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From haploid to reference: a new milestone in poplar genomics

  • # Authors contributed equally: Shihui Niu, Quanzi Li

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  • Passiflora plants are lianas with axillar tendrils and nectaries; their sexual organs are merged into a structure named the androginophore[1]. Passiflora is a genus with nearly 600 species; 95% of them are American natives, mainly from South America and Mesoamerica (from Central Mexico to Panama)[2]. More than 60 species of Passiflora produce large edible fruits, and nearly 25 species are cultivated. The economically important edible juice producers are Passiflora edulis, P. edulis f. flavicarpa, P. ligularis, P. quadrangularis, and P. tripartita var. mollissima; moreover, the fruits of P. tripartita, P. tarminiana, P. maliformis, P. alata, P. hannii, P. laurifolia, P. popenovii, and P. setacea are consumed locally elsewhere[3]. Approximately 1.5 million tons of passion fruit (Passiflora edulis) are produced worldwide, with Brazil being the main producer and consumer[4].

    Although most Passiflora species are American native, research on those species involved worldwide scientific groups. For example, due to their, actual and potential ecological and economic roles, in several world regions, such as China, projects for cropping and breeding Passiflora are being developed[5]. Medical researchers are determining the potential of Passiflora plant organs to recover physical and psychiatric human health[6,7].

    In Mexico, 91 Passiflora species, native and introduced, have been reported, indicating that, for this genus, this country is the fifth in worldwide diversity ranking[8]. Within Mexico, one of the areas with greater Passiflora diversity are the areas belonging to the southern states of Campeche, Chiapas, Yucatán, and Quintana Roo[9]. In Chiapas state there are, at least, two endemic species, P. pendens and P. tacanensis[8].

    The land area of those southern states is 215,047 km2, representing approximately 10% of the total Mexican territory. Nowadays, its current inhabitants belong to different ethnic groups and mestizo people[10]. Nevertheless, before Spanish irruption in Mexico, this area was inhabited by several groups belonging to ancient Mayan culture, including yucatecos in the states of the Yucatan Peninsula (Campeche, Yucatán, and Quintana Roo), and choles, tsetales, tsotsiles, tojolabanes, and lacandones in Chiapas state[11,12].

    As Mexico is one of the main land reserves for Passiflora plants, scientific efforts to claim further national studies on this plant genus must be performed. This review presents a list of the Passiflora species botanically recorded in four southern Mexican states. Then reports related to previous, actual, and potential uses for those species are briefly summarized. This review aims to point out the importance of the conservation of Passiflora genetic resources in southern Mexico.

    According to the herbaria MEXU[13], HERBANMEX[14], CICY[15], and CHAPA[16], thereafter confirmed in the specialized platform 'Plants of the word on line'[8], in the states under study, there are 55 Passiflora species (Table 1). Chiapas state accounts for 90% of those species, followed by Quintana Roo, Campeche, and Yucatán states[9].

