Dataset Information

Reference genome and demographic history of the most endangered marine mammal, the vaquita.

ABSTRACT: The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

SUBMITTER: Morin PA

PROVIDER: S-EPMC8247363 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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Reference genome and demographic history of the most endangered marine mammal, the vaquita.

Morin Phillip A PA Archer Frederick I FI Avila Catherine D CD Balacco Jennifer R JR Bukhman Yury V YV Chow William W Fedrigo Olivier O Formenti Giulio G Fronczek Julie A JA Fungtammasan Arkarachai A Gulland Frances M D FMD Haase Bettina B Peter Heide-Jorgensen Mads M Houck Marlys L ML Howe Kerstin K Misuraca Ann C AC Mountcastle Jacquelyn J Musser Whitney W Paez Sadye S Pelan Sarah S Phillippy Adam A Rhie Arang A Robinson Jacqueline J Rojas-Bracho Lorenzo L Rowles Teri K TK Ryder Oliver A OA Smith Cynthia R CR Stevenson Sacha S Taylor Barbara L BL Teilmann Jonas J Torrance James J Wells Randall S RS Westgate Andrew J AJ Jarvis Erich D ED

Molecular ecology resources 20201120 4

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated re ...[more]

PMID: 33089966

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Project description:IntroductionWhole-genome resequencing technology covers almost all nucleotide variations in the genome, which makes it possible to carry out conservation genomics research on endangered species at the whole-genome level.MethodsIn this study, based on the whole-genome resequencing data of 101 critically endangered Artocarpus nanchuanensis individuals, we evaluated the genetic diversity and population structure, inferred the demographic history and genetic load, predicted the potential distributions in the past, present and future, and classified conservation units to propose targeted suggestions for the conservation of this critically endangered species.ResultsWhole-genome resequencing for A. nanchuanensis generated approximately 2 Tb of data. Based on abundant mutation sites (25,312,571 single nucleotide polymorphisms sites), we revealed that the average genetic diversity (nucleotide diversity, π) of different populations of A. nanchuanensis was relatively low compared with other trees that have been studied. And we also revealed that the NHZ and QJT populations harboured unique genetic backgrounds and were significantly separated from the other five populations. In addition, positive genetic selective signals, significantly enriched in biological processes related to terpene synthesis, were identified in the NHZ population. The analysis of demographic history of A. nanchuanensis revealed the existence of three genetic bottleneck events. Moreover, abundant genetic loads (48.56% protein-coding genes) were identified in Artocarpus nanchuanensis, especially in genes related to early development and immune function of plants. The predication analysis of suitable habitat areas indicated that the past suitable habitat areas shifted from the north to the south due to global temperature decline. However, in the future, the actual distribution area of A. nanchuanensis will still maintain high suitability.DiscussionBased on total analyses, we divided the populations of A. nanchuanensis into four conservation units and proposed a number of practical management suggestions for each conservation unit. Overall, our study provides meaningful guidance for the protection of A. nanchuanensis and important insight into conservation genomics research.

Dataset Information

Reference genome and demographic history of the most endangered marine mammal, the vaquita.

Publications

Reference genome and demographic history of the most endangered marine mammal, the vaquita.

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