaa P. TCP and MADS-Box Transcription Factor Networks Regulate Heteromorphic Flower Type Identity in Gerbera hybrida. Plant Physiol. 2020 Nov;184(3):1455-1468. doi: 10.1104/pp.20.00702.
    • Xu Z, Pu X, Gao R, Demurtas OC, Fleck SJ, Richter M, He C, Ji A, Sun W, Kong J, Hu K, Ren F, Song J, Wang Z, Gao T, Xiong C, Yu H, Xin T, Albert VA, Giuliano G, Chen S, Song J. Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants. BMC Biol. 2020 Jun 18;18(1):63. doi: 10.1186/s12915-020-00795-3. 
    • Oropeza-Aburto A, Cervantes-Pérez SA, Albert VA, Herrera-Estrella L. Agrobacterium tumefaciens mediated transformation of the aquatic carnivorous plant Utricularia gibba. Plant Methods. 2020 Apr 10;16:50. doi: 10.1186/s13007-020-00592-7.
    • Albert VA, Renner T. Aquatic angiosperm ambiguities answered. Nat Plants. 2020 Mar;6(3):181-183. doi: 10.1038/s41477-020-0607-5.
    • Zhang T, Zhao Y, Juntheikki I, Mouhu K, Broholm SK, Rijpkema AS, Kins L, Lan T, Albert VA, Teeri TH, Elomaa P. Dissecting functions of SEPALLATA-like MADS box genes in patterning of the pseudanthial inflorescence of Gerbera hybrida. New Phytol. 2017 Nov;216(3):939-954. doi: 10.1111/nph.14707.
    • Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274
    • Amborella Genome Project. The Amborella genome and the evolution of flowering plants. Science. 2013 Dec 20;342(6165):1241089. doi: 10.1126/science.1241089
    • Ibarra-Laclette E, Lyons E, Hernández-Guzmán G, Pérez-Torres CA, Carretero-Paulet L, Chang TH, Lan T, Welch AJ, Juárez MJ, Simpson J, Fernández-Cortés A, Arteaga-Vázquez M, Góngora-Castillo E, Acevedo-Hernández G, Schuster SC, Himmelbauer H, Minoche AE, Xu S, Lynch M, Oropeza-Aburto A, Cervantes-Pérez SA, de Jesús Ortega-Estrada M, Cervantes-Luevano JI, Michael TP, Mockler T, Bryant D, Herrera-Estrella A, Albert VA, Herrera-Estrella L. Architecture and evolution of a minute plant genome. Nature. 2013 Jun 6;498(7452):94-8. doi: 10.1038/nature12132.
    • Rendón-Anaya M, Ibarra-Laclette E, Méndez-Bravo A, Lan T, Zheng C,Carretero-Paulet L, Perez-Torres CA, Chacón-López A, Hernandez-Guzmán G, ChangTH, Farr KM, Barbazuk WB, Chamala S, Mutwil M, Shivhare D, Alvarez-Ponce D,Mitter N, Hayward A, Fletcher S, Rozas J, Sánchez Gracia A, Kuhn D, Barrientos-Priego AF, Salojärvi J, Librado P, Sankoff D, Herrera-Estrella A, Albert VA, Herrera-Estrella L.  The avocado genome informs deep angiospermphylogeny, highlights introgressive hybridization, and revealspathogen-influenced gene space adaptation. Proc Natl Acad Sci U S A. 2019 Aug 20; 116(34):17081-17089.
    • Salojärvi J, Smolander OP, Nieminen K, Rajaraman S, Safronov O, Safdari P, Lamminmäki A, Immanen J, Lan T, Tanskanen J, Rastas P, Amiryousefi A, Jayaprakash B, Kammonen JI, Hagqvist R, Eswaran G, Ahonen VH, Serra JA, Asiegbu FO, de Dios Barajas-Lopez J, Blande D, Blokhina O, Blomster T, Broholm S, Brosché M, Cui F, Dardick C, Ehonen SE, Elomaa P, Escamez S, Fagerstedt KV, Fujii H, Gauthier A, Gollan PJ, Halimaa P, Heino PI, Himanen K, Hollender C, Kangasjärvi S, Kauppinen L, Kelleher CT, Kontunen-Soppela S, Koskinen JP, Kovalchuk A, Kärenlampi SO, Kärkönen AK, Lim KJ, Leppälä J, Macpherson L, Mikola J, Mouhu K, Mähönen AP, Niinemets Ü, Oksanen E, Overmyer K, Palva ET, Pazouki L, Pennanen V, Puhakainen T, Poczai P, Possen BJHM, Punkkinen M, Rahikainen MM, Rousi M, Ruonala R, van der Schoot C, Shapiguzov A, Sierla M, Sipilä TP, Sutela S, Teeri TH, Tervahauta AI, Vaattovaara A, Vahala J, Vetchinnikova L, Welling A, Wrzaczek M, Xu E, Paulin LG, Schulman AH, Lascoux M, Albert VA, Auvinen P, Helariutta Y, Kangasjärvi J. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat Genet. 2017 May 8.
    • Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang TH, Cervantes-Pérez SA, Zheng C, Sankoff D, Tang H, Purbojati RW, Putra A, Drautz-Moses DI, Schuster SC, Herrera-Estrella L, Albert VA. Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome. Proc Natl Acad Sci U S A. 2017 May 15. pii: 201702072.
    • Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang T-H, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, Pálfalvi G, Pollard ST, Rozas J, Sánchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, Hasebe M. Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nature Ecology & Evolution. 2017 Feb 6;1:0059.
    • Juntheikki-Palovaara I, Tähtiharju S, Lan T, Broholm SK, Rijpkema AS, Ruonala R, Kale L, Albert VA, Teeri TH, Elomaa P. Functional diversification of duplicated CYC2 clade genes in regulation of inflorescence development in Gerbera hybrida (Asteraceae). Plant Journal. 2014 Sep;79(5):783-96.