    Table 1.  Passiflora species botanically registered in the states of Chiapas, Campeche, Quintana Roo, and Yucatán, Mexico; and their names in Spanish (S), Yucatec Maya (Y), Lacandón Maya (L), Tseltal Maya (T), and English (E).
    No. Species Location Name
    1 P. adenopoda DC. Chiapas (L): k'um sek; ucumin sek
    2 P. alata Curtis Chiapas (E): winged-stem passion flower
    3 P. ambigua Hemsl. Chiapas, Quintana Roo & Yucatán (S): granadilla de monte; ingo; jugito; jugo; (L): ch'um ak'
    4 P. apetala Killip Chiapas No information
    5 P. bicornis Mill. Campeche, Chiapas, Quintana Roo & Yucatán (S): ojo de luna; (Y): poch k' aak' ; kasu' uk; (E): wing-leaf passionfruit
    6 P. biflora Lam. Campeche, Chiapas, Quintana Roo & Yucatán (S): calzón de niño; bejuco de guaco; hoja de murcielago; (Y): poch aak'; (L): k'um sek (ah); (T): mayil poch;
    (E): twoflower passion-flower
    7 P. bryonioides Kunth Chiapas (S): granada cimarrona; (E): cupped passion flower
    8 P. capsularis L. Quintana Roo No information
    9 P. ciliata Aiton Campeche, Chiapas, Quintana Roo & Yucatán (S): maracuyá; sipolan; (Y): poch k' aak' ; poch kaki; xpoch aki; (E): fringed passion flower
    10 P. clypeophylla Mast. ex Don.Sm. Chiapas No information
    11 P. cobanensis Killip Campeche, Chiapas & Quintana Roo No information
    12 P. conzattiana Killip Campeche, Chiapas & Quintana Roo (S): hoja de vampiro
    13 P. dolichocarpa Killip Chiapas No information
    14 P. edulis Sims Campeche, Chiapas & Yucatán (S): maracuyá; flor de pasión; maracuyá morado;
    (Y): xton kee jil; (E): yellow passion fruit, purple passion fruit
    15 P. exsudans Zucc. Campeche (S): bolsa de gato; té de insomnio
    16 P. filipes Benth Chiapas (S): frijolillo; granadilla(E): slender passion flower
    17 P. foetida L. Campeche, Chiapas, Quintana Roo & Yucatán (S): amapola; maracuyá silvestre; granadillo; cinco llagas(Y): poch; túubok; poch' aak' ; poch' iil(E): stinking passion fruit; fetid passion flower; rambusa
    18 P. hahnii (E.Fourn.) Mast. Chiapas (S): granadilla chos
    19 P. helleri Peyr. Chiapas, Quintana Roo & Yucatán No information
    20 P. holosericea L. Chiapas No information
    21 P. itzensis (J.M.MacDougal) Port.-Ult. Chiapas, Quintana Roo & Yucatán (Y): maak xikin soots'
    22 P. jorullensis Kunth Chiapas (S): golondrina; tijerilla
    23 P. lancearia Mast. Chiapas No information
    24 P. ligularis Juss. Chiapas (S): granadilla; granada de moco; (E): sweet granadilla
    25 P. mayarum J.M.MacDougal Campeche, Chiapas & Quintana Roo (S): granadillo; (Y): toon ts' iimim; poch aak'; (E): wild passion flower
    26 P. membranacea Benth. Chiapas (S): granadilla; granada; (T): karanotozak; karanato rak'
    27 P. mexicana Juss. Chiapas No information
    28 P. morifolia Mast. Chiapas (E): woodland passion flower
    29 P. obovata Killip Campeche, Chiapas, Quintana Roo & Yucatán No information
    30 P. oerstedii Mast. Chiapas (S): granadilla chos
    31 P. ornithoura Mast. Campeche, Chiapas & Quintana Roo No information
    32 P. pallida L. Campeche, Chiapas, Quintana Roo & Yucatán (Y): sak aak' ; soots' aak' ; ts' unyajil
    33 P. pavonis Mast. Chiapas No information
    34 P. pedata L. Campeche, Quintana Roo & Yucatàn (Y): toom ts' iimin; tontotzimin
    35 P. pendens J.M.MacDougal Chiapas No information
    36 P. pilosa Ruiz & Pav. ex DC. Chiapas (S): granadilla; granada de zorro
    37 P. platyloba Killip Chiapas & Quintana Roo (S): granadilla de monte
    38 P. porphyretica Mast. Chiapas (T): schelchikin chinzak
    39 P. prolata Mast. Campeche, Chiapas & Quintana Roo (S): granadilla de monte
    40 P. quetzal J.M.MacDougal Chiapas No information
    41 P. rovirosae Killip Campeche, Chiapas & Quintana Roo No information
    42 P. sanctae-mariae J.M.MacDougal Chiapas No information
    43 P. seemannii Griseb Chiapas No information
    44 P. serratifolia L. Campeche, Chiapas, Quintana Roo & Yucatán (S): amapola; jujito amarillo; maracuyá de monte; pasionaria; granada de ratón; (Y): pooch aak' ; ya' ax pooch; (L): poochin; (E): broken ridge granadillo
    45 P. sexflora Juss. Chiapas & Campeche (S): granadilla chos;
    (T): schelchikinchinak; shel chikin chinzak; shel chikin
    46 P. sexocellata Schltdl. Campeche, Chiapas & Yucatàn (S) ala de murciélago; granada de ratón;
    (Y): xikin sots' ; xiik' sots'
    47 P. sicyoides Schltdl. & Cham. Chiapas (S) granadilla
    48 P. standleyi Killip Chiapas No information
    49 P. suberosa L. Campeche, Chiapas, Quintana Roo & Yucatán (S): granadilla roja; granadita de ratón; pata de pollo;
    (Y): kansel-ak; zal-kansel-ak; (I): cork-barked passion-flower, corky passion fruit
    50 P. sublanceolata (Killip) J.M.MacDougal Campeche, Quintana Roo & Yucatán (S) jujo; (Y): pooch k' aak'
    51 P. subpeltata Ortega Campeche & Chiapas (S) pasionaria, granadina, aretitos, granada de zorra, jujo
    52 P. tacanensis Port.-Utl. Chiapas No information
    53 P. tarminiana Coppens & V.E.Barney Chiapas No information
    54 P. xiikzodz J.M.MacDougal Campeche, Chiapas, Quintana Roo & Yucatán (Y): maak xikin soots'
    55 P. yucatanensis Killip ex Standl. Campeche, Quintana Roo & Yucatán (S): flor de la pasión de Yucatán; (E): Yucatan passion flower
    References[5,6,8,9,1318].
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    Chiapas state presents five biogeographical provinces related to a specific natural area in relation to its endemic biota. Those five provinces are, the 'Gulf of Mexico lowland', 'Chiapas central plateau', 'Chiapas central depression', 'Madre mountain range', and 'coastal lowland'. In contrast, within the Campeche state area, there are two biographical provinces, the 'Gulf of Mexico lowland' and the 'Yucatán lowland'. Whereas Yucatán and Quintana Roo states belong only to the province named 'Yucatán lowland'[19]. Thus, the presence of different biogeographical provinces, implying different climates and ecological conditions, might influence Passiflora diversity. For example, in Mexico, Chiapas state is known to be the second state with a relatively high total plant diversity, with over 10,000 plant species[20].

