Evidence map›Paper›PMID 36435969›Full record

ArticlePlant communications2023

Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution.

Salih Kafkas, Xiaokai Ma, Xingtan Zhang, Hayat Topçu, Rafael Navajas-Pérez, Ching Man Wai, Haibao Tang, Xuming Xu, Mortaza Khodaeiaminjan, Murat Güney and 26 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Plant communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
2.4field-weighted citation impact, top 10% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed, 31 citations in OpenAlex.

  1. Article
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  3. Management and Genetic Diversity of an ItalianInternational journal of molecular sciences · 2025
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

36 authors at 10 institutions in 6 countries.

Salih KafkasDepartment of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey. Electronic address: skafkas@cu.edu.tr.
Xiaokai MaCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, Fujian Agriculture and Forestry University, Fuzhou, China.
Xingtan ZhangCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
Hayat TopçuDepartment of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
Rafael Navajas-PérezDepartamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
Ching Man WaiDepartment of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Haibao TangCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
Xuming XuCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
Mortaza KhodaeiaminjanDepartment of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
Murat GüneyDepartment of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
Aibibula PaizilaDepartment of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
Harun KarcıDepartment of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
Xiaodan ZhangDepartment of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Jing LinCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
Han LinCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
Roberto de la HerránDepartamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
Carmelo Ruiz RejónDepartamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
Jerson Alexander García-ZeaDepartamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
Francisca RoblesDepartamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain.
Coral Del Val MuñozDepartment of Computer Science, University of Granada, Granada, Spain; Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI Institute), 18014 Granada, Spain.
Agnes Hotz-WagenblattGerman Cancer Research Center, Omics IT and Data Management Core Facility, Heidelberg, Germany.
Xiangjia Jack MinDepartment of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA.
Hakan ÖzkanDepartment of Field Crops, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
Elmira Ziya MotalebipourDepartment of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
Hatice GozelPistachio Research Institute, Şahinbey, Gaziantep 27060, Turkey.
Nergiz ÇobanPistachio Research Institute, Şahinbey, Gaziantep 27060, Turkey.
Nesibe Ebru KafkasDepartment of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
Andrej KilianDiversity Arrays Technology, University of Canberra, Canberra, ACT, Australia.
HuaXing HuangCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
Xuanrui LvCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
Kunpeng LiuCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
Qilin HuCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China.
Ewelina JacygradGenome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.
William PalmerGenome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.
Richard MichelmoreGenome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.
Ray MingDepartment of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address: rayming@illinois.edu.
Cukurova University · TRFujian Agriculture and Forestry University · CNUniversidad de Granada · ESUniversity of Illinois Urbana-Champaign · USGaziantep Children's Hospital · TRUniversity of California, Davis · USGerman Cancer Research Center · DEUniversity of Canberra · AUXiamen University · CNYoungstown State University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.

Indexed as

PistaciaDomesticationNutsSex ChromosomesTreesdomesticationpistachioPistacia verareference genomesequencingsex chromosome

Identifiers

PMID36435969
PMCPMC10203267
OpenAlexW4310059429

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.