10KP: A phylodiverse genome sequencing plan

Abstract

Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here.

Figure 1:

A phylogeny of seed plants (dated phylogeny based on Smith and Brown, in press). Colors correspond to the number of species in the subtending lineage (red = lower to blue = higher). Some larger clades are highlighted around the phylogeny along with the estimated number of genomes to be sequenced by 10KP in bold below the name. Smaller numbers and arrows inside the phylogeny indicate estimates of some of the already available genomes within the identified clade.

Figure 2:

Summary tree of nonseed plants (based on the 1KP Capstone Analysis, in press). This shows the phylogenetic relationships for the 5 major categories of seed-free plants, including bryophytes (hornworts, liverworts, mosses), lycophytes, and ferns.

Figure 3:

Summary tree of eukaryotes. Schematic diagram shows the known or predicted relationships among the major eukaryotic groups, based on multi-gene analyses, featuring diverse eukaryotic microbes (algae and protists) [10]. Lineages with 1 or more photosynthetic/plastid-bearing groups are highlighted with a square. The Archaeplastida are the eukaryotic “supergroup” to which green algae and embryophytes belong. Protist genomes sequenced as part of 10KP will come from diverse lineages but exclude true fungi and animals.

Figure 4:

Distribution of species/genus/family abundance across the major clades of embryophytes. Most species belong to the eudicot clade, for which the largest families include Asteraceae, Orchidaceae, Fabaceae, Rubiaceae, and Poaceae.

Figure 5:

Representative images of species from different clades/families of flowering plants. The species names presented here are: a. Canella winterana (L.) Gaertn. (Angiosperms, Magnoliids, Canellales, Canellaceae). Flowers and inflorescence. Photo credit: Walter Judd. b. Austrobaileya scandens C.T. White (Angiosperms, Austrobaileyales, Austrobaileyaceae). Flower. Photo credit: Walter Judd. c. Ceratophyllum demersum L. (Angiosperms, Ceratophyllales, Ceratophyllaceae). Habit and inflorescence. Photo credit adapted from Christian Fischer, CC BY SA 3.0 Wikimedia Commons. d. Illicium floridanum J.Ellis (Angiosperms, Austrobaileyales, Schisandraceae). Flower. Photo credit: Walter Judd. e. Piper neesianum C. DC. (Angiosperms, Magnoliids, Piperales, Piperaceae). Habit and inflorescence. Photo credit: Walter Judd. f. Myrothamnus flabellifolius Welw. (Angiosperms, Eudicots, Gunnerales, Myrothamnaceae). Habit and leaves. Photo credit adapted from JMK, CC BY SA 3.0 Wikimedia Commons. g. Dillenia indica L. (Angiosperms, Eudicots, Dilleniales, Dilleniaceae). Photo credit: Walter Judd.

Figure 6:

Representative images of species from various clades/families of nonflowering plants. The species names presented here are: a. Picea abies (L.) H. Karst. (Pinophyta, Pinales, Pinaceae). Shoots and female cones. Photo credit adapted from Magnus Manske (CC BY SA 3.0 Wikimedia Commons). b. Ginkgo biloba L. (Ginkgophyta, Ginkgoales, Ginkgoaceae). Leaves and male inflorescence. Photo credit adapted from Sten, CC-BY SA 3.0 Wikimedia Commons. c. Cibotium barometz (L.) J.Sm. (Polypodiopsida, Cyatheales, Cibotiaceae). Fronds (leaves). Photo credit: Pi-Fong Lu. d. Adiantum caudatum Klotzsch (Polypodiopsida, Polypodiales, Pteridaceae). Fronds (leaves) and habit. Photo credit: Pi-Fong Lu. e. Marsilea crenata C.Presl (Polypodiopsida, Salviniales, Marsileaceae). Fronds (leaves) and habit. Photo credit: Pi-Fong Lu. f. Asplenium viride Huds. (Polypodiopsida, Polypodiales, Aspleniaceae). Fronds (leaves) and habit. Photo credit: Pi-Fong Lu. g. Diphasiastrum complanatum (L.) Holub. (Lycopodiopsida, Lycopodiales, Lycopodiaceae. Habit. Photo credit: Pi-Fong Lu. h. Bryum capilare Hedwig (Bryopsida, Bryales, Bryaceae). Gametophyte and Sporophyte. Photo Credit adapted from Lairich Rig (CC BY SA 2.0 Wikimedia Commons). i. Marchantia polymorpha L. (Marchantiopsida, Marchantiales, Marchantiaceae). Thalli with gemmae (asexual reproductive structures). Photo Credit adapted from Holger Casselmann (CC-BY SA 3.0 Wikimedia Commons).

Figure 7:

Light micrographs of diverse protists, including members of different eukaryotic “supergroups.” a. Stylonema (Archaeplastida [Plantae], red alga). b. Cyanoptyche (Archaeplastida [Plantae], glaucophyte). c. Scherffelia (Archaeplastida [Plantae], Viridiplantae, chlorophyte). d. Stephanosphaera (Archaeplastida [Plantae], Viridiplantae, chlorophyte). e. Chaetosphaeridium (Archaeplastida [Plantae], Viridiplantae, streptophyte). f. Mallomonas (stramenopiles, chrysophyte). g. Coscinodiscus (stramenopiles, diatom). h. Synedra (stramenopiles, diatom). i. Sphacelaria (stramenopiles, brown alga). j. Trithigmostoma (alveolates, ciliate). k. Cryptomonas (Cryptista). l. Paramoeba (Amoebozoa). Micrographs courtesy of Gerd Günther (http://www.mikroskopia.de/index.html), Sebastian Hess (Halifax; Scherffelia), and Ivan Fiala (Czech Republic; Paramoeba).

Figure 8:

Sample submission portal from the CNGB/10KP website. Figure shows the sample submission portal (as well as the underlying database management) on the 10KP website https://db.cngb.org/10kp/; this website (version 1.0) is still evovling. This sample submission portal is prepared specifically for land plants; most samples will come from botanical gardens or botany research centers/laboratories worldwide. A global community effort is crucial to help supply all families and all genera. For stage 1, we anticipate more active involvement of highly motivated and skilled laboratories, whereas for stage 2, we anticipate more of a community effort to supply the majority of the remaining genera. For algae and protists, all samples will come from the public collections and channelled through the Culture Collection of Algae at the University of Cologne, where quality controls will be enforced.

Figure 9:

An overview of the 10KP strategy.