    For Chiapas state, there are botanical reports of Passiflora in 65 of the 126 municipalities, with a greater presence in Ocosingo (19 species), Unión Juárez (nine species), and Palenque (eight species). Including the four states under study, the municipality of Othón P. Blanco, Quintana Roo state (11 species), follows Ococingo, and then, the list continues with Calakmul, Campeche State (11 species). For Yucatán state, a greater Passiflora presence has been reported in Progreso (five species) (Fig. 1).

    Figure 1.  Municipalities within Peninsula de Yucatán and Chiapas, Mexico, with greater botanical reports of Passiflora species. Chiapas (yellow) [Ococingo (19), Unión Juárez (9), and Palenque (8)], Campeche (red) [Calakmul (11), Holpechén (6), Campeche (5), and Champotón (5)], Yucatán (black) [Progreso (5)], and Quintana Roo (purple) [Othón P. Blanco (11), Felipe Carrillo Puerto (8), and José María Morelos (5)]. Four Passiflora species illustrate this genus diversity. Data of present work were marked on a map sourced from Google Earth.

    The number of Passiflora species recorded in Ocosingo is greater than the number of Passiflora species reported in each of the other 18 states in Mexico[9]. Additionally, Unión Juárez must be valorized for its Passiflora richness, as the municipality area is only 62 km2[10].

    Passiflora species grow mainly in family orchards and jungle systems[12,21]; the latter system is very sensitive to overexploitation of natural resources, pollution, and climatic change. Moreover, it is very responsive to demographic changes, public policies, and local technological projects[22].

    To our knowledge, there are no reports of the use of Passiflora plants by ancient Mayan culture. However, ethnobotanical reports, written in the last three decades, indicate that in the Lacandón forest, native people eat the fruits of 'ch'um ak'' (P. ambigua), 'ch'ink ak'il' (Passiflora sp.) 'poochin' (P. serratifolia) and P. hahnii[12,13]. A recent review confirmed the consumption of P. ambigua, P. bicornis, P. ciliata, P. foetida, P. hahnii, P. ligularis, P. mayarum, P. serratifolia, and P. yucatensis fruits in communities of Chiapas and the Yucatan Peninsula[23].

