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opencc-by-4.0Jan 2021View details →

New genetic markers for Sapotaceae phylogenomics: more than 600 nuclear genes applicable from family to population levels

Some tropical plant families, such as the Sapotaceae, have a complex taxonomy, which can be resolved using Next Generation Sequencing (NGS). For most groups however, methodological protocols are still missing. Here we identified 531 monocopy genes and 227 Short tandem repeats (STR) markers and tested them on Sapotaceae using target capture and NGS. The probes were designed using two genome skimming samples fromCapurodendron delphinense and Bemangidia lowryi, both from the Tseboneae tribe, as well as the published Manilkara zapota transcriptome from the Sapotoideae tribe. We combined our probes with 261 additional ones previously published and designed for the entire angiosperm group. On a total of 792 low-copy genes, 638 showed no signs of paralogy and were used to build a phylogeny of the family with 231 individuals from all main lineages. A highly supported topology was obtained at high taxonomic ranks but also at the species level. This phylogeny revealed the existence of more than 20 putative new species. Single nucleotide polymorphisms (SNPs) extracted from the 638 genes were able to distinguish lineages within a species complex and to highlight geographical structuration. STR were recovered efficiently for the species used as reference (C. delphinense) but the recovery rate decreased dramatically with the phylogenetic distance to the focal species. All together, the new loci will help reaching a sound taxonomic understanding of the family Sapotaceae for which many circumscriptions and relationships are still debated, at the species, genus and tribe levels.

opencc-by-4.0Dec 2002View details →

Sideroxylon lycioides (Sapotaceae) - bark - of a medium tree or large branch

Image of Sideroxylon lycioides (Sapotaceae) - bark - of a medium tree or large branch

Sideroxylon lycioides (Sapotaceae) - twig - orientation of petioles

Image of Sideroxylon lycioides (Sapotaceae) - twig - orientation of petioles

Sideroxylon lycioides (Sapotaceae) - whole tree (or vine) - general

Image of Sideroxylon lycioides (Sapotaceae) - whole tree (or vine) - general

Sideroxylon lycioides (Sapotaceae) - leaf - whole upper surface

Image of Sideroxylon lycioides (Sapotaceae) - leaf - whole upper surface

Sideroxylon lycioides (Sapotaceae) - bark - of a large tree

Image of Sideroxylon lycioides (Sapotaceae) - bark - of a large tree

Sideroxylon lycioides (Sapotaceae) - twig - orientation of petioles

Image of Sideroxylon lycioides (Sapotaceae) - twig - orientation of petioles

Fig. 2 in Three Critically Endangered new species of Capurodendron (Sapotaceae) from Madagascar

Fig. 2. - Field photograph of the type collection of Capurodendron schatzii L. Gaut. & Naciri. [Photo: G.E. Schatz]

Fig. 3 in Three Critically Endangered new species of Capurodendron (Sapotaceae) from Madagascar

Fig. 3. - Known distribution of (A-B) Capurodendron sahafariense L. Gaut. & Naciri (green), (A, C) C. schatzii L. Gaut. & Naciri (pink), and (A, D) C. nanophyllum L. Gaut. & Naciri (blue). Limits of protected areas in yellow. [Google Earth Images. Copyright 2018 DigitalGlobe. Reproduced per attribution guidelines]

Fig. 5 in Three Critically Endangered new species of Capurodendron (Sapotaceae) from Madagascar

Fig. 5. - Field photograph of the type collection of Capurodendron sahafariense L. Gaut. & Naciri. [Photo: F. Ratovoson]

Fig. 4. - Capurodendron sahafariense L. Gaut. & Naciri. A in Three Critically Endangered new species of Capurodendron (Sapotaceae) from Madagascar

Fig. 4. - Capurodendron sahafariense L. Gaut. & Naciri. A. Longitudinal section of flower; B. Flower; C. Corolla opened seen from inside; D. Corolla opened seen from outside; E. Brachyblast with leaves and post-anthesis flower; F. Branch with flowers and fruit; G. Fruit; H. Transverse section of ovary. [Drawings: G. Loza]

Fig. 4. – A in Mimusops coriacea (A. DC.) Miq. (Sapotaceae): nomenclature, distribution and ecology

Fig. 4. – A tree of Mimusops coriacea (A. DC.) Miq. preserved in the city of Masoala, Eastern Madagascar. [Photo: L. Gautier]

Fig. 2 in Mimusops coriacea (A. DC.) Miq. (Sapotaceae): nomenclature, distribution and ecology

Fig. 2. – Natural range of Mimusops coriacea (A. DC.) Miq. in Madagascar, plotted on HUMBERT (1955) map of phytogeographical domains (102 specimens georeferenced with <5 km incertainity).

