Application of a Simplified Method of Chloroplast Enrichment to Small Amounts of Tissue for Chloroplast Genome Sequencing

Premise of the study: High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. Methods: Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing. Results: Using this simple method, significant enrichment of chloroplast DNA-derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully. Discussion: This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species)

Une nouvelle espèce micro-endémique de Scaevola L. (Goodeniaceae) de Nouvelle-Calédonie en danger critique d'extinction

ACL-12-57International audienceA new narrow endemic endangered species of Scaevola (Goodeniaceae) from New Caledonia. A new endemic species of the pantropical genus Scaevola L., S. barrierei A.S. Wulff & Munzinger, sp. nov. is described from New Caledonia. It grows in open shrub land on ultramafic substrate. It is characterized by its coriaceous and pubescent leafs on the abaxial side and its raised yellow flowers, pubescent on the exterior. This species is preliminarily assigned as "critically endangered" (CR) following IUCN Red List Categories and Criteria

Conservation Priorities in a Biodiversity Hotspot: Analysis of Narrow Endemic Plant Species in New Caledonia

<div><p>New Caledonia is a global biodiversity hotspot facing extreme environmental degradation. Given the urgent need for conservation prioritisation, we have made a first-pass quantitative assessment of the distribution of Narrow Endemic Species (NES) in the flora to identify species and sites that are potentially important for conservation action. We assessed the distributional status of all angiosperm and gymnosperm species using data from taxonomic descriptions and herbarium samples. We characterised species as being NES if they occurred in 3 or fewer locations. In total, 635 of the 2930 assessed species were classed as NES, of which only 150 have been subjected to the IUCN conservation assessment. As the distributional patterns of un-assessed species from one or two locations correspond well with assessed species which have been classified as Critically Endangered or Endangered respectively, we suggest that our distributional data can be used to prioritise species for IUCN assessment. We also used the distributional data to produce a map of “Hotspots of Plant Narrow Endemism” (HPNE). Combined, we used these data to evaluate the coincidence of NES with mining activities (a major source of threat on New Caledonia) and also areas of conservation protection. This is to identify species and locations in most urgent need of further conservation assessment and subsequent action. Finally, we grouped the NES based on the environments they occurred in and modelled the habitat distribution of these groups with a Maximum Entropy Species Distribution Model (MaxEnt). The NES were separable into three different groups based primarily on geological differences. The distribution of the habitat types for each group coincide partially with the HPNE described above and also indicates some areas which have high habitat suitability but few recorded NES. Some of these areas may represent under-sampled hotspots of narrow endemism and are priorities for further field work.</p></div

Map of “Hotspots of Plant Narrow Endemism” and protected areas in New Caledonia.

<p>Values given per cell are the total number of NES summing NES 1, 2 & 3. Red ellipses indicate collections of cells that fall within named geographical locations such as mountains or valleys. The total number of NES in the red ellipses is indicated in brackets beside the name of site, numbers in red refer to the total number of NES 1. The line in the middle of Grande Terre (the main island) is the separation between the north and the south provinces.</p

Predicted distributions of the three groups of NES.

<p>For each group, the map of potential distribution (colour according to probability of the habitat being suitable), and the name of location presenting the highest probabilities for a suitable habitat are detailed (Areas already identified as HPNE are in bold).</p

Hotspots of narrow endemism (HPNE) in the New Caledonia flora where >7 NES are found per 2×2 km cell (see also Fig. 2).

<p>The province of each “hotspot” is noted at the end of the name (PN: North province, PS: South province). An asterisk indicates that the site is potentially threatened by mining impacts. An “X” in the “Protected area” column indicates that the “hotspot” is protected. In the substrate column, “V” indicates a volcano-sedimentary substrate; “U” indicates an ultramafic substrate.</p