    In Yucatán state, the P. ciliata plant is used to treat hysteria, sleeplessness, and child convulsion; local people assign this species narcotic and sedative properties[24]. In the Chiapas High Valleys, P. membranacea liana is used as a rope to tie tools or help build rudimentary houses[21].

    In the municipality of Solidaridad, Quintana Roo State, the staff of the butterfly pavilion of a theme park, crop at least two Passiflora species, one allegedly to be P. lobata ('pata de gallo' in Spanish), to raise butterfly larvae. The information within the park, mentions that they raise the butterflies Agraulis vanillae, Dryas iulias, Heliconius erato, and H. charithonia. Scientific literature supports the preference of butterfly larvae for P. lobata[25].

    For centuries, some effects on the human body have been assigned to Passiflora plants. Moreover, in the Spanish language, the name of passion fruit was misunderstood, and many people have given aphrodisiac properties to Passiflora species, instead of relating its name to the passion of Christ[1]. Moreover, in plants of this genus, several molecules with spasmolytic, sedative, anxiolytic, and blood pressure modulation properties have been identified. One of those molecules is passicol, which has antibacterial properties. P. foetida leaf extracts reduce the growth of Pseudomonas putida, Vidrio cholerae, Shigella flexneri, and Streptococcus pyogenes, supporting the use of this plant in ethnopharmacology to treat fiber, diarrhea, stomach and throat pains, and ear and skin infections[26].

    It has been suggested that the anthocyanin present in the peel of P. biflora might be used as an additive to increase color and antioxidant capacity in some human foods[27]. Additionally, pectin can be extracted from the Passiflora peel for human consumption[28], and it has been proposed to transform peel into biofuels[29]. As Brazil is a high yellow passion fruit producer, it has been proposed to produce passion fruit seed oil there. The oil might be used in human foods or transformed into creams, shampoos, and pharmacology products[30]. In addition, among the seed components, there are stilbenes, which are excellent antioxidants, enhance human skin conditions, and present hypoglycemic properties[31].

    In the Yucatan Peninsula, Passiflora is among the top five plant genera with relatively high diversity[17]. This richness might be used to breed, aiming for genotypes producing high-quality fruits and suitable for cropping in new areas[5,32]. Nevertheless, land use change represents one of the greatest risks to conserving actual biodiversity; this factor also contributes to increasing the rate of climatic change and affects ecosystem sustainability[33].

    Quintana Roo state is one of the main tourist region's in Mexico, Cancun resort area is located there, and further luxury resorts are still planned. Mexican environmental law protects approximately 30% of the land of the municipality of Othón P. Blanco, Quintana Roo state[34]; and this municipality started policy programs for sustainable bay management, keeping its vegetation, including several medicinal plants[35]. In this sense, recently, the Mexican government involved some institutes in flora conservation. In the municipality of Solidaridad, Quintana Roo state, the Botanical Garden 'Dr. Alfredo Barrera Marín' belonging to the 'Centro de Investigaciones de Quintana Roo' is the repository of the flora native of the section North 5 of the project Maya Railway.

    In general, in the four states under study herein, there are important archeological and touristic venues; thus, Passiflora conservation in southern Mexico might involve ethno-tourism, ecotourism, and other local developmental projects. Moreover, in the Yucatan Peninsula and Chiapas there are almost 17 areas named Nature Reserves. They are: 'Pantanos de Centla', 'Río Celestum', 'Río Lagartos', 'Sian Ka'an' 'Chinchorro', 'Caribe Mexicano', 'Tiburón ballena', 'El triunfo', 'La Encrucijada', 'La Sepultura', 'Lacan tún', 'Montes azules', 'Selva El Ocote', 'Volcán Tacaná', 'Calakmul', 'Balam ku', and 'Los Peténes'. Therefore, according to UNESCO, in nature reserves, effective fauna and flora protection policies might be observed[36].