Fig. 3 in Mimusops coriacea (A. DC.) Miq. (Sapotaceae): nomenclature, distribution and ecology

Fig. 3. – Phenology of Mimusops coriacea (A. DC.) Miq. in Madagascar (number of specimens having flower buds, flowers, young fruits or fruits per month)

Fig. 1 in Mimusops coriacea (A. DC.) Miq. (Sapotaceae): nomenclature, distribution and ecology

Fig. 1. – Mimusops coriacea (A. DC.) Miq. A. In fruit near Masoala, Eastern Madagascar; B. Flower in Orangea, ntsiranana. [Photo: A: L. Gautier; B: R. Randrianaivo]

opencc-by-4.0May 2020View details →

Fig. 1. – Labramia ambondrombeensis L. Gaut. & Randriarisoa. A in Labramia ambondrombeensis (Sapotaceae), a Critically Endangered new species from Madagascar.

Fig. 1. – Labramia ambondrombeensis L. Gaut. & Randriarisoa. A. Flowering branch; B. Leaf with venation details (a: upper side; b: lower side); C. Flower; D. Flower in longitudinal section; E. Detached corolla spread opened (c: outer side, with appendages folded down and one lobe removed to show one lobe and one stamen; d: inner side, with two stamens removed to show inner side of lobes); F. Transversal section of the ovary. [Razakamalala et al. 1077, G] [Drawing: G. Loza]

Fig. 9. – Englerophytum ferrugineum L. Gaut. & O. Lachenaud. A in Five new species of Englerophytum K. Krause (Sapotaceae) from central Africa

Fig. 9. – Englerophytum ferrugineum L. Gaut. & O. Lachenaud. A. Inflorescence; B. Flower bud; C. Longitudinal section of flower; D. Longitudinal section of corolla; E. Leaf blade detail, upper surface; F. Leaf blade detail, lower surface; G. Branch apex showing stipules; H. Extremity of twig with leaves. [Drawing: G. Loza]

Fig. 8 in Five new species of Englerophytum K. Krause (Sapotaceae) from central Africa

Fig. 8. – Field photographs of Englerophytum sylverianum Kenfack & L. Gaut. A. Leaves; B. Fruits; C. Seeds; D. Inflorescence. [Photos: A, C: D. Kenfack B: X. van der Burgt, D: M. Sainge]

Fig. 7 in Five new species of Englerophytum K. Krause (Sapotaceae) from central Africa

Fig. 7. – Englerophytum sylverianum Kenfack & L. Gaut. A. Leafy twig; B. Detail of the lower surface of the leaf, showing venation; C. Branch apex with leaves removed, showing stipules; D. Inflorescence; E. Flower; F. Flower viewed from above, showing the united stamens; G. Corolla longitudinally sectioned and opened, with ovary; H. Fruit; I. Seed, ventral view. [A-G: Kenfack 764; H-I: Sainge & Kenfack 2245] [Drawing: Alice Tangerini]

Fig. 6. – Englerophytum libenii O. Lachenaud & L. Gaut. A in Five new species of Englerophytum K. Krause (Sapotaceae) from central Africa

Fig. 6. – Englerophytum libenii O. Lachenaud & L. Gaut. A. Leafy twig; B. Portion of twig with stipules and base of petioles; C. Detail of lower surface of the leaf, showing venation; D. Inflorescence; E. Flower, side view; F. Flower, longitudinal section; G. Portion of corolla with stamens, seen from inside; H. Flower, viewed from above; I-J. Fruits (dry condition); K. Seed, ventral view; L. Seed, lateral view. [A-C: Champluvier 6101, BR; D-H: Breteler et al. 8125, BR; I-L: Champluvier 6106, BR] [Drawing: A. Fernandez]