    The role of Passiflora plant species in conserving local fauna, and, by a consequence, help to keep the ecosystem balance, must be carefully understood. Several Passiflora species included in Table 1 have been reported to be good feed sources for animals. For example, P. biflora may play a role in conserving bats in the Lacandón forest[9]. For Passiflora species being bat-pollinated, it has been observed that their flowers are well adapted to bat behavior, as their flowers secrete nectar at night[37]. Moreover, it has been reported that some years after introducing Passiflora plants, the population of butterflies and bees was increased[9]. Some studies have revealed that P. suberosa is a good feed source for A. vanillae maculosa larvae, although less preferred by D. iulia caterpillar, who prefers leaves of P. misera[38,39].

    Although tropical forest regeneration is possible, the predicted growth of urban areas is a risk factor[33] in reducing Passiflora diversity. On the other hand, some researchers have suggested that rural families contribute strongly to maintaining plant species[40]. Thus, reducing the poverty factor might be included in national, state, and municipality politics to recognize the importance of native and original communities in conserving plant genetic resources. For example, within the three municipalities with the greatest presence of Passiflora species, only Othón P. Blanco has less than 45% of its population living in poverty, whereas over 80% of the populations of Ocosingo and Calakmul live in poverty. In five of the six municipalities with a greater presence of Passiflora, the human population living in poverty is greater than 70%[41].

    Although some countries offer payments to conserve plant genetic resources, they are limited to plant species presenting economic importance[42]. Thus, to involve local people in plant genetic conservation, projects aimed at sustainability, environment conservation, prosperity, and human welfare must be offered. The municipality, state, and national governments must establish laws and regulations to save jungles and mangroves. Further efforts to keep flora and fauna, in this case Passiflora species, in the areas with a higher presence of this genus, are expected to keep its holistic value and diversity.

    The high diversity of Passiflora plants in Chiapas state seems to be related to the presence of five biographical provinces: 'Gulf of Mexico lowland', 'Chiapas central plateau', 'Chiapas central depression', 'Madre mountain range', and 'coastal lowland'. Within Chiapas state, Ococingo is the municipality with the highest Passiflora diversity.

    Although there are no reports of the use of Passiflora in ancient Maya culture living in Chiapas, Campeche, Yucatán, or Quintana Roo states, the actual use of Passiflora suggests inherited knowledge. On the other hand, the agro-industrial and pharmacological potential of this plant genus might help promote sustainable regional development. The rescue of traditional fruit species and their ancient knowledge might enhance the local economy and maintain ecological balance.

  • The authors confirm contribution to the paper as follows: study conception and design: Franco-Mora O; data collection: Franco-Mora O, Moreno-Jiménez A; analysis and interpretation of results: Franco-Mora O, Sánchez-Pale JR; draft manuscript preparation: Franco-Mora O, Castañeda-Vildózola Á. All authors reviewed the results and approved the final version of the manuscript.

  • The herbarium MEXU, HERBANMEX, and CICY offers free access to their on line database; they are cited in the References section[1315]. Data from herbaria CHAPA (16) is available at the Institute.

  • The herbaria exemplars, consulted herein, represent the work of several botanists. The picture of Passiflora ciliata was kindly donated by Prof. Elia Ballesteros-Rodríguez (CICY, Yucatán, Mexico).

  • The authors declare that they have no conflict of interest.

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  • Cite this article

    Niu S, Li Q. 2024. From haploid to reference: a new milestone in poplar genomics. Forestry Research 4:e020 doi: 10.48130/forres-0024-0018
    Niu S, Li Q. 2024. From haploid to reference: a new milestone in poplar genomics. Forestry Research 4:e020 doi: 10.48130/forres-0024-0018

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COMMENTARY   Open Access    

From haploid to reference: a new milestone in poplar genomics

Forestry Research  4 Article number: e020  (2024)  |  Cite this article
  • As the first tree species to undergo whole-genome sequencing, the completion of the Populus trichocarpa (black cottonwood) genome sequencing in 2006 marked a significant breakthrough in forest genomics research[1]. It greatly facilitates the adoption of poplar trees as a model species for genomics in the realm of forest trees[2]. The reference genome, serving as the bedrock of research plays an indispensable role in advancing genetic improvement of trees, research on adaptability, and ecosystem management. It enables scientists to more accurately pinpoint the genes that control important traits, thereby achieving more efficient variety breeding and resource utilization in forestry practice.

    Genomics has advanced at an unprecedented rate in the past three years, especially in the technologies and strategies for genome assembly. For instance, the use of long-read sequencing technologies such as PacBio and Nanopore, in conjunction with high-throughput chromosome conformation capture (Hi-C) technology, has significantly improved the continuity and accuracy of genome assembly. To date, at least 3,517 genome datasets from 1,575 plant species have been released, 67% of which were completed in the past three years, including 73% of the newly published genomes that have been assembled to the chromosomal level[3]. Furthermore, the pan-genome studies have been introduced into forestry research, allowing researchers to explore the diversity and complexity within species' genomes[4]. Nonetheless, due to high heterozygosity and the presence of complex genomic regions, including centromeres and ribosomal RNA gene clusters (rDNA regions), the assembly of a truly complete genome is still a challenge[5], even for model plants with smaller genomes like Arabidopsis thaliana[6]. The current v4.1version of the P. trichocarpa genome, as the highest quality among all the published poplar genomes, there are still 59 unresolved gaps which account for about ~3.32% of the genome. The ultimate goal of the T2T genome assembly is to achieve a completely gapless genome sequence, which is crucial for revealing the full biological information of the genome[7].

    The haploid materials have the characteristics of genotypic homozygous, which can obtain high-quality genome sequencing results, and have important application value in genetic engineering research[8]. A recent study by Liu et al., titled 'A nearly gapless, highly contiguous reference genome for a doubled haploid line of Populus ussuriensis, enabling advanced genomic studies'[7], has successfully induced a double haploid (DH) callus line, referred to as DH15, from anthers of P. ussuriensis[9]. Utilizing this DH line, the authors have achieved a telomere-to-telomere (T2T) assembly of 19 chromosomes in the DH15 genome. Notably, this study has identified and annotated the centromere regions of the DH genome, marking a significant milestone as it reveals the content of the centromere complex regions within a poplar genome for the first time. This study has annotated 465 more genes than the annotation of P. trichocarpa genome. These advancements render a valuable resource for various studies on poplar genomes. In addition, the quality of the genome assembly has been greatly improved, from both the length of N50 and the number of gap sites, and the improved integrity of the genome significantly fills gaps present in the P. trichocarpa genome.

    The availability of the T2T P. ussuriensis reference genome not only establishes a solid foundation for a deeper understanding of genomic structure and functions in poplar but also provides valuable resources for poplar genomic and evolutionary studies. In particular, the in-depth annotation of centromeric regions offers new insights into the mechanisms of chromosome distribution and cell division in plants. Furthermore, comparative analysis with other poplar genomes has revealed gene family expansion and contraction within the Populus genus, as well as the potential role of specific gene families in adaptive traits. These findings are crucial for understanding the biological characteristics of poplar trees. Through comparative genomics, researchers can identify gene families that are unique or expanded in poplars, which may be associated with the adaptability of poplars to environmental changes. This provides targets for further functional research and molecular breeding.

    Although most gaps are nearly closed, a few remaining ones consist of the rDNA region, which bears the 18S-5.8S-25S ribosomal RNA genes also called nucleolus organizer regions (NORs) or 45S rDNA sites, presenting challenges for assembly due to their repetitive nature, copy number variation, and sequence complexity, which requires resolution in future research endeavors.

  • Shihui Niu and Quanzi Li contributed equally for original draft and review the manuscript.

  • Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.

    • The authors declare that they have no conflict of interest.

    • # Authors contributed equally: Shihui Niu, Quanzi Li

    • Copyright: © 2024 by the author(s). Published by Maximum Academic Press, Fayetteville, GA. This article is an open access article distributed under Creative Commons Attribution License (CC BY 4.0), visit https://creativecommons.org/licenses/by/4.0/.
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    Niu S, Li Q. 2024. From haploid to reference: a new milestone in poplar genomics. Forestry Research 4:e020 doi: 10.48130/forres-0024-0018
    Niu S, Li Q. 2024. From haploid to reference: a new milestone in poplar genomics. Forestry Research 4:e020 doi: 10.48130/forres-0024-